DreINT0050375 @ danRer10
Intron Retention
Gene
ENSDARG00000021720 | col7a1
Description
collagen, type VII, alpha 1 [Source:ZFIN;Acc:ZDB-GENE-030131-2427]
Coordinates
chr6:40215963-40218443:-
Coord C1 exon
chr6:40218408-40218443
Coord A exon
chr6:40216044-40218407
Coord C2 exon
chr6:40215963-40216043
Length
2364 bp
Sequences
Splice sites
5' ss Seq
GTGGTGAGT
5' ss Score
8.95
3' ss Seq
TAACATGATTTGATAAACAGGGA
3' ss Score
4.41
Exon sequences
Seq C1 exon
GGACCACAAGGACCTCAAGGGCTTCCAGGACAAGTG
Seq A exon
GTGAGTAAATAAACATACCAGACAAGCTAATGTATTACAGAGAATTTGCGAAATGACAATTTTACCTCTTCAAGTAATTGGCATAATGGTGAAAGTGAGGCAAAGCTTGATTGCGGGTCCATGCAACAAATGACAAGTGTCCGCTGTGGGAGAGCACTTGACTTTAGATTTGAACAACAATATAGCCGTTCAGTCACTAATGCTTCTCTGAGGTTGAACTCACAGTTCACTCTCAAACGAATACATTTGCTCTCGGTCAAGCAGTTTCAGGCTCAATCCAGTTATGTGATTGTGGTGTATATATTGCATGGATATGTGTTTTATTTTGAGGTGGTTGGCAATACTCAGACTTATTTTTATTTAAAAAATGTTCTGCCTACATAGACTTTTGAAAAACAGGGCATTCCATAGACGTCTGTAGGGATGTTCGCAGGGTCTTAAAAAATGTATTAAAAGTTGATAAATCAATTATGAGAAAATTAAGGCCCTTAAAAGGTATTGAAAAGTCTTTATTTTACGAGGTATTTTTTGTTCAAGCGTTGTCCAAAACTTTTAACTCCAAAATATGTATATTTATTTTCCTCCTAATATTAACAACGGCATGCTCGATCCACGTAATTGGTTCGGGCCAGGGCGCGTCAGGCTAAGCTCATCTGTCTGGGTGATGTCACGTAATTTGCGAAAGACTCGGAAAGGTGATGTGACGCACTCAACATGTAGCAAAACCATAGAGCAAAACAGGCGGAAAATGTATGTTTGCGTACTCCTGGTAAACAGTGGCAATGTTTAAACAGTGGCTGAAGCCTGTCACTGAAAACAACCACGTAATTTATTCTTTCAAGCTTTGTGTCTTCTGATCTTATCTGAGTTCTGTTACATGGTTGTGCTTCATTGATTTATTTAACTAAAACTTTTTATTAACAACTGTTTATAAAGTTAAATGTTTTACTTATACTGAGTAGAACTTGAAGTGGTGATGAGGTCTTAAAATATTCTGATAAGGTCTTTAAAAAGGTTTTGAAATTATCTTTAGGATTGCTGCATATACCTTCTAACCAATTCCCTAAACAATGAAAGTTTCAAGGTATTCTGTTTATTTATATGCAGGTTTTATGCATTAAAGGGATTGGGTAACACAAAAATCTAAATTTACTGACTATTTACTAGGGGTGTGAACCTACACTACACTGAACACCTCTCACTGTTCGGTTCAGTTTACGATTATCATGTCATCAATTCGGTTCAATTCGATATCTTGGTGCATTGACAATGATTTCCACATACATTTATCATTTTTTCTACACAACAAGATTCTTGAACTAAAATTTTCAAACATATTTATATTTATACTATAGTATTTGTAATCCAATTTTGTCCTTTAACACAAGCACTCAGAAATATAATCTGTACCTTTAATTTTATCTGCTCAAAGGAAACCTTTTTGAATGTTTCAAGCAAAACTCAAATAAAATCACAGAAGACAACATGAGCATTTATAGTAAATGAACTAATGTAAATATTATTCAGCTTGCTTTTTGAGCATTGTTGAGCATTTAATCAGCGCTTAACAGAAAAGGCTGCGATTGGCTCTAAAACTGACAATACTGTTGCCCGATGAGTGAGGTGGACATTGAAGAATGTGCGTTAACAGTCTATATGCACGTAATAATCACAGCTGATCTGTAACAAACATCGTGGAGAAAACTCAATCTACAGACACACTCGTGTCAGGATCCACAAGTATCACTTTAGTCCAGCAAACTTGCATTCGCTTAATAGTGCACAGTTGTCTGCTTTTTAGGTAGTTGGAGCATTTTAATTACTCGCCCTCGCCTTGTTCGAATAGTATTCTACTGTGACATAGCGCTTCTGAGATCAAGGACGTCAGTATGTTAAAACCGGTGATAATCAATGAATGAACTGATACTGAATTGTCCACATCTGCATCACGGTGCACTAAAGAAACAATTAATTTTGACACCCCTACTTTTTACCAAGAAGATGGATTAAAAGAAGCTATAAACCTGTACCCACTGACTTCCATACTATAAAACAGATAAGAAATAAGTCAGTGGTTTCCAGCTACTTTCAGTATCTTCTTGTGTGTTCAATGGAAGAAAGAAAGTCTAACAGGTTTGGATCAAGTAAATAGTGAGTAAATAATGACAGAACTTCCAGTTTTGGGTGAACTATCCCTTTAACACAGACAAAAATCTATTTTATACACTGCATTTTATTGAATTAATTTGAATAGTTTGTTGTTTGTGACTGGTAATAATGAATTTGTTTGCTTATGTAATGTGACTGAGGCCTGGCACTTGTTACAGTAATGAGGTTATCTCTTTAACATGATTTGATAAACAG
Seq C2 exon
GGAGAGGGGGGCAAGCCTGGGGTCCCAGGAAGAGACGGTGCTCCGGGTAAAGATGGCCTGCCAGGCTTAAATGGTAAACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000021720:ENSDART00000154878:85
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=FE(14.1=100),PF0139113=Collagen=PU(13.8=91.7)
A:
NA
C2:
PF0139113=Collagen=PD(34.5=74.1),PF0139113=Collagen=PU(27.9=63.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]