BtaINT0078130 @ 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
chr13:20281513-20282633:+
Coord C1 exon
chr13:20281513-20281735
Coord A exon
chr13:20281736-20282400
Coord C2 exon
chr13:20282401-20282633
Length
665 bp
Sequences
Splice sites
5' ss Seq
TAAGTAAGT
5' ss Score
8.07
3' ss Seq
AATCATTTGCATTTTAACAGAGA
3' ss Score
6.03
Exon sequences
Seq C1 exon
GAAATGGTGTTTGCAAGTGTCGAGTGTGTGAGTGCAACCCTAACTACACCGGCAGCGCCTGTGACTGTTCTCTGGATACCACTTCCTGCATGGCCGTGAATGGACAGATCTGCAATGGCCGCGGCGTCTGCGAGTGTGGTGCCTGTAAGTGTACAGACCCCAAGTTCCAAGGGCCAACCTGTGAGATGTGTCAGACCTGCCTTGGAGTCTGTGCTGAGCATAA
Seq A exon
GTAAGTATTTCTCAGTTGCTTGAAATAGGTGATTGCTCACTGTTCGCCTGTGTATGAACACACGGTCCATAGAACAGTGCTAATACTAGGCCACGCTGTAAATAAAGTATCTGTCACATTGAAGCCCACTTTTTAAATCTAAAAATTCTCAATCGCTAGTGTTTGCACATGATAGTGAATTGTATCCTATGAGGGTGGTGGTACCATTATTTCAACCTGAATTTTGTATTTAATTGAATCCATGTGGTAACCTTTGTTAAATTAGTATTACCAATTGCTAATTAATTTATTTACTGCCTTTTGACTAAATAAAATGGAAGGTTTTGTCCCTTGCAGAAAGAACCATAATACCAGCAATACATTTCAAAAGTTATTTTGGCTTTATATTGTATATTTCATATCTGATAGGGCTAGTTTTAGCTTACTACTGTTATTTCTTTTGGAGGATTTTAGTTTGGGCTGTAATAAATCTGTAATTTCACTTAGGAAGCTAGCGTCTTTATGTTTAGTTTTCCCACCAAGAAATGTCATATGTTTTTTCATTTATTCATATCTTCTTTCATCTCTCTTGGCCTAATTTGGTCAAATTTTGAGTCTAGCACAGAAAATAATCTTTAAGCAAATATTATTATAAATAATAAATATAATCATTTGCATTTTAACAG
Seq C2 exon
AGAATGTGTTCAGTGCCGAGCCTTCAATAAAGGAGAGAAGAAAGACACATGTGCTCAGGAATGTTCACATTTCAACATTACCAAGGTTGAAAATCGGGACAAATTGCCCCAGCCAGGCCAGGTGGATCCCTTGTCCCACTGTAAGGAGAAGGACGTTGACGACTGCTGGTTCTACTTCACATACTCCGTGAATGGGAACAATGAGGCCACTGTTCATGTTGTAGAGACTCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000015910:ENSBTAT00000056716:13
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=0.013
Domain overlap (PFAM):
C1:
PF079748=EGF_2=PD(64.5=26.7),PF079748=EGF_2=WD(100=42.7),PF079657=Integrin_B_tail=PU(4.5=5.3)
A:
NA
C2:
PF079657=Integrin_B_tail=FE(87.6=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:
GTGCAACCCTAACTACACCGG
R:
AGTCGTCAACGTCCTTCTCCT
Band lengths:
356-1021
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development