BtaINT0007562 @ bosTau6
Intron Retention
Description
Bos taurus major histocompatibility complex, class I (LOC512672), mRNA. [Source:RefSeq mRNA;Acc:NM_001076841]
Coordinates
chr23:28302427-28304970:+
Coord C1 exon
chr23:28302427-28302723
Coord A exon
chr23:28302724-28304694
Coord C2 exon
chr23:28304695-28304970
Length
1971 bp
Sequences
Splice sites
5' ss Seq
CAAGTAGGT
5' ss Score
7.33
3' ss Seq
ACTGTCCTGGGGCTGGGCAGGCC
3' ss Score
4.96
Exon sequences
Seq C1 exon
GATCACACTCTCTGCAGTATTTCTACTCAGTTGTGTCTGAACCGGGTCCAGGAGTCCCTTCATTTATGGCTTTTGGCTTCGTGGACAACCAGCCCTTCATTCGCTATGACAGTGAAGAGATGAAGGCAAAGTCTTGTGTTCATTGGTTGAGGGAGGAGCCAAGTTACTTTGATGATGAGACCAAGATCTTCACAAGTCGGATGAAGATTTTCCACTTAAATCTGAGGAATGTACAGCAATATTACAACCAAACCAAGGAGGATGGTCTGAACAGAGCGCTGGCACAAAAGCAAACAA
Seq A exon
GTAGGTGCCTCAGAGAAAGCAGAGGGAAGTGGTGCTTGTCACTTCGTACCAATCCCCAGGGGTGAAAGGCTCTTGACAAGTGTTCCCATAGGGTCAGGCTGGGGCAGAAGAACATGTACAAGTTATCACTTGAGAATGAAAGCTGAGCTGGTCTGGTCACAATGGTGTAGGGTCTGTGTGACGAGAATTAATAATTAATAGATTAATTAAGCAGTTTTACTGGGTCATGGATATATGCTGAACATCTTTTGAGTGCTAGAAATGGGGACCCAGAAGAGTATAAACTGATGTTTGTCTTCAAAGAGCTTATAATTCATATGGGAAGGTACTCACACTTCTGTGAAAAGTTTATTGACCCTTCACTGCATACCCAGAGATGTCAAAGACAGGAACCTCCTTGAATGCCATAGTTTACTGAGATTCATAGATGAGATACCCCAGTGGTCAGAGTTTCATGAATGAGGCAGAACTTTATATAGAACCAGGTGGATATGTATTACTTAGGTCTATGAAGAACATAAAAGACGTTCCAAGCAGTAGGAAATTAGGGTGGAGCAAGTCGTGGGGTAGGATTTGTCTTAGTGAGCTCAAGGGATGGACTGAAATTTAATCATTTCTAGTTAATGGCTCTTGAGACTTTAGGTCTGTTGAAACAAGTTTGTAAAGGGCCTTGAAGCCCAATCAAGGCATAAGCCAGTGAGAAGTATAATTCAAGCTGAATACTGAGGCTGCTCAGCTTTTTCCCGTTGATCCTTCTAGGAACATGAATTCAACAAAGGTTTATCCGATGGTTACTTTACAGGCACTGATGTAGACTCTGCCTTTCAAGGGCTCACAGTATAAGAAGAGAGTGATGGTACACAATAAAGTTATAGTATGCAAGTTTGTTAGACTAGGAACTTGAGCTGGGAATCTGTGGAAACTTAGAAGCATGTGTGCTGAATCCAGGCTGCAGTGATCTCAGATTTATTCATATTTGGCTTTGAAATTCATTTGAGAAATTTTTCAGCAGTTTGGGCTTGTTGATGCTATTTGCTTTCTCTAGTATCTTGTGTTGTTGTCCTTTCGTCGCTAAGTTGGGTTGCAAAAGAGTTGGACACAGCCTAGTGACTAAACAGCAAGTGACCTGACTTAGCGATTAAACAACAACAGTAAGAATATTAGTCTGCCTGGCCTACCATGACAAAATACCACAGACTGCATGATTTAAGCACCAGAAATTTATCTTCTGACTGTTCTAGAGACTGGAAGGTCTAAGGTCAAGATTCAGCAGGGTTCTCTGTGGTGAGGGCTCACTTCCTGGCTTGCAGTCGGCCACATTCTCGCTTTCCTTGGTGTGTGCCCATGGAGTGAGGGAGAGAGCTCCTTAACCCCTCTTGTCCTTGTTGGATTAGGGCGCCACTCTCGTGACTTCATTTAAACTTAATTACTTGCTAGTATCTCCGAATACAGTTACATCAAGGGTTAGGGGTTCCACATAGTGAATATTGGAGGGATAAAATTTGGTCCATAGCTGTCAAGGAAAACTACTCAGTACATTGTCCCCTCCTGTGTTAATGCTGTGTAGTGTGGTCCTGTTCTCAGGAACTTGAGCTTAGACTCTGAGGCTGTTAGCCTAGAAGAGACCTGTTAGGTCATAATCTAACCCTCTTTTTATACAAGATAAATGTAGAATGAATAACTTGCCCAGATCACACAGTTCATGGCAGAGTTCAAATCTGTAACTCCCAATCCATGGCCTTTTCAATACCTCCTGGAACCAACCATAGACCATTCCTCAAGCAGAACTGACTGTAATGAAAAGAGATCGTTATTAGGGCAAAACTAGTTTGTCTATGGAATTTGAATGTCCTCTAAGGAGAAGATAAGAGATGGGAAGGTATCGGGGGGCTGGAACCTTGGGTGGGAGGCCTTGGGGGCAGACTGTGCCCAACTGACACTGGCTGACACCACTGTCCTGGGGCTGGGCAG
Seq C2 exon
GCCCCCACACCCTCCAGTTCACCTACGGCTGTGAGCTCCTGGAGGACGGCAGGACCACGTGGCACTGGCAGTATGGCTATGATGGTGAGGACTACCTGAGCTTGCATATGGACCCTCTGCAATACACAGCAGCCACATTCGTTGCTCAGTACACCAAACAAAAATGGGAGGCCGGTGGGAACTTCATAGAGAGAGACAAGAACTACTTGGAGAAGGAATGCATCCTGTGGTTGTGGAGATACTTGACGTTTGGAGGGGAGAGCTTGAACCGCACTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000038619:ENSBTAT00000052679:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.040 A=NA C2=0.022
Domain overlap (PFAM):
C1:
PF0012913=MHC_I=PU(52.7=99.0)
A:
NA
C2:
PF0012913=MHC_I=PD(46.8=94.6)
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:
TTTTGGCTTCGTGGACAACCA
R:
GCTGTGTATTGCAGAGGGTCC
Band lengths:
357-2328
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]