BtaINT0042308 @ bosTau6
Intron Retention
Gene
ENSBTAG00000019081 | COL7A1
Description
collagen, type VII, alpha 1 [Source:HGNC Symbol;Acc:HGNC:2214]
Coordinates
chr22:51870171-51870458:+
Coord C1 exon
chr22:51870171-51870206
Coord A exon
chr22:51870207-51870386
Coord C2 exon
chr22:51870387-51870458
Length
180 bp
Sequences
Splice sites
5' ss Seq
CCGGTAGGT
5' ss Score
9.39
3' ss Seq
TGCTGTTCTCTATCCTGCAGGGA
3' ss Score
11.27
Exon sequences
Seq C1 exon
GGAGAGCGAGGACCTCGAGGCCCAAAGGGGGAGCCG
Seq A exon
GTAGGTGAAGGACGGAGGGGAGGGAACCAAGCTGGATGTCCCGGGGGGAGCAGAGTTGCCCCCCAGCCTGACACTGTGCAGGGCCTAAGGCATCATGAGGAATAGCTGGGGACCTCTGGGGCTTCTCCCACCTCAGGGTTCCCATACCCTGAATCCTGCCTGCTGTTCTCTATCCTGCAG
Seq C2 exon
GGAGAGCCTGGACAAGTCATTGGAGGCGAGGGCCCAGGGCTTCCTGGGCAGAAAGGGGACCCTGGACCTCCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000019081:ENSBTAT00000025418:34
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(16.7=100)
A:
NA
C2:
PF0139113=Collagen=PD(16.7=45.8),PF0139113=Collagen=PU(27.4=70.8)
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:
GAGGACCTCGAGGCCCAAAG
R:
GAGGTCCAGGGTCCCCTTTC
Band lengths:
99-279
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]