BtaINT0042263 @ bosTau6
Intron Retention
Gene
ENSBTAG00000019081 | COL7A1
Description
collagen, type VII, alpha 1 [Source:HGNC Symbol;Acc:HGNC:2214]
Coordinates
chr22:51859652-51860389:+
Coord C1 exon
chr22:51859652-51859736
Coord A exon
chr22:51859737-51860202
Coord C2 exon
chr22:51860203-51860389
Length
466 bp
Sequences
Splice sites
5' ss Seq
GAGGTGGGT
5' ss Score
7.07
3' ss Seq
ACCCTGATGACTCTTGCCGGCCA
3' ss Score
-5.11
Exon sequences
Seq C1 exon
ATGAGGCTGCGGCTCCTGGTGGCTGCGCTCTGCGCCGGGATCCTGGCAGGGGCTCCCCGAGTGTGGGCCCAGCCCAGGGAGAGAG
Seq A exon
GTGGGTACGGCAGGGAAGGACCCCATCCAGGGCACTGCACCTTGTCACCCGGCTCCACTCGGCCTTCATCCTAGAGCCCGCTTCCCACCCGCTGCAACTCCGCGGGCATTTCTCCTAACTCTCCCCCGGACTCCCCAAACCCTCCGCGATCCACGCTGCGTCTCCCCAACTGCATCCAGATGTCCGTGGGTCCCCTACCCCTATGACAGTCTGCGCTGGTCCCCAGAGGCCAACCTCAGTCCCTGATTCACCCCCACACCAGCGACTCTGCCTCCCCACCAATCCTCCGCGGGAGAGTCCGCTCCGGGCTCCACCTCTGCTCCCTCCACCGCTCCCAGGCCCAAGCCAGCCTGGGCCGGTTTGCACAGTGGATGAGGCCCACCCGCCCCCTCCCCAGCCCCAGGGGACCACTGTGAGGGGAGAGGGTAGGTGGGCTCCAGGAAGAAACCCTGATGACTCTTGCCGG
Seq C2 exon
CCACAGTGAGCTGCACGCGCCTCTACGCCGCTGACATCGTGTTCCTCCTTGACGGCTCCTCGTCCATCGGCCGAAGCAACTTCCGCGAAGTGCGGGGTTTCCTTGAGGGGCTGGTGCTGCCCTTCTCCGGGGCAGCTGGGGCACAGGGTGTGCGCTTCGCGGCCGTGCAGTACAGCGACGACCCACG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000019081:ENSBTAT00000025418:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0009223=VWA=PU(29.5=81.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTCTGCGCCGGGATCCTG
R:
GGTCGTCGCTGTACTGCAC
Band lengths:
241-707
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]