DreINT0050352 @ danRer10
Intron Retention
Gene
ENSDARG00000021720 | col7a1
Description
collagen, type VII, alpha 1 [Source:ZFIN;Acc:ZDB-GENE-030131-2427]
Coordinates
chr6:40228430-40230597:-
Coord C1 exon
chr6:40230553-40230597
Coord A exon
chr6:40228466-40230552
Coord C2 exon
chr6:40228430-40228465
Length
2087 bp
Sequences
Splice sites
5' ss Seq
ACTGTAAGT
5' ss Score
8.59
3' ss Seq
TCTATCGAACTTTTTTTCAGGGC
3' ss Score
8.5
Exon sequences
Seq C1 exon
GGTAAAGCAGGGGAGGACGGCAAATCAGGACTGCCTGGAAAGACT
Seq A exon
GTAAGTGAAGTTATAATTATTCATTCATTCAATCATGTTCTTTTTGGCTTAGTCCCTTTATTAATCCGGGGTCGCCACAACGGAATGAACCGCCAAATTATCCGGCACATGTTTTAAGCAGCGGATGCCCTTCCAGCTGCAACCCATCACTGGGAAACACCCATACACTTCCATTCACACACATACACTACGGACAATTTAGCCTACCCAATTTACCTATATCACATGTATTTTGAACTTGTGGGGGAAACCAGAACGCCCAGAGGAAACCCACGCAAACATGCAAACTCCACACAGCAACTGACTCAGCCGAGGCTTGAACCAGCGACCTTCTTGCTGTGAGGCGAGAGCACAAACCATTGCGCCACCGTGCTGTCCAGCTATAATTATATATTCTTTCAAAAGTATATTTACATCTACAGTACATGCTGGGTACATTTCTCTTGACATTTTCAACAACTCCATTGTAATATAAGTCGCATGCAGTGCTTTCCACACATAAACGCTTATATTAATGGCCGGCCATTTATATAAATTTTTTTTTACCAATATTATCATCCTATTTCACCTTTTTTGTATCCGCCAAAGATAACCAAACATCCTCGTTCAATTAACCAGTGGAAAATCTTCTCTCGCCCTGCACATTTCATACTGCTCATTGTGTGCGTGAACTGTAAACAACAGTTCCTCAGACAGTCTCACGCGCTCTAGAGACCCACAGAGATGTGACTTTTTTAGGCTTGAAAATGCATTCAGCAACTTCAACCAATGATTCTAAATCTCCTAAAATGTCCGGGAGTCGATTTTGGCTTTGGCTTTCTAAAGTTGTTGCGTTTTTGCATTACTTTTTTATTTAAGACTACTTTCCGCTTGGCTTCACAGCTGCCAGCGTGTACACAGCTGCGAGACCGAGAGAAAAAGTAAATAATAGATTCTTTAATCTAAACGACTCAAAAAACTTTACTAAATACTCGGACAAATACATATTAATACAAATATATGTACACCATTATAAATGAGCAATCGACTCATTTGCCTTAAATAAACAATCCACACTTTTTATTTTAGGTATTAATAATTGTTATTAAATATCCATTTTAGAGATATCGTCTGTTTTTATTCATTTTTCCTGTAATTTATTTCTCATTTGCCGTATATAATATTAATTTGATGATGTTAATACATTACATATTTTATACATATCTAATAGGCTTTGGCAATACTGTATTAATGTCATGCCAATAAAGCAACCTGAACTTGAGAGAGAGAATGCAGCTGTGTGCACATGGCTCCTAAATAGCATCATTTTTTTATTTTTTTCAACAGCCATTTCAAATAAACTGTATAACAGTGTCATAATAAATACCAGTATTGTTAAAAATCACATTATTTTTGTTTCACGTGTAGTTAACCATTTATGTGCCATGAGTAAAAGATGTGTTTCAATACGGCTACCACTGCAAGTATATTTCAAACCTGTGGGAAGCACTGCACATGTATGGATTTCCAATCAATTTTTTTTCTCAGATCAGCTCCATCTAGAATGCAGACACTCATTCTAGTTTAGTAGCCACACCAGAGCCCTTGTTCTCCATAAAAGAGACGATTAAACCATCCTGCTGATTATAAATCACCCTCTTAGCAGCCGTTCAGTGGGAGGCAACGCAGCCTAATAAACGCTTTATAGTTCAAATATGTGAGGAGTTTCAGTCAGCCATGTACTAATGTTCGGTTAACCTGACTCAGATAGATTACACCGCTGGCGCCGAGCTTACGCAAATCCCGCTCGTCCTGCAGTTTCTACTGATTTACTGATCACAGCCCCGAACCAGCTGTGGTAATTGCAGGAGCTATATCGGGCTGGATGGCACCCGTCATATATCTGTAATATAAGGCTGCGCGTCGCATGAAGCGTTTAGAAGAGAAATTACTGCTTGAATGAGCCACACAAAATTACAAGAGTTCTCATACCAAAACAGGAAGAGCTGATTACAGGAAGTCTTGATTACAGAAATTATGAAATCGCGCCTTGCACTCCTCCAGATGTCTGTGTTTAGCACCTCGTTTTCTATCGAACTTTTTTTCAG
Seq C2 exon
GGCGAAGATGGCGTGCCAGGAGAGGATGGTCGAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000021720:ENSDART00000154878:64
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(17.1=100)
A:
NA
C2:
PF0139113=Collagen=FE(13.4=100),PF0139113=Collagen=PU(18.3=91.7)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
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]