BtaINT0041323 @ bosTau6
Intron Retention
Gene
ENSBTAG00000004582 | COL20A1
Description
collagen, type XX, alpha 1 [Source:HGNC Symbol;Acc:HGNC:14670]
Coordinates
chr13:54736838-54738839:-
Coord C1 exon
chr13:54738786-54738839
Coord A exon
chr13:54736892-54738785
Coord C2 exon
chr13:54736838-54736891
Length
1894 bp
Sequences
Splice sites
5' ss Seq
AGGGTGAGT
5' ss Score
9.25
3' ss Seq
AGTCCATCTTCCCCCTCCAGGGT
3' ss Score
9.54
Exon sequences
Seq C1 exon
GGCCTCCCCGGGCGGAACGGAGCCCCAGGAGAGCAAGGCTTCCCAGGGCCCAGG
Seq A exon
GTGAGTCATGGGGCATCCTGGGGGTGGGTGCAGGAGTGAGCGCCCTGCAGTCCAACCCTAGGCAGGAGGGGGACCACAGCCTGGGCACCGTGTGACGGGCAGTCTTGGGCGCCGGCCGGGCCACGTGTGCTCTGCCCTCCCCTGTGTTTCTCCCTTTAGCCGCTCCACCCCCTTGGAAGTTGCTGGCATTTTATTGTTGGATGCATGTCTTCGGGCCCCGTTCGACTGGCTTTTCTCCTTCATTCGAGGAGCTCTAGGTTTTCTGGGAACCCTGTGCTCTGAGCTGTGACTAGTGTACCGAGTCGTGGTCTCCTGACCTGGCTTATGATATGTGTGGCAGGCAGATTTAGGATCCACTTTGTCTCATCGGCTGTGTCGGCTGTGTGGGTCTGTCTCCACGGCTCCTGACTCGCTTTGTATTTAAAGGCCTTCCCTTAGTCTGTGAGGACCACCTCCTCATGGGCCTTGAAGTGCTTCTAGCACCTTCCAGCCTGGAACTGTGGTTCCTCCTTCCTCCCCAGACCACTGCCCCTCGGTCCTCTATTTATTGAGTAGCCATTCCCCCACCCCCGCCACTTCAAATGCGGTCTAATCACATCACCAGCTTTGCACGGAGTCCAGAATCCAAATAGCTCTTCAGACACAGGAGCAGCCACCGTCCTGGCAGGGATGGGTCCAGCTCTACATCCTCTCCCCTAAACCCCCTGTCCTCTCTGTGTATTGTTTTTGGGCCCCATTTCTTACTCAATTACCTTATTTGCAATTGTTTTTTAATTTCATATGGTTTCCTTGGACTTTCCTGGTTTTTATTTACAGCACCTGTGAAAAATCATATCACTGTCTCCTTTTCAATTTTCTCTTTCTTTTTAAAATTTTTTTCTTGCTTATTTCTCTGGTGTGGGTGACACTCCAGAGTTTGTTAAGGAAGCCCGGTGATAGCAGACATGTCCATGTTAGCTTCACAGAAATGCTTCTGGGGTTTGCCCGTTGAGTGTGGGGCCGGCCTGGGAGCTGAGACAGATGGATTTTGTCATGTGATAGTCAAATCCTAACCTTATTTTATTAGGAGACTTTAAAAATCAAGAATGGGTGTTAAATAAGATTTAGTGCCTCATCAGCTGCTCTGAACACAAGCAAATCGTTTTCCTTTTTGGAGCTATTAGTTTGGTGAATGATTTAATCTCTCTCGAATGCTGAACTCTTCCTGCTCCCGCTAGAAGCCGGCATGGTCACTGAGCCCTCACCACTCATTTAACAGGCTGCAGGCTTCTGTGTGCTCATGTTTTATTTAGGATTTTCACATTGATATTCGCAAATGGGAATGCCTGTGGTTTTCTTTATAGAATTTGGTGCATTGATATGCTTTAACTCTCAATTATTTGAAAGCATTCTTTAAAAAAAAACCAAAAAACTGCAAATCAAGCCATTTAAATGGTGTTGGTGGCCTCTGTCCCTTAGAGGTTTGGTAGGATGTTTCGGTGTCTGGGGTTCGAAGCTCTGTGACTGGACTGTCAGAGCTGGCCCAGCTCCTAGCTATAGAGTGGGGTTGCAGCAGGACCCTCTCAGGGTGGGCCGTGAGGGTGAAGATGCCTGTGTGTGGGCGGGTCTGCCCCGCCCCCCCCGCCCCCCCCCCCCGCCCCCCGCCGACCCAGGGCAGGATCAAAGGAGGGGCTGTAGGAGGAGCCATGTGCCTCCTCAGCCCCCATCTCCCATGTCTCCAGGGAGAGCCCGGGCCACCTGGACAGATGGGACCCGAGGGTCCTGGGGGTCAGCAGGGGTCACCGGGCACCCAGGGCCGCACCATCCAGGGACCCGTGGTAGGTGCTGCATCCCCCCGCCCTGTCCCCCCACCCCCTCCCCTCGCCTTCCCGCCCAGTCCATCTTCCCCCTCCAG
Seq C2 exon
GGTCCGCCAGGGGTCAAAGGAGAGAAGGGGGACCACGGACACCCCGGCTTGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000004582:ENSBTAT00000065814:27
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=FE(28.8=100)
A:
NA
C2:
PF0139113=Collagen=FE(30.9=100)
Main Inclusion Isoform:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development