BtaINT0042292 @ bosTau6
Intron Retention
Gene
ENSBTAG00000019081 | COL7A1
Description
collagen, type VII, alpha 1 [Source:HGNC Symbol;Acc:HGNC:2214]
Coordinates
chr22:51860203-51861205:+
Coord C1 exon
chr22:51860203-51860389
Coord A exon
chr22:51860390-51861045
Coord C2 exon
chr22:51861046-51861205
Length
656 bp
Sequences
Splice sites
5' ss Seq
ACGGTCAGT
5' ss Score
8.02
3' ss Seq
TGCCACCTGCCTCCCCACAGGAC
3' ss Score
12.07
Exon sequences
Seq C1 exon
CCACAGTGAGCTGCACGCGCCTCTACGCCGCTGACATCGTGTTCCTCCTTGACGGCTCCTCGTCCATCGGCCGAAGCAACTTCCGCGAAGTGCGGGGTTTCCTTGAGGGGCTGGTGCTGCCCTTCTCCGGGGCAGCTGGGGCACAGGGTGTGCGCTTCGCGGCCGTGCAGTACAGCGACGACCCACG
Seq A exon
GTCAGTGGACCCCCACAACTGGACCCACGAGGAATCTTCCCCCAGTCAGAAGCAGAGAGCTCCAAGCCCCTGGGTCAGGTTTTAGGGAATCCAGGGGGTCCCCTCCTTCCACCGTCCAAGGCATCCTTTTAAGAAGCAGGGATCTCCCAGGTGGAGCCCTGACACCTGAGACCCGGCTACCCACTGGCTCCTGCCAAAGTCAGGGGCTCTGTTTTCTGATCTGGAGATGGAGAGCCTGTGGGGGAGGCCAGGGGCTTGAGATGGCCTGGGTCTGCTGGATTCCCCATGTTCTAGCCTCCTGATGCCCGTCAGCCTCTCATTCAGCAGAGGGCCTCCCTGTCTGGCCAGTGTCCACCTCCGTACAACAGGGCCCTTCCTCCTACCATTATTTAATTAAACAGACATCCCGGCCCCTGAGCCTGGGAGCCCCACTGGGGCCAGGCCTGCTCAAGCCCAGCCCCAGGCAGGACACAGAGAGGCACCTAATCACTTTGTTGGCTTGGGAGCTTCAGGGATGGAGGGAATCACAGAATCAGAGAACGGAGAGGACCCTCAAGGGGGCCTGATAACTCACCACCCTCACCCTAGAGACCTCTGAGAGGCCAAGGCCAGCACAGGTTCTTGTCCCTAGCCTGCTGCCACCTGCCTCCCCACAG
Seq C2 exon
GACAGAATTTGACCTGGATGCACTTGGCTCAGGCGGAGATGTGATCCGTGCCATCCGAGAGCTCAGCTACAAGGGGGGCAACACGCGCACAGGGGCCGCGATTCTCCACGTGGCTGACCGCGTCTTCCTGCCCCAGCTGGCCCGACCTGGTGTCCCCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000019081:ENSBTAT00000025418:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0009223=VWA=PU(29.5=81.0)
A:
NA
C2:
PF0009223=VWA=FE(30.6=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GAGCTGCACGCGCCTCTA
R:
GACACCAGGTCGGGCCAG
Band lengths:
334-990
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]