BtaINT0078164 @ bosTau6
Intron Retention
Gene
ENSBTAG00000017060 | ITGB2
Description
Bos taurus integrin, beta 2 (complement component 3 receptor 3 and 4 subunit) (ITGB2), mRNA. [Source:RefSeq mRNA;Acc:NM_175781]
Coordinates
chr1:145108130-145109920:-
Coord C1 exon
chr1:145109780-145109920
Coord A exon
chr1:145108318-145109779
Coord C2 exon
chr1:145108130-145108317
Length
1462 bp
Sequences
Splice sites
5' ss Seq
CCGGTGAGG
5' ss Score
9.35
3' ss Seq
GCTCTACGTTCCCATGACAGATC
3' ss Score
9
Exon sequences
Seq C1 exon
AAACTGTCCTCCAGAGTCTTCCTGGATCACAGCACCCTCCCTGACACCCTGAAAGTCACCTACGACTCCTTCTGCAGTAACGGGAAATCGCAGGTGGACCAGCCCAGAGGGGACTGCGACGGCGTCCAGATCAACGTCCCG
Seq A exon
GTGAGGCTCCCTCCCAGCCTCTGGAAGGGGTTCCCCTTGGACAGCAAGAGGGTGTGCCCTGGCCAATGGCCTACCATGGATCAGCTAAGAGGTTGGGCCTGTCCACCTTCGGTCCAGTTCCTTCCTTTTAAAATCCACAAACGCTGTGGCCTGATGTGGACAGACCCCAGCGCCCCCTGGTGGCAAATGCTGGGCATAGCACCACATGCCTAAAAAGGGCATTCCTTCCCCTCTGGGCATCTGCTTTGGTTTGATTTTCCTGATTTTTGTGGTTTTGTTTATTGTTATTATTGTTATGAATTTATTTATTTGGCTGCGTCAGATCTTTGTTGTGGCACATGGGCTCTCCAGTTGTGGTGAGCGGGCTTAGTTGCCCCTTGGCATGTGGGATCTTAGTTCCCCAACCTGGGATGGAACCCAAGTCCCCTGCATTGGAAGGCAGATTCTCAACCCCTGGACCACCAGGGAAGTCCCTGTTTTTTGACAAAGACATTAAAGCAGGGGCCACACAGATGATTACAAGCAGGCAGTGAGTTGTTTCTCTAATAGTTTAAATTTGTCATGACCAGGAATGATTCAACGTTTCCTTTCACCAGCTGTGAATTAATATTCAGCAAAATACTTCCTTTTATTTCTGAATGACATTGAAATTCTTTCAAATATGTGACTTACTAAGTGCATGTGAACTTTGACTGAAATCTCTGCCCCTCTTACTGGGGGATCCATACCCGAATGTACTCAGTGTTGACTGCCTGATTCCTCCCTGATGTTTCTGCTCTGTCTTCATGTACTGGGTGGAGACTCACTTACGTTGACCGGCAGTGAGGCTGAGCGGGTGCTCCCTGAAGCTCCCTGAGGGCTGAGCAGCAGAGCAGTGTGTGTGTGTGTGTGTGGTGGGGTGGGGTGGGGGTGGGGGTGGGGCTCTGTGCTGCCAGCTCAGTTCTTCTGGGGCATTCAGGCTCAAGATACACCTTCACATGCAGAATCTAGGACTTCCTATGGTATTCTGACATCTTAGCCTCTGGGCTTCAGGACAAAATACCTGGAGAAAATATACATCATTTATTAATACGAAGTCACTTTAAAATCCCTTTAAGAGATGCATGATTAAAAGAATTCTAAAGACACCTCCGCGCAAGTCCAGGCCACCTGAGGATGGAGGGTGGGGGGAGCTGGGTGGGGGTGCATGTTGCAGCATGTCCGAGTTTACAGCTCTCATCTTCTCCCTCATCTCCCTTCCTGAGCCCTGGAGCCACCTGGAATGTCCCTGTCCTTTCCCTCTCCCACCGCGATCCACTCCTTCCCTGGCCCAGCAGAGGCAGCACCCTACCAGCCTGGTAGCAGAGGGTGGTGGCCCTTCCCCTTCTAGGCTGTGCCCTTGTTCATGCTGCCCAGAGGAGATCAGAGCAGGGTCATGAGCCTGGGGTCCCATGCTCACCTGAGCTCTACGTTCCCATGACAG
Seq C2 exon
ATCACCTTCCAGGTGAAGGTCACAGCCACCGAGTGCATCCAGCAGCAGTCCTTCACCATCCGGGCGCTGGGCTTCACGGACACGGTGACCGTGCGGGTCCTCCCCCAGTGCGAGTGCCAATGCCGGGACGCCAGCAGGGACGGCAGCATCTGCGGCGGCAGAGGCTCGATGGAGTGCGGCGTCTGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000017060:ENSBTAT00000022687:10
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(11.1=100)
A:
NA
C2:
PF0036213=Integrin_beta=PD(9.1=60.3),PF126612=hEGF=PU(15.4=3.2)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AAACTGTCCTCCAGAGTCTTCCT
R:
CAGACGCCGCACTCCATC
Band lengths:
326-1788
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development