BtaINT0041326 @ bosTau6
Intron Retention
Gene
ENSBTAG00000004582 | COL20A1
Description
collagen, type XX, alpha 1 [Source:HGNC Symbol;Acc:HGNC:14670]
Coordinates
chr13:54751752-54753272:-
Coord C1 exon
chr13:54753162-54753272
Coord A exon
chr13:54751896-54753161
Coord C2 exon
chr13:54751752-54751895
Length
1266 bp
Sequences
Splice sites
5' ss Seq
CAGGTAGGG
5' ss Score
9.46
3' ss Seq
TCTCCCCAACCCCACCCTAGGGG
3' ss Score
7.56
Exon sequences
Seq C1 exon
CGAGTGGCCGCCTGAGGCTGGCGGTGCTGCCTGAGGACCGGCTGCAGATGAAGTGGAGAGAGTCAGAAGGGAGCAGCCTCGGCTACCTGGTGCAGGTGAAGCCCAGGGCAG
Seq A exon
GTAGGGGCCTGCGCCTTGCCTCTGTGCAGACCGACGGTGAACACGCTCAGCACGGCGGTCGCAGTGCTGGTTCCCCTGGGCTCTGCCCTACCTCCTCGCTGTCTCCCCACTAGCACAGGGAGGTTGTGGCGGGAGAACAGGGCCCTTAATGTCCCCGCCGTGTGTCCCCACACCTGGCACTTGCAGAAGGCAGTCAACGACTTTGCAAAAAAAGGGCCCTCCCCCAGCTTAGAGTTCTCAGGGCCCTGACAGTGCCAAGCCCGAGTGGCAGACTCGCTCCATTTTAGGAGTTAAGGTTGTTTGACATTGGGCTTCAGCTGTTTCAAGAGCTGACCTGTCCTCAGAAACCCTTACACCTGGGTGGAGCTCTTCAGGGTCTCAACCCCAAAGAATTAGGAGGGGGGATGTGCCAAGGATGCACTCTTCAGAGGACCTGCCTGTCCATCCCTCCCTGGAAGGCAGCAGGAACCCAACAGACCTGGGCTTAAATCCTGATTCCGAGCAACTGTGTGACTCGATTTCCCATCTACAAAACGGGTGGGGGCTTGTGAAAATTATGCAGCTTGAGTCACGTGAAGCACCTGGGACCTCACCCTCCTGGCCTGTGCCACCTCCCCATGCAGGGCTGGGCCCAGGCTGGGGGCTGTCCACCTTGCAGGATGTTGGACAGTGGGCAGGCTTGTGAGTCCTTCCTCTCTGAGTCCCCTTTCTAGCACCTGAGGTCCAAGAATTGCCAGGTATTCCTGACCTCTGATCAGTCGCTCCTATCACCTCCGTGGCCGCCTCCCCTGAGAGCATGGCAGCATGCCCTTGGAATTGTTTCTTTGTTTTTAGCATAGACTCACAGTCACACTGGGACGTGCTTACAGGTTCACTGCCATGTGCTATCCAGCCCCTGTGCACAGGCGGCAGGCCCCCCCCCACGTGCAGCCCTGTCTGCACAGACACCTCCATGGTGTCCCCAGCGCTGCTCTGATGGCACCTGGAGAACTTACAGATCCCCCGGTGGACCCTGAGATGAGTCCCTCTGGGGAGGAGCACAGGCCACTCCCATCAGGTCCTAGAGAGAGACACACAGACCTCTCCCCCTACTCCCTCCCCTGGCCCAAAGGGAGGAACTAGGGGAGGGGAAAGAGGGGTGCCAGGCAGATTTCACCACTCCTAACACACATGTACACATATGCACACCTCAGGCATAAGTGCACACACGCATGCAGATACCACCCACCTCAGCTGCCTTGATCCCTCTCCCCAACCCCACCCTAG
Seq C2 exon
GGGACCCAGAGCAGGAGGTGATGCTGACCACCAAGACCCCCAAGGCCACTGTGGGGGGCCTGAGCCCCTCCAAGGGGTACACCTTGCAGATCTTCGAGCTCACTGGCTCAGGGAACATCCTGCTGGCTCGCAGGGAGTTTGTGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000004582:ENSBTAT00000065814:3
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.132 A=NA C2=0.374
Domain overlap (PFAM):
C1:
PF0004116=fn3=PU(48.1=97.4)
A:
NA
C2:
PF0004116=fn3=PD(50.6=79.6)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Chicken
(galGal4)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTGCTGCCTGAGGACCGG
R:
CACAAACTCCCTGCGAGCC
Band lengths:
231-1497
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development