BtaINT0078168 @ 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
chr1:145105076-145107224:-
Coord C1 exon
chr1:145107022-145107224
Coord A exon
chr1:145105243-145107021
Coord C2 exon
chr1:145105076-145105242
Length
1779 bp
Sequences
Splice sites
5' ss Seq
TCGGTGAGC
5' ss Score
9.1
3' ss Seq
ACACCACATGTGTGCCCTAGAGT
3' ss Score
6.08
Exon sequences
Seq C1 exon
CCCCTGCACAGAGTGCCTGAAGTTCGACAAGGGCCCCTTCGCCAAGAACTGCAGCGCAGCGTGCGGGCAGACGAAGCTGCTGTCCAGCCCGGTGCCCGGCCGCAAGTGCAAGGAGCGCGACTCCGAGGGCTGCTGGATGACCTACACCCTGGTGCAGCGCGACGGGCGGGACAGATACGACGTGCACGTGGACGACATGCTCG
Seq A exon
GTGAGCCCGGGATGGGGGTGGGGGTGTCGGGAAGAGTCCCCTCCGCGCCCCTACTCTCCACCCCGGGGCCATGCATCTCTCAAACCCGCCCCCGCCGCACCCCCACCATACCCCGCCCCCACCTCATCTCTCAGCCCGCCCCCGTCGTTGTGGGCGGTGGGCTGTCCCACAGTAGAGCTTCCCCAAGCCGAGCGGGTCCTGAGAACCGGGCGGAGGGGATCGTGGGGACCTCCAGACCCAAGTCCAGCCCTTGCCCTGGAGGGGCCTGCAGAGCTGCTGCTCTCTTCCCCAGATGCCCACTACCCTCCAGTCACCCGGCTCTGCCCAGGACCCAGAGACCAGCGCAGTCTTCATAGGTCCCCTGGGGACATATGAGCAGGTTCTGAGGGGCAAAGACTCCAGCGGGGCCTGTTTCTGAGGTCAGAGGTCAGAAGGTATCTCTAAGGAGGACAGTTGCAGATAGTTGGAGAAGGTTTCAGGTGCTGGGCTGGGCACTTACTGGACCCCTGAGAGTCCAGGGGAGCCTTAGGTCTTTTCCCAGACATAAAAGGAGGCTGCCAACAGCTTTCAGAGGAGCTTTCAGAAGCCGGACACACACCTGGGAAGGGCCACAGCCCGGCCCAGGCACTGAGCAGGGCTGGGTTGGGGCCCTGGGGGCGGCGTGGACAGAGCCTGCTCTGGAATGTAACTCTGGGCAGGATCGAAAGGGACAGGTGATGAGTGGGGGCAGAGGGTGGGTCAGTTTCAAGGAGGTACATTGAGTGATGATGACATTTTGAGATGGAGGGACTTAGAACAACAGACCCCTGAGGGAATGAGTGTAAGGGTTGGAGCAGCAGCACCCAGAGCCATCTGGACACCAGATCTGAGTACCCCACCCTTCCCACTCAGAGAGGCTGAGGGTACGAGCACAGGCTTCCAGGCCAGCCTCCAGGGTGACCGCAGCAGACATGTGGCAGCTGTCCACCCAGGTTCTTGCAAGACTGGGATCTGCTCCCGCTCTCCCTCCCCAGGAAAGGACCCCCAGGAAGGCATGTGGGGCCCAGTCCATTGTGTATCCCCAGGGCTGCAGAGCCCAGCCTGCTGGGGTGGATGGCTCTCCCTGGGTTTTCAGAGTAGATGTGCCGTCAGGTCTGGATTGGGGCAGCTGTGGCTACGGTGTTTAGTCTCTAAGGACATGAGGCTCCCTGGAAAGGCCAGGGTGATGAACGAGGGAGCACCACGGACTCCGGTGCCCTCAGCCAGGCAGACAGTGAGGGGCTTGCACCAAGTGCGGTGCTTCTGTCGGCAACCAGAGGGGGGCTTGCACCAAGTTTGGTGCCTTTGTCGGCAGCCAAAGTGGGCATGTGGCAGTCCAGAGACCCCCACCTGAGCTCAGCAGGAGGCTGGGTGCAGCCCCCTTGGGCACTGGGACCCTGCCTCCCATTCCCAAGGCTGCTGCTGTGAGTCTCCCCGGGAATGCTTGCATGAGGAGAGTCCCCCCTAAACTCTGATACAGTGTGGTCTGGGTGGGAGGCCAGAGTCTGGCCCTGGTTTCTGGCAATCCGGGCCCCCCTTTCCTTCTCTGTAAACAAGGGCCCTCTCGACTTCATTGGGAACCGCGGAGCCTGGCCTTGTGCTCAGCTCTGGGCTCTCCTGGGCTGGGGGCCGGGGCCAGGGCTGGTTTGCTTACTACCTGCCACAGAGATCTGGCAGTGGGACCTGGACACCGTGCAGGGACAGGGCTGACACCCGGGGCCTGGGAGCCGGGGCAGCCTTGACACCACATGTGTGCCCTAG
Seq C2 exon
AGTGTGTGAAGGGCCCCAACATCGCTGCCATCGTGGGGGGCACCGTGGGGGGCGTCGTGCTCGTCGGCATCCTCCTGCTGGTCATCTGGAAGGCCCTGACACACCTGAGCGACCTCAGGGAGTACCATCGCTTTGAGAAGGAGAAGCTCAAGTCCCAGTGGAACAAC
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000017060:ENSBTAT00000022687:14
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:
PF079657=Integrin_B_tail=FE(86.1=100)
A:
NA
C2:
PF079657=Integrin_B_tail=PD(7.6=10.7),PF087256=Integrin_b_cyt=PU(54.3=44.6)
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:
AGTGCCTGAAGTTCGACAAGG
R:
TCCACTGGGACTTGAGCTTCT
Band lengths:
354-2133
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development