BtaINT0041336 @ bosTau6
Intron Retention
Gene
ENSBTAG00000004582 | COL20A1
Description
collagen, type XX, alpha 1 [Source:HGNC Symbol;Acc:HGNC:14670]
Coordinates
chr13:54747513-54748027:-
Coord C1 exon
chr13:54747863-54748027
Coord A exon
chr13:54747668-54747862
Coord C2 exon
chr13:54747513-54747667
Length
195 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGC
5' ss Score
9.6
3' ss Seq
GGCTCCTCTCCCTCCCACAGCTA
3' ss Score
9.88
Exon sequences
Seq C1 exon
GCGTGAAGAATGCCGACGAAACCGAGTTGAGGCTCCTGGCATCCCAGCCGCTGGACATCACCGTCCACAATGTGCAGGACTTCCCCCAGCTCAGCACACTCTCCGGCCTACTCAGCCGGCTCATCTGCCAGAAGGTCCAGGGCAGGAGCCCGCGTGGGAGCCCAG
Seq A exon
GTGAGCGACGCGGCTGGGGCAGGGGCAGGGTTGCCACACCAGGTGCAGCCCCACCAGGTCCCCTCCCACTGGGCTCTCAGGGCTCCCAGGACAACTGGGGAGCCCCTGTCCTTCCTGGAAGTGGCCGCCAGGGGGCGCAGGCAGAGCCACTGACACCAGCCTCCCCCTGGGCCTGGGCTCCTCTCCCTCCCACAG
Seq C2 exon
CTACACCGGCCCTGGATCCCCCTCCTGCTCCCACAAGGCTGGTCCTGACCCAAGTGACCTCCTCCAGCGTCCTCTTGTCCTGGAGCCCGGCCCCACAGCCGCCCCTCAAGTACCTGATTGTGTGGAGGCCTTCCAAGGGCGGCACCCCCAGGGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000004582:ENSBTAT00000065814:9
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.143 A=NA C2=0.308
Domain overlap (PFAM):
C1:
PF0009223=VWA=PD(21.4=66.1)
A:
NA
C2:
PF0004116=fn3=PU(53.8=82.7)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ATCACCGTCCACAATGTGCAG
R:
GAAGGCCTCCACACAATCAGG
Band lengths:
242-437
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development