BtaINT0041591 @ bosTau6
Intron Retention
Gene
ENSBTAG00000013155 | COL2A1
Description
Bos taurus collagen, type II, alpha 1 (COL2A1), transcript variant 2, mRNA. [Source:RefSeq mRNA;Acc:NM_001113224]
Coordinates
chr5:32458913-32459666:+
Coord C1 exon
chr5:32458913-32458990
Coord A exon
chr5:32458991-32459621
Coord C2 exon
chr5:32459622-32459666
Length
631 bp
Sequences
Splice sites
5' ss Seq
ATGGTAAGA
5' ss Score
9.48
3' ss Seq
CATTTTCTGTTCCAATGCAGGGC
3' ss Score
9.29
Exon sequences
Seq C1 exon
AACTTTGCTGCCCAGATGGCTGGTGGATTTGATGAGAAGGCTGGTGGCGCCCAGATGGGAGTAATGCAGGGACCAATG
Seq A exon
GTAAGAAAAGGCACCAGTTCTTTGCAGCCAAAATGGCAAGAGGTGGCCCTCAGCAGAGCCAGGGACTCTGACAACCTCACTTTAGAGATAATTACTTGGAGCGGCCCTTCCCCATCAGTTATATAACCTCCCATTTAGCTAGCCCAGAGCATTTGGTTTTTAATGGCGATGGATGCCAGTTTTAATGATGCGCTGGAGTGACTAAGAAGAATGAGGATGGAGAGAGGCATATAGGCTGATCTGTCAGAAGGCCAGTTGCTATTGCTCTTGGAATGAGAACTGAAGAATGCAGACAGCAGCCACTGTTCTCCAGCATCCACAAGACTTCCAGCAGGAAATCTCAGCCCCGCAGCTCCCACTTGGCACATGCTAAATGAAACTCAGACTTTAGTAAACATGGCTGCTGTCCAGGGGAAAGCAAGGCCAGCTTCTCTGTCCAAATGGTACCTATAAATAAAAATAGAATGTTGCAAGGGGAGAGGGAAATGAGAGGGAGCAGCCCCTGCCGGCCCCCTGCTCACAGAGTAACTCCTTGTCCTTTGTCTGGACTGTTGGCTGGGAGGCGGCAGCACCATGGAGGCCGAGGGTGAAGCCTTTCCAGTAAAGCTCCTCATTTTCTGTTCCAATGCAG
Seq C2 exon
GGCCCCATGGGACCTCGGGGACCCCCAGGCCCTGCTGGTGCTCCC
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000013155:ENSBTAT00000017509:7
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=PD(4.5=11.5),PF0139113=Collagen=PU(6.6=15.4)
A:
NA
C2:
PF0139113=Collagen=FE(23.0=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
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]