BtaINT0042000 @ bosTau6
Intron Retention
Gene
ENSBTAG00000047998 | COL5A1
Description
collagen, type V, alpha 1 [Source:HGNC Symbol;Acc:HGNC:2209]
Coordinates
chr11:106875912-106876370:-
Coord C1 exon
chr11:106876317-106876370
Coord A exon
chr11:106876020-106876316
Coord C2 exon
chr11:106875912-106876019
Length
297 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGT
5' ss Score
10.47
3' ss Seq
TGCCCCTTTCATTCCCACAGGGT
3' ss Score
11.93
Exon sequences
Seq C1 exon
GGCCCCCCAGGACTCCCCGGCCTCAAAGGAGACTCTGGACCCAAAGGAGAGAAG
Seq A exon
GTGAGTGGCCTGCAGGCGCCCGTGCGGCTGAAGTGTGGGCCCCCTGAGAGCCTGTGCCTCGGGCCTCACAAGGTCTGGCTCGTCCCTGCCAGCGTCACCTGCTCGGGGTGGCGACTCGAAGGGAACAGATCCGTGTGGCTTGGAGACCCGGCCGCTGCCCGCTGTCGGGGCCGGCCTGGGGCACATTTCCACTGCAGGAGCTTCGAGCAGGGCGGAAGGCAGCGCTGCCGCTTCTGGCTGGGCCACGCGGCCGGACGTGAGGCGTTGCCACCACAAATGCCCCTTTCATTCCCACAG
Seq C2 exon
GGTCACCCAGGCTTGATCGGCCTCATCGGACCTCCGGGCGAACAGGGAGAAAAGGGTGACCGCGGAGTCCCCGGCCCCCAGGGCTCCTCGGGCCCTAAGGGAGAACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000047998:ENSBTAT00000063052:64
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=FE(25.0=100),PF0139113=Collagen=PU(22.4=94.4)
A:
NA
C2:
PF0139113=Collagen=PD(10.3=19.4),PF0139113=Collagen=FE(46.1=100)
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:
CTCCCCGGCCTCAAAGGA
R:
GTTCTCCCTTAGGGCCCGAG
Band lengths:
148-445
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development