BtaINT0078140 @ bosTau6
Intron Retention
Gene
ENSBTAG00000015910 | ITGB1
Description
Bos taurus integrin, beta 1 (fibronectin receptor, beta polypeptide, antigen CD29 includes MDF2, MSK12) (ITGB1), mRNA. [Source:RefSeq mRNA;Acc:NM_174368]
Coordinates
chr13:20277065-20277529:+
Coord C1 exon
chr13:20277065-20277160
Coord A exon
chr13:20277161-20277439
Coord C2 exon
chr13:20277440-20277529
Length
279 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAAT
5' ss Score
8.88
3' ss Seq
GTTTTATCTTTTAATTGCAGGAA
3' ss Score
9.49
Exon sequences
Seq C1 exon
GATTATCCTTCTATTGCTCACCTTGTCCAGAAACTAAGCGAAAATAACATTCAGACGATTTTTGCAGTTACTGAAGAATTTCAGCCTGTTTACAAG
Seq A exon
GTAAATATATACTTGTGAGATCAAAATAGGAACACATTTCTAGATCCTTATTGTTTAGTCATCAAAGGCAAAATGATATGTCTGAATTGAAATGTGGGAAAATGTCATCAGATAGGCTAGATTTTACAAATGTGGTATTTTAATTACATTGCAAAACTAGTTTTTAGGTCTGACTCCTTATTTAGGATATATATCTAGAAATGGTTTTTAAAAATAAATAGTAGGCACTCAGTAGATGCTAATTAGTCAGATTTTATAGGTTTTATCTTTTAATTGCAG
Seq C2 exon
GAACTGAAAAATTTGATCCCTAAGTCAGCGGTAGGAACATTATCTGCAAATTCCAGCAATGTGATTCAGTTGATCATCGATGCGTACAAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000015910:ENSBTAT00000056716:8
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0036213=Integrin_beta=FE(7.2=100)
A:
NA
C2:
PF0036213=Integrin_beta=FE(6.7=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:
TCCTTCTATTGCTCACCTTGTCC
R:
TTGTACGCATCGATGATCAACTGA
Band lengths:
180-459
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development