BtaINT0041335 @ bosTau6
Intron Retention
Gene
ENSBTAG00000004582 | COL20A1
Description
collagen, type XX, alpha 1 [Source:HGNC Symbol;Acc:HGNC:14670]
Coordinates
chr13:54747863-54748887:-
Coord C1 exon
chr13:54748723-54748887
Coord A exon
chr13:54748028-54748722
Coord C2 exon
chr13:54747863-54748027
Length
695 bp
Sequences
Splice sites
5' ss Seq
TGGGTGAGC
5' ss Score
7.23
3' ss Seq
TTCTCTCAACACTGCGGCAGGCG
3' ss Score
2.83
Exon sequences
Seq C1 exon
GCCTGGCCCTGACCCACGTGCTGGAGCAGAACCTGAAGCCCAGAGCAGGTCTCCGTCCAGAGGCGGCCAAGCTGGTGATTCTGGTGACAGATGGCAAGTCCCAGGATGATGCCCACACTGCTGGCCACGTGCTCAAGGGTCTGGGTGTCGACATCTTTGCTGTGG
Seq A exon
GTGAGCAGCACCCCCCCGGGCTCTCAGTGGGCATTCTCACAGAACACAGCAGGGTGGCTCCCGGCTCCCCAAGCTGCAGGTCTTGTGGCCTCTGAGCCTCAGCACCTGCTCCCGCCCCCCAACCCCATCTATGAATGGGAGGAAGAGTCCCTGCTCTGAAGACCTGAGTTCCCACCTGGACAATTGGAGGTGGCCACACAAGTTGGCGTGGGCAGCCTGGCCACTCCCTGGTGAAGTGGCCAGTTGGCAGAGTCATCTGTGGACATGTTTGTGGCCCCTCCCTGTTCCCCACACCATATGCCCTGGGGACCTCTCTCTGCTACCATAGCCAGCCAGTCACTAACTCCATCCCTTGGGAGGGAACTCCAGACCTGGGGGCAGGGTTTCTGGAAGCAGAGACCCTGCTCTGTGCCTGACCCCAGCCCCTGGGTGAACAGGACCCCAAGGAAAGCACACTGACCTCTCTCCTGGCTGCAAGCTCCACAGAGACCTGGGCAGGCATGCCACAGGCACCTTCACACCAACCTGTCTCTCATGGGCACCTGGCCAGGTGACCCCATTCCGGGGCCTGTGGGGTCTGGGGTCCTTGGGAAGGGCTCTCTGCCGACTGGGTGACCAGCAGGGGCCCAGTGGTCCTGACTGCACAACAAACATGGGTGCTGAGTGGGCTAACCCTTCTCTCAACACTGCGGCAG
Seq C2 exon
GCGTGAAGAATGCCGACGAAACCGAGTTGAGGCTCCTGGCATCCCAGCCGCTGGACATCACCGTCCACAATGTGCAGGACTTCCCCCAGCTCAGCACACTCTCCGGCCTACTCAGCCGGCTCATCTGCCAGAAGGTCCAGGGCAGGAGCCCGCGTGGGAGCCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000004582:ENSBTAT00000065814:8
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.054 A=NA C2=0.143
Domain overlap (PFAM):
C1:
PF0009223=VWA=FE(31.8=100)
A:
NA
C2:
PF0009223=VWA=PD(21.4=66.1)
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:
CTGGCCCTGACCCACGTG
R:
CTCCTGCCCTGGACCTTCTG
Band lengths:
311-1006
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development