DreINT0050289 @ danRer10
Intron Retention
Gene
ENSDARG00000021720 | col7a1
Description
collagen, type VII, alpha 1 [Source:ZFIN;Acc:ZDB-GENE-030131-2427]
Coordinates
chr6:40196207-40197805:-
Coord C1 exon
chr6:40197757-40197805
Coord A exon
chr6:40196216-40197756
Coord C2 exon
chr6:40196207-40196215
Length
1541 bp
Sequences
Splice sites
5' ss Seq
GTGGTGAGT
5' ss Score
8.95
3' ss Seq
TTTCTCTTTTTGTCTCAAAGCTT
3' ss Score
8.7
Exon sequences
Seq C1 exon
GAGGATGAGATTCGGACTTATGTTCGATCTGAGATGAACCAGCACTGTG
Seq A exon
GTGAGTGGATCTTTCATAATCGTCATTTATCTACAACAATTTACCATTTTCAATAATGAGGGTTTCAATTTCTGTGTCCAATTTTCTATATTGACATTTTATTTAAAGCTGCGCTTAAAGAAACAGAGGGCCCTATCATACACCCGGCGCAATCATTCACAAGACGTGTTTGGTGCGATTTGTTGCTATTTTCAGACCAGCACAACCCTAATTTTCATGTTTTGTGCAACATTGTTTAAATTGAAAATCCATTTGCGCCCAATTGTGGACTCATGGGTGAGCTGATGTTAAAAGAAAGTGGGTTAAGGTGCATTGTTGGCGCGTTGCTATTTTGAGGAACTGAAATAGACTGCATCACTGACTAACTAAAACCTGGTCTAAAGTCCAGCACAGAGTGTGCTAATTATGCACCTTTGCAGGTCCAAAACACTTACACATTGCTTAATATACACAGGATGTACAGCAATACACACATTTCTTTACATATTCAAAAAGTTAAAGGAATTAAATGTTACAAAAATTATTATTTTCTACATAAATATAAAAATCACTACCTTCATGCCTTATCTGGAGTGCTTTTTCAGTATATTCATGACAATTTGCATTTGTATAATGTTATTATTATTAATATTATTATTTATTATATGCATATTTATATTTGTTTTAATAAGAACAACTTTAGATTTGTTTAGAACTTTAGAAATGTACGCATCACCACAAAGGGGTAAAAGAATAGGACGTGTGTTTGGATATAGCTCAGTTTTTTGACCACAAATAACAATTTAACAACTTTGTTATTATTGTTAATTTATTTGTTGGCTAGAAATTAGAACTGAATTTAGAAATAGGTTTGAAACAAGTCTTTGCGCTTAACATTTAAATATGTAGGCTTATGGATGTCTTCAGTGGAGTGCATACAACACTGTTTCGGTATCCATGAAAGTGCAGGAGTAAAATAAAGAGTAAAAGTAAAGAGAAAAAGAAAGTAAAGAGGCCGAATGGAGGAGGCTCATTCTTTATCTTTGTGCTGCAGATGCTCTGTTTAACTATTCTCTCACTAGTGAAGTGTTCAGTTTTATCACTTTCAAACTCTGCCATGTAAATAGCAAATCCGCCATGGCGTGACACAACTAACTCTTAAAGGGAATGTGAGATGAGACTCTGATTGCTTTAATGACGATAGGCTCAAAACACATGCACAACTCATTAAAAGAATAAGCACAACCCTGTTAGACCATGCGCCAGAGCGCAGAGTGTATTTTTCTGTCCCTAAAATAGCAAAAGTGGATTCGGACATGTGCTTAATGCTTTTGCGCCATTCACTTTAGACTTTGCGCCTAGATCATTAAAATATAGCCCAGAATGTTAAAGGCATAGTTCACCCTTCGTCGACAAATGATATTTTTGTTGAACAAAAAGTATTTCTTTTCACTTAGAAATACACTTTACAGAACTAAAATAGATTGCAAATGCTGATTTTTATATCATTCTTCCTTTGTTCTCTCGATTTAAGTTTCTCTTTTTCTCTTTTTGTCTCAAAG
Seq C2 exon
CTTGTGGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000021720:ENSDART00000154878:112
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.750 A=NA C2=0.533
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
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]