BtaINT0041306 @ bosTau6
Intron Retention
Gene
ENSBTAG00000004582 | COL20A1
Description
collagen, type XX, alpha 1 [Source:HGNC Symbol;Acc:HGNC:14670]
Coordinates
chr13:54746168-54747237:-
Coord C1 exon
chr13:54747108-54747237
Coord A exon
chr13:54746314-54747107
Coord C2 exon
chr13:54746168-54746313
Length
794 bp
Sequences
Splice sites
5' ss Seq
CAGGTGTGT
5' ss Score
6.99
3' ss Seq
TCTGCTCCCGTCTCCCCCAGCAC
3' ss Score
9.59
Exon sequences
Seq C1 exon
GTGGTGGTGGAAGGGCCCACCTCGTCAGCACAGCTGCACAACCTGACCTCCAGCACCGAGTACCTGGTCTCTGTGTTCCCCCTCTACAAGGCTGGCGTCGGCGAGGGCCTGCAGGGCCTGGCGACCACAG
Seq A exon
GTGTGTGCGTGAGCTGAGGGTTGTAGGGGCTCCCCCCACCTGCAGCCTCCCCTTGGAGCCCGGCACCCTCAAGGCGGTCTGAACCCAGGCAGGGTACCACACCCAACAAAGGCCGAGTCACTGGGCCGCTCTGACCCTCAGTGTCCTCTTCTGAGCACAAGTGACATCCTTTGTATCACATCCCTAACACACAGGGACCCATCACTGTTGCTGCCACACTGTGGAGCTCCCACCCTGCCTGGCCTGCAGTTCCCCCAGGACTGCGTGAGACCCGCCACCTGGCGACTTTATTGAGATACACCCCACAGTCACCTGTTCACAGCGGGTGATACTGTTGTTTTCCATATAGTCCCAGCATTGTGCACCCGTCACCCTGAAGGGGGCCCCACACCTTAGTGGTCACCCCAATCCTCCCCTCCCCCACAGTCCCTGCCGACCCCTGATCTGCTCTCTGTCTCTGGGGTTTGCGGATCCTGGACCCTCCATCTAAATGGGACCACACAGGCTGTGGCCTCTTAACCCCAGGCCACGGCCCTCTCACCCTCAGGGCAGGTGGCCTTAACAGAAACCTGCGGGGCGGTCCAGAGTGAAATAAGTTCCAGGACTTACAGTCAGTTGTCTGTCCTCCCCTACCCCTGCTGGTCTTCCCCTCTCTGTGTCTCCATCTGGACACACCTAGCCTGCGCCTACCAAGGGACTGACAGGTGTCTGTCCTCCCCCGACTCCCGCTGGTTGATAGGTCTGATTTCTGCCTGCTGCTGCATTTTTAAACTTTCTGCTCCCGTCTCCCCCAG
Seq C2 exon
CACCCCTGCCCCCACCCCAGGCGCTGACCCTGGCTGCAGTGACACCCAAAACTGTCCGCCTCACCTGGCAGCCCTCGGCAGAGGCCACCCAGTACCTGGTGCGGTGGTCACCTGCCTCCCCCAAGGGCGAGGAGGAGAGGAGAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000004582:ENSBTAT00000065814:11
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.386 A=NA C2=0.510
Domain overlap (PFAM):
C1:
PF0004116=fn3=PD(43.8=79.5)
A:
NA
C2:
PF0004116=fn3=PU(55.6=91.8)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTGGTGGTGGAAGGGCCC
R:
CTCTCTCCTCTCCTCCTCGC
Band lengths:
276-1070
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development