L1Base
Browse the Database of full-length, intact LINE-1 Elements
 

ID (uid)

Description: ID of the L1 element in the Database

candUID (cand_uid)

Description: Candidate uid of the L1 element in the Database, for identifications purposes throughout the passes of L1Xplorer

Chr (contig)

Description: Chromosome

Start (contig_start)

Description: Start of the locus containing the L1 element on the Chromosome (Goldenpath)

End (contig_end)

Description: End of the locus containing the L1 element on the Chromosome (Goldenpath)

Query Start (query_start)

Description: Start of the alignment on the query L1 [nt]

Query End (query_end)

Description: End of the alignment on the query L1 [nt]

Strand (contig_strand)

Description: Strand of the L1 element on the Chromosome (Goldenpath)

ORF1 conserved (orf1_cons)

Description: 0 if ORF1 is not conserved (no significant TFASTX alignment found), 1 if conserved

ORF1 Start (orf1_start)

Description: Start [nt] of ORF1 relatively to the L1 element

ORF1 End (orf1_end)

Description: End [nt] of ORF1 relatively to the L1 element

ORF1 Q-Start (orf1_l1_start)

Description: Start [aa] of the TFASTX alignment on the Query ORF1

ORF1 Q-End (orf1_l1_end)

Description: End [aa] of the TFASTX alignment on the Query ORF1

ORF1 gaps (orf1_gaps)

Description: Number of gap characters in the TFASTX alignment of ORF1

ORF1 frameshifts (orf1_frameshifts)

Description: Number of frameshifts in the TFASTX alignment of ORF1

ORF1 stops (orf1_stops)

Description: Number of STOP codons (TAA, TAG, TGA) in ORF1

ORF2 conserved (orf2_cons)

Description: 0 if ORF2 is not conserved (no significant TFASTX alignment found), 1 if conserved

ORF2 Start (orf2_start)

Description: Start [nt] of ORF2 relatively to the L1 element

ORF2 End (orf2_end)

Description: End [nt] of ORF2 relatively to the L1 element

ORF2 Q-Start (orf2_l1_start)

Description: Start [aa] of the TFASTX alignment on the Query ORF2

ORF2 Q-End (orf2_l1_end)

Description: End [aa] of the TFASTX alignment on the Query ORF2

ORF2 gaps (orf2_gaps)

Description: Number of gap characters in the TFASTX alignment of ORF2

ORF2 frameshifts (orf2_frameshifts)

Description: Number of frameshifts in the TFASTX alignment of ORF2

ORF2 stops (orf2_stops)

Description: Number of STOP codons (TAA, TAG, TGA) in ORF2

Ta SSVs (ta)

L1 Part inspected: 3' UTR Nucleotide Sequence
Format: <nts corresponding to 5930-2 L1.2><nt corresponding to 6015 L1.2> (<Classification based on Literature>)
Type: HMMer directed conservation check
Scoring: no
Description: Inspects the family determining Ta locus of the L1 element identified. Family classifications are:
  • GAGA - L1PA2-L1PA5
  • GAGG (intermediate L1)
  • GCGA (intermediate L1)
  • ACGA (preTa L1)
  • ACGG (preTa L1)
  • ACAG (Ta Element)

References
  • Salem, et al., J Mol Biol (2003) 326, 1127-46 Pubmed
  • Boissinot, et al., Mol Biol Evol (2000) 17, 915-28 Pubmed
  • Boissinot, et al., Genome Res (2004) 14, 1221-31 Pubmed
  • Ovchinnikov, et al., Proc Natl Acad Sci U S A (2002) 99, 10522-7 Pubmed

Ta0/Ta1 SSVs (ta01)

L1 Part inspected: ORF2 Nucleotide Sequence
Format: {L1PA5|Ta-0/L1PA2|Ta-1|non canonical}
Type: HMMer directed conservation check
Scoring: no
Description: Inspects the family determining Ta0-1 locus of the L1 element identified. Classification according to references below.
References
  • Salem, et al., J Mol Biol (2003) 326, 1127-46 Pubmed
  • Boissinot, et al., Mol Biol Evol (2000) 17, 915-28 Pubmed
  • Boissinot, et al., Genome Res (2004) 14, 1221-31 Pubmed

Ta1-nd/d (tand)

L1 Part inspected: 5' UTR Nucleotide Sequence
Format: {Ta1-d|Ta1-nd|non canonical}
Type: HMMer directed conservation check
Scoring: no
Description: Checks for the family determining Tad/nd deletion in the 5'UTR of the L1 element identified. Classification according to references below.
References
  • Boissinot, et al., Mol Biol Evol (2000) 17, 915-28 Pubmed

L1M/L1PA Discrimination (l1mvspa)

L1 Part inspected: ORF2 Nucleotide Sequence
Format: {L1PA|L1M}
Type: HMMer against HMM db
Scoring: no
Description: Checks through a HMM a diagnostic part of ORF2, which discriminates L1M and L1PA families.
References
  • Smit, et al., J Mol Biol (1995) 246, 401-417 Pubmed

Poly-A (polya)

L1 Part inspected: 3' UTR Nucleotide Sequence
Format: <# of nt of pure poly(a)> pure/<# of nt of estimated poly(a)> (kim dist=<float result of kimura dist>)
Type: Poly-A Estimation
Scoring: no
Description: Identifies the position of the Poly-A signal and determines the length of the pure Poly-A tail, as well as the length of an estimated Poly-A Tail (containing mutations). Calculates as well a Kimura distance to a pure Poly-A tail of the length of the estimated sequences. Distance is not available when mutation rate is too high.
References
  • Roy-Engel, et al., Genome Res (2002) 12, 1333-44 Pubmed

PolyA Signal (polyasig)

L1 Part inspected: 3' UTR Nucleotide Sequence
Format: {cons|mut}
Type: HMMer directed conservation check
Scoring: yes
Description: Test the sequence for an intact Poly-A signal. Poly-A signals that fulfill the consensus AATAAA or AATTAAA will be consideres as valid signals.
References
  • Boeke, Nat Genet (1997) 16, 6-7 Pubmed

Runx3 Site (runx3_1)

L1 Part inspected: 5' UTR Nucleotide Sequence
Format: {cons|mut}
Type: HMMer directed conservation check
Scoring: yes
Description: Checks for the presence of an intact RUNX3 binding motif in the 5'UTR of the L1 Element.
References
  • Yang, et al., Nucleic Acids Res (2003) 31, 4929-40 Pubmed

Runx3 ASP (runx3_3)

L1 Part inspected: 5' UTR Nucleotide Sequence
Format: {cons|mut}
Type: HMMer directed conservation check
Scoring: yes
Description: Checks for the presence of an intact RUNX3 Anti-Sense-Promoter binding motif in the 5'UTR of the L1 Element.
References
  • Yang, et al., Nucleic Acids Res (2003) 31, 4929-40 Pubmed

SRY Site 1 (sry1)

L1 Part inspected: 5' UTR Nucleotide Sequence
Format: {cons|mut}
Type: HMMer directed conservation check
Scoring: yes
Description: Checks for the presence of an intact first SRY1 binding motif in the 5'UTR of the L1 Element.
References
  • Tchenio, et al., Nucleic Acids Res (2000) 28, 411-5 Pubmed

SRY Site 2 (sry2)

L1 Part inspected: 5' UTR Nucleotide Sequence
Format: {cons|mut}
Type: HMMer directed conservation check
Scoring: yes
Description: Checks for the presence of an second first SRY1 binding motif in the 5'UTR of the L1 Element.
References
  • Tchenio, et al., Nucleic Acids Res (2000) 28, 411-5 Pubmed

YY1 BoxA+BoxA (yy1)

L1 Part inspected: 5' UTR Nucleotide Sequence
Format: {cons|mut}
Type: HMMer directed conservation check
Scoring: yes
Description: Checks for the presence of an intact YY1 binding motif at the very beginning of the L1 Element.
References
  • Kurose, et al., Nucleic Acids Res (1995) 23, 3704-9 Pubmed
  • Becker, et al., Hum Mol Genet (1993) 2, 1697-702 Pubmed
  • Hyde-DeRuyscher, et al., Nucleic Acids Res (1995) 23, 4457-65 Pubmed

TF nkx-2.5 (nkx25)

L1 Part inspected: 5' UTR Nucleotide Sequence
Format: {cons|mut}
Type: HMMer directed conservation check
Scoring: no
Description: Checks the sequences for intactness of the first putative nkx2-5 site.
References
  • Durocher, et al., Mol Cell Biol (1996) 16, 4648-55 Pubmed

TF nkx-2.5B (nkx25b)

L1 Part inspected: 5' UTR Nucleotide Sequence
Format: {cons|mut}
Type: HMMer directed conservation check
Scoring: no
Description: Checks the sequences for intactness of the second putative nkx2-5 site.
References
  • Durocher, et al., Mol Cell Biol (1996) 16, 4648-55 Pubmed

find TSDs (tsdsearch)

L1 Part inspected: Whole Nucleotide Sequence
Format: <# of nt> nt
Type: TSD search
Scoring: no
Description: Searches for target-site-duplications flanking the L1 Element. Only TSDs of a length greater than 10 will be considered as valid TSDs.
References
  • Szak, et al., Genome Biol (2003) 4, R30 Pubmed
  • Szak, et al., Genome Biol (2002) 3, research0052 Pubmed

REKG235 (rekg235)

L1 Part inspected: ORF1 Aminoacid Sequence
Format: {cons|mut}
Type: HMMer directed conservation check
Scoring: yes
Description: Checks the sequence for intactness of REKG235 locus in ORF1.
References
  • Moran, et al., Cell (1996) 87, 917-27 Pubmed

ARR260 (arr260)

L1 Part inspected: ORF1 Aminoacid Sequence
Format: {cons|mut}
Type: HMMer directed conservation check
Scoring: yes
Description: Checks the sequence for intactness of ARR260 locus in ORF1.
References
  • Moran, et al., Cell (1996) 87, 917-27 Pubmed

YPAKLS282 (ypakls282)

L1 Part inspected: ORF1 Aminoacid Sequence
Format: {cons|mut}
Type: HMMer directed conservation check
Scoring: yes
Description: Checks the sequence for intactness of YPAKLS282 locus in ORF1.
References
  • Moran, et al., Cell (1996) 87, 917-27 Pubmed

N14 (n14)

L1 Part inspected: ORF2 Aminoacid Sequence
Format: {cons|mut}
Type: HMMer directed conservation check
Scoring: yes
Description: Checks the sequence for intactness of N14 locus in ORF2.
References
  • Feng, et al., Cell (1996) 87, 905-16 Pubmed

E43 (e43)

L1 Part inspected: ORF2 Aminoacid Sequence
Format: {cons|mut}
Type: HMMer directed conservation check
Scoring: yes
Description: Checks the sequence for intactness of E43 locus in ORF2.
References
  • Feng, et al., Cell (1996) 87, 905-16 Pubmed

Y115 (y115)

L1 Part inspected: ORF2 Aminoacid Sequence
Format: {cons|mut}
Type: HMMer directed conservation check
Scoring: yes
Description: Checks the sequence for intactness of Y115 locus in ORF2.
References
  • Feng, et al., Cell (1996) 87, 905-16 Pubmed

D145 (d145)

L1 Part inspected: ORF2 Aminoacid Sequence
Format: {cons|mut}
Type: HMMer directed conservation check
Scoring: yes
Description: Checks the sequence for intactness of D145 in ORF2.
References
  • Feng, et al., Cell (1996) 87, 905-16 Pubmed

N147 (n147)

L1 Part inspected: ORF2 Aminoacid Sequence
Format: {cons|mut}
Type: HMMer directed conservation check
Scoring: yes
Description: Checks the sequence for intactness of N147 in ORF2.
References
  • Feng, et al., Cell (1996) 87, 905-16 Pubmed

T192 (t192)

L1 Part inspected: ORF2 Aminoacid Sequence
Format: {cons|mut}
Type: HMMer directed conservation check
Scoring: yes
Description: Checks the sequence for intactness of T192 in ORF2.
References
  • Feng, et al., Cell (1996) 87, 905-16 Pubmed

D205 (d205)

L1 Part inspected: ORF2 Aminoacid Sequence
Format: {cons|mut}
Type: HMMer directed conservation check
Scoring: yes
Description: Checks the sequence for intactness of D205 in ORF2.
References
  • Feng, et al., Cell (1996) 87, 905-16 Pubmed

SDH228 (sdh228)

L1 Part inspected: ORF2 Aminoacid Sequence
Format: {cons|mut}
Type: HMMer directed conservation check
Scoring: yes
Description: Checks the sequence for intactness of SDH228 locus in ORF2.
References
  • Feng, et al., Cell (1996) 87, 905-16 Pubmed

R363 (r363g)

L1 Part inspected: ORF2 Aminoacid Sequence
Format: {cons|mut}
Type: HMMer directed conservation check
Scoring: yes
Description: Checks the sequence for intactness of R363 locus in ORF2. R to G mutation is known to limit retrotransposition rate.
References
  • Lutz, et al., Am J Hum Genet (2003) 73, 1431-7 Pubmed

FADD700 (fadd700)

L1 Part inspected: ORF2 Aminoacid Sequence
Format: {cons|mut}
Type: HMMer directed conservation check
Scoring: yes
Description: Checks the sequence for intactness of FADD700 locus in ORF2.
References
  • Feng, et al., Cell (1996) 87, 905-16 Pubmed

HMKK1091 (hmkk1091)

L1 Part inspected: ORF2 Aminoacid Sequence
Format: {cons|mut}
Type: HMMer directed conservation check
Scoring: yes
Description: Checks the sequence for intactness of HMKK1091 locus in ORF2.
References
  • Moran, et al., Cell (1996) 87, 917-27 Pubmed

SSS1096 (sss1096)

L1 Part inspected: ORF2 Aminoacid Sequence
Format: {cons|mut}
Type: HMMer directed conservation check
Scoring: yes
Description: Checks the sequence for intactness of SSS1096 locus in ORF2.
References
  • Moran, et al., Cell (1996) 87, 917-27 Pubmed

I1220 (i1220m)

L1 Part inspected: ORF2 Aminoacid Sequence
Format: {cons|mut}
Type: HMMer directed conservation check
Scoring: yes
Description: Checks the sequence for intactness of I1220 locus in ORF2. I to M mutation is known to limit retrotransposition rate.
References
  • Lutz, et al., Am J Hum Genet (2003) 73, 1431-7 Pubmed

S1259 (s1259l)

L1 Part inspected: ORF2 Aminoacid Sequence
Format: {cons|mut}
Type: HMMer directed conservation check
Scoring: yes
Description: Checks the sequence for intactness of S1259 locus in ORF2. S to L mutation is known to limit retrotransposition rate.
References
  • Lutz, et al., Am J Hum Genet (2003) 73, 1431-7 Pubmed

ORF StartStop (orfclass)

L1 Part inspected: Whole Nucleotide Sequence
Format: {cons|mut} (<ORF1 {M|non-M codon}{*|non-Stop codon}>, <ORF2 {M|non-M codon}{*|non-Stop codon}>
Type: ORF Classifications
Scoring: yes
Description: Checks the ORFs of the L1 for presence of valid methionine start codons and stop codons. (M*,M*) indicates conserved start and stop codons in both ORFs.
References

    G-C Content (gccontent)

    L1 Part inspected: Whole Nucleotide Sequence
    Format: % value
    Type: GC-Content
    Scoring: no
    Description: Calculates the %G-C of the L1 Element in a 50nt window.
    References
    • Furano, Prog Nucleic Acid Res Mol Biol (2000) 64, 255-94 Pubmed

    Repeat Annontation (ensrepeats)

    L1 Part inspected: No Sequence
    Format: Comma-Separated list of repeat names
    Type: Ensembl DB Link Repeats
    Scoring: no
    Description: Digs the Ensembl Database for Repeatmasker annotations of the Current L1. Results are given as / +
    References
    • Smit, et al., J Mol Biol (1995) 246, 401-417 Pubmed

    Look for SNPs (enssnp)

    L1 Part inspected: Whole Nucleotide Sequence
    Format: <Total #> of SNPS (ORF1:<ORF1 # of SNPs>/ORF2:<ORF2 # of SNPs/STOPS:<# of stop-causing SNPs/AACHANGE:<# of AA changing SNPs/FS:<# of frameshift-causing SNPs>)
    Type: Ensembl DB Link SNPs
    Scoring: no
    Description: Adds SNPs from the correspondent Ensembl release to the annotation, and shows aminoacid exchanges (only for L1Base)
    References
    • Birney, et al., Nucleic Acids Res (2004) 32 Database issue, D468-70 Pubmed
    • Sherry, et al., Nucleic Acids Res (2001) 29, 308-11 Pubmed

    Genome Vicinity (ensgenes)

    L1 Part inspected: Whole Nucleotide Sequence
    Format: <Ensembl Gene Name> plus for every transcript a representation of the exon positions relatively to the L1, "--" = exon sits before the L1, "++" = Exons sits after the L1.
    Type: Ensembl DB Link Genes
    Scoring: no
    Description: Checks the presence of genes within the surrounding 50000nt. Exons that lie before the L1 are marked as [Exon Nr]--, exons after the L1 as ++[Exon Nr].
    References
    • Birney, et al., Nucleic Acids Res (2004) 32 Database issue, D468-70 Pubmed

    ORF1 %A (orf1acont)

    L1 Part inspected: ORF1 Nucleotide Sequence
    Format: % value
    Type: Nucleotide Statistics
    Scoring: no
    Description: Evaluates the A-content of ORF1 (see reference)
    References
    • Han and Boeke, Nature (2004) 429, 314-8 Pubmed

    ORF1 %T (orf1tcont)

    L1 Part inspected: ORF1 Nucleotide Sequence
    Format: % value
    Type: Nucleotide Statistics
    Scoring: no
    Description: Evaluates the T-content of ORF1 (see reference)
    References
    • Han and Boeke, Nature (2004) 429, 314-8 Pubmed

    ORF2 %A (orf2acont)

    L1 Part inspected: ORF2 Nucleotide Sequence
    Format: % value
    Type: Nucleotide Statistics
    Scoring: no
    Description: Evaluates the A-content of ORF2 (see reference)
    References
    • Han and Boeke, Nature (2004) 429, 314-8 Pubmed

    ORF2 %T (orf2tcont)

    L1 Part inspected: ORF2 Nucleotide Sequence
    Format: % value
    Type: Nucleotide Statistics
    Scoring: no
    Description: Evaluates the T-content of ORF2 (see reference)
    References
    • Han and Boeke, Nature (2004) 429, 314-8 Pubmed

    ORF1&2 %A (orfsacont)

    L1 Part inspected: Both ORFS Nucleotide Sequence
    Format: % value
    Type: Nucleotide Statistics
    Scoring: no
    Description: Evaluates the A-content of both ORF1 and ORF2 (see reference)
    References
    • Han and Boeke, Nature (2004) 429, 314-8 Pubmed

    ORF1&2 %T (orfstcont)

    L1 Part inspected: Both ORFS Nucleotide Sequence
    Format: % value
    Type: Nucleotide Statistics
    Scoring: no
    Description: Evaluates the T-content of both ORF1 and ORF2 (see reference)
    References
    • Han and Boeke, Nature (2004) 429, 314-8 Pubmed

    CPG Islands (cpg)

    L1 Part inspected: Whole Nucleotide Sequence
    Format: # islands
    Type: CpG Search
    Scoring: no
    Description: Annotates CPG-islands in the L1.
    References
    • Furano, Prog Nucleic Acid Res Mol Biol (2000) 64, 255-94 Pubmed

    ORF1 CAI (caiorf1)

    L1 Part inspected: ORF1 Nucleotide Sequence
    Format: % value
    Type: Codon Adaptation Index
    Scoring: no
    Description: Calculates the Codon Adaptation Index of ORF1 (Meaningful for Intact ORFs)
    References
    • Sharp and Li, Nucleic Acids Res (1987) 15, 1281-95 Pubmed

    ORF2 CAI (caiorf2)

    L1 Part inspected: ORF2 Nucleotide Sequence
    Format: % value
    Type: Codon Adaptation Index
    Scoring: no
    Description: Calculates the Codon Adaptation Index of ORF2 (Meaningful for Intact ORFs)
    References
    • Sharp and Li, Nucleic Acids Res (1987) 15, 1281-95 Pubmed

    Intactness Score (intactness)

    L1 Part inspected: No Sequence
    Format: Point score (integer)
    Type: Intactness Scoring
    Scoring: no
    Description: Calculates an intactness measure for the L1 annotated. Each feature putatively contributing to activity awards for one point when conserved.
    References

      Search Monomers (simaf)

      L1 Part inspected: 5' UTR Nucleotide Sequence
      Format: {A-Monomer I-VI|G.F-Monomer|T.F-Monomer|F-Monomer}*
      Type: Simsearch
      Scoring: no
      Description: Searches the L1 for Mouse L1 promotor monomers. Detected Monomers are A-Monomer I, A-Monomer II, A-Monomer III, A-Monomer IV, A-Monomer V, A-Monomer VI, T.F-Monomer, F-Monomer, G.F-Monomer.
      References
      • Schichman, et al., Mol Biol Evol (1993) 10, 552-70 Pubmed
      • Goodier, et al., Genome Res (2001) 11, 1677-85 Pubmed

      66/42 Monomers (sim6642)

      L1 Part inspected: ORF1 Nucleotide Sequence
      Format: {66-Monomer|42-Monomer1-3}*
      Type: Simsearch
      Scoring: no
      Description: Searches the L1 for Mouse L1 ORF1 monomers (LPR, aka 66-42-42 monomers).
      References
      • Goodier, et al., Genome Res (2001) 11, 1677-85 Pubmed

      L1.3/L1.4/L1mlvi2 (mlvi2)

      L1 Part inspected: 3' UTR Nucleotide Sequence
      Format: {TCG (L1.3)|ACG (L1.4|TTA (L1.mlvi2)|Unknown Variant} }
      Type: HMMer directed conservation check
      Scoring: yes
      Description: Discriminates via SSVs between L1.3, L1.4 and L1mlvi2.
      References
      • Usdin, et al., Mol Biol Evol (1995) 12, 73-82 Pubmed
      Tomasz Zemojtel, Institute for Molecular Genetics, Max-Plack Institute Berlin
      Tobias Penzkofer, Department of Bioinformatics, University of Würzburg