BtaINT0042372 @ bosTau6
Intron Retention
Gene
ENSBTAG00000019081 | COL7A1
Description
collagen, type VII, alpha 1 [Source:HGNC Symbol;Acc:HGNC:2214]
Coordinates
chr22:51882902-51883260:+
Coord C1 exon
chr22:51882902-51883009
Coord A exon
chr22:51883010-51883188
Coord C2 exon
chr22:51883189-51883260
Length
179 bp
Sequences
Splice sites
5' ss Seq
CGGGTAAGG
5' ss Score
10.17
3' ss Seq
TTGCCTCATTTTTACCATAGGGT
3' ss Score
9.18
Exon sequences
Seq C1 exon
GGAGACTCAGGGCCCCCCGGATCCCCCGGACCTCCTGGTATTGTGGGGTTCCCCGGTCAGACAGGCCCTCGAGGAGAGCTGGGGCAGCCGGGCCCCAGTGGAGAGCGG
Seq A exon
GTAAGGGGGCCAAGGGCTGCGTGTAGGGATTTGCTGGGCCCAGGACCTCTGGATCTGGTTGCGGGTGAGGAAGAGGAGGGGACCCAGCCCTGCCCAGGGGGCTCCTGTTCTTGGGGGAACAGCATGGGAGGAAGGTTCCCCAATCTCCCTTCCTCTCTCTTGCCTCATTTTTACCATAG
Seq C2 exon
GGTCTGGCAGGTGCCCCAGGGAGAGAGGGAGCCCCAGGTCCCTTGGGGCCGCCTGGACCACCTGGGTCAGCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000019081:ENSBTAT00000025418:94
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(64.8=100),PF0139113=Collagen=PU(28.3=47.2)
A:
NA
C2:
PF0139113=Collagen=PD(0.1=0.0),PF0139113=Collagen=FE(38.3=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GATCCCCCGGACCTCCTG
R:
CAAGGGACCTGGGGCTCC
Band lengths:
134-313
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]