BtaINT0042004 @ bosTau6
Intron Retention
Gene
ENSBTAG00000047998 | COL5A1
Description
collagen, type V, alpha 1 [Source:HGNC Symbol;Acc:HGNC:2209]
Coordinates
chr11:106872754-106873512:-
Coord C1 exon
chr11:106873459-106873512
Coord A exon
chr11:106873010-106873458
Coord C2 exon
chr11:106872754-106873009
Length
449 bp
Sequences
Splice sites
5' ss Seq
CCAGTGAGT
5' ss Score
8.28
3' ss Seq
CTGCCCTCTTCCGCACCCAGGGC
3' ss Score
9.62
Exon sequences
Seq C1 exon
GGTCCCACTGGCCCGAAGGGTGAGGCAGGCCAGCCAGGACCCCCTGGCCCACCA
Seq A exon
GTGAGTAGCCCTTGAGGACTCGGGAGTTGGGGGGTCCCCTGATGCTGAGGGAATTGTGTGGTTTGATCCCAAAACATTCTTAACAATGTGTGACGTGTGGTGGGGCGGGGCCTGGCCCTGGACACAGGTCAGCCCATGGCGCCTCGCCCTCGGAAGTATGGCTGGGGAGAGATGAAGGGTGAGCAAACACACACGTGTGTGTGTGTGTGCACCCACATACCTCTGTGTGAACAGGTGTGTATGCACGCATATGCGTGTGTGTGTGCACACATGCGTGTGTTGGGCAGGGGTCAGGCAGCACCGGGCAAGGCCTTGCGGGATCATGTGGAATGTTCCAGAGACATAGAAAAGGGAAGAAGACTGTGCTGAGATGGACAGGCGCCTGCAGCTGCGGCCCTGGCTGTGGGCCCTGCCCTGCCCCACCCACCACTGCCCTCTTCCGCACCCAG
Seq C2 exon
GGCCCCCCAGGCGAGGTCATCCAGCCCCTGCCGATCCAGGCATCCAGGACCCGGCGGAATATCGATGCCAGCCAGCTGATGGACGACGCAGAGGGCGAGCAGTACATGGACTATGCGGATGGCATGGAGGAGATCTTCGGCTCGCTCAACTCCCTGAAGCTGGAGATCGAGCAGATGAAGCGGCCGCTGGGCACACCGCAGAACCCCGCACGCACCTGCAAAGACCTCCAGCTCTGCCACCCCGACTTCCCTGACG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000047998:ENSBTAT00000063052:68
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=0.791
Domain overlap (PFAM):
C1:
PF0139113=Collagen=FE(30.4=100)
A:
NA
C2:
PF0139113=Collagen=PD(14.3=9.3),PF0141013=COLFI=PU(12.7=31.4)
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:
GGTCCCACTGGCCCGAAG
R:
CGTCAGGGAAGTCGGGGT
Band lengths:
310-759
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development