DreINT0050283 @ danRer10
Intron Retention
Gene
ENSDARG00000021720 | col7a1
Description
collagen, type VII, alpha 1 [Source:ZFIN;Acc:ZDB-GENE-030131-2427]
Coordinates
chr6:40199459-40201791:-
Coord C1 exon
chr6:40201729-40201791
Coord A exon
chr6:40199522-40201728
Coord C2 exon
chr6:40199459-40199521
Length
2207 bp
Sequences
Splice sites
5' ss Seq
AAGGTTGGA
5' ss Score
5.64
3' ss Seq
ACATTTCCTTTGATGCCCAGGGG
3' ss Score
4.81
Exon sequences
Seq C1 exon
GGTGAAGTCGGGCTTCAAGGACCCATTGGAAGTCCAGGGAAGGAGGGACTCATTGGAGCCAAG
Seq A exon
GTTGGAGGATAATGCCAGTTTGACATTTACACTGCCGTTTCAGTCATTTTTAAACTGTTGAACAAACTTTAGTATTTGAGTTTTTTTTAGTAATATAAAGGTCAGAGACAAACAAGTGTGTCATTGAGTTTAGTAATTTGAAATTTTTGTCTGTATTTGTAATGTGTGCTGTTTAAATTTAAACCTTTTTAGCAAAATAATTGATGACTAATGTTCATTTTAACAATAATTTACAGAAACCACTCACAAAAATGTCAGTTAGTGTAAATATATTTTTGGATATCAAACAATTTGGTCAGGAATACTGTACATATCAACTCTATTTAAGCATTACAATACATAATTAAAATACATATATTTTACTCATCCTAATTTTAGTATTTATTTTTGTAATCTTTAGAAATAAACACTTTAAATCTTGTTTCTTTTTTTCAAACCATTACGTGTTACAGCTTTGTCAGGAAGTTGTCAGTTGTAATATTCATTCATTCATTCATTTTCTTTTCGACTTAGTCCGTTTATTAATCCGGGGTCACCACAGCGGAATGAACCATCAACTTATCAAGCACGTTTTTATGCAGCGGATGCCCTTCCAGCTGCAACCCATCTCTGGGAAACATCCACACACACTCATTCACACTCATACACTAGGGACAATTTAGGCCACCCAATTGTTTGGACTGTGGGGGAAACCGGAGCACCCGGAGGAAACCCACCCGAACACAGGGAGAACATGCAAACTCCAAACAGAAACATCAACTGACCCAGGCGAGGCTCGAACCAGCGACCTGTAAGGCGACACCCTACTGCGCCACTGCATCACCCAGTTGTAATATTATATTATATTATATTATATTATATTATATTTATTATATTATATTATATTATATTATATTATATTATATTATATTATATTATATTATATTATATTATATTATATTATATCATATTATATCATATTATATCATATTATATTAAATATTACAAGTACAGATTAGAAATTTTTACCAGATGTTGGTAACAATCAAAGAAATCTATGTATGACACATATGAAATGACTCATTGAAAATGAAAAAATGATGAACAAATAAAGAAGGGGAGCTTTAAAAAGGCAGTAGCTGAAATCTTTCAGTAGCTCTTCAGCAACCCTCTACCCTTTCTCATTGTAAATTAACATTAGCTGCTTCAGTTTAAACATCTACATTACCAGGATGATGCCAATCACCTGACTTTTATCCAATAGAAAATACAAAATAAAGGTCAGATTTGATTACCTCATTTTGGATATGAGAGGCTGCCATCACAAAAAAAGCCTTTAATATAAAGTATTAAATACATTTCAGTAGTTCAGTACTTTCTCCTTGTGGCAGTCCATTGTTATTACACATAATTTTTCCAGATTTATTTTGTTTTGTTATATTATTTTGTTTATATTGTTTGGGCCTTTAACAAAATCTGGTTCAATTCTTGCTTTTAGGAAAGTTTTTCCAAAAAAAAAAAAACTGTGACCTTTTGAATACTTTTTCCCCACTGTATCTGTTACACTGAACAACTATGAAACATGCCTTTTTATTCATGCTATTTTGAAACATTAAAGCACTTGTTTTGTAATATAATTTCTATGTAAATGAAATATCTTTCGTACATTTAATTTAATGCACACGCCAAAATGAAACCTCTTGTCTTTGACCAACAATATTATTATAAAATATTCAAAATGTCATTTTAACATGTCCTTTTGCCTAATTGTAAGTACATGTGATGTGCAATATGTACATTTAGAGCCAATAAATAAATAAAAAATTAAATAAATAATTAAAAATATATCAATGTTAGAAAAGAAATCACAAATAATTATTTAACTATAGAGACTTTGTTTTCAGCTTAACAATCTTATTGTAATGTATGCAATCTAATTAAACAATTGTATGATATTATAATGTATGATACAATCTGTAAATGTAATTGGTGCATACAGCATTGATGTGGAGATTGTTTTGACCTGAGTTTGTACTAGCTGTGTTTTATCTTTATTTTATGATTGATTGGCACAAAAATACTGGTTCTTTTAATAATCAAGAAGACAACTACATTAACACAGCTATGCTCTACTTTCCACTTTACAGTCTTTGTTATTCAAAGCATAAAGTTGAAAAATGTGCACTGAAACATTAAACAAACTGTGTAACATTTCCTTTGATGCCCAG
Seq C2 exon
GGGGACAGAGGTTTTGATGGCGTTACAGGGCCAAAGGGAGCACAAGGAGAGAAGGGTGAACGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000021720:ENSDART00000154878:107
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(25.6=100)
A:
NA
C2:
PF0139113=Collagen=PD(14.1=52.4)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping 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]