BtaINT0007561 @ bosTau6
Intron Retention
Description
Bos taurus major histocompatibility complex, class I (LOC512672), mRNA. [Source:RefSeq mRNA;Acc:NM_001076841]
Coordinates
chr23:28299437-28302723:+
Coord C1 exon
chr23:28299437-28299573
Coord A exon
chr23:28299574-28302426
Coord C2 exon
chr23:28302427-28302723
Length
2853 bp
Sequences
Splice sites
5' ss Seq
CCCGTGAGT
5' ss Score
8.4
3' ss Seq
GTTGCTTGTTCTCACCTCAGGAT
3' ss Score
7.59
Exon sequences
Seq C1 exon
GTGAAGCCGGTGGTCTCCGAGCTGTGTGCCACAGCCGTGCCCGGAAGTCTTGGGGCCAATCGGAACAGCCAAGGCGATGCTGTGGGGCCCTGTCCTCTTGTATTTCTTCCTAGCATACCTGCCAGAGACACAAACCC
Seq A exon
GTGAGTTGGGAGCGAGGGGTGGCGGGCTGGGAGAGTGGAAGAAGCTGAAACCGGACGAGAGTGGAATTTTTCAGATCACTGGAAGCTTAGTGGTGACTTTGAAAATCTTGGTGCAGGCCGTCACTGGCTTATTTGTGCGGGCTCTGTCAATAAGGGCAGCTAGTGTAAACAAGAGGAGAAAAATGGCAACCTACTCCAGTATTCTTGCCTGGAGAATCCCGTGGGTGGAGGAGCCTGGTGGGCTGCCGTCTTTGGGGTCGCAGAGTCGAACACGACTGAAGCGACTTAGCAGCAGCAGCAGTGTAAACAAGAAAGAAGTTGGCAGATCTCTGAACCAGGTCAGAAGTCATAATTCTGTAGTCTTGCTCAGAATAGATGTTCCTGGTTTCCCACTCCAGTATTCTTGCCTGGAGAATCCCCCAGGATTTTGGCGGGCTACAGTCTATGCGCGGTCGCAAGGAGTCGGACACAACTGAGCGACTGAACTAAACTGAACTGAACAGTCTATGCGGTCGTTCAGGAGGGAGCGACTAACACTTTCGCTTTTACTTTTAAAGTCTTTGGAAGGGCAAAGGCACAGCCAGAAGCAAAAATTTGGTATGGATGGTATTCAAGGTTTTAGATCATCTTTCTTTACAATTTAGAGTGTGTTTATTTATTTACAAAGTATGTGCATATTCCATTATAGCAGTACATTATGTTGAGTATACGAATTTACAGAAACAAATCCAAAAAGATGAGATAAAATATTTTAAATAACTTAAAAAAAATTGATCACAAGCTTGATTAATGACAGAACTGAAAGAAAATAACGTAGCACACACATTCATCTTTTATTCATATGGGGAAAGGGCTTCACTGAAGTGTTTGTTTAAATATGGCTCATCCAGGAAAACCCCATAGGGACAGTATGCAAAACTCTCACCACCCACTAAGCTACAATTTTTGCATTTTCCTACATGCAGGTTATTTGCAAAACCATTGTTCCCAGCCACAGGTCTCCTAGCACAGTTTCTCAGCAGCTATTATTGCGCTCCAGACTCTAGAAGTGTACCAAGAAAGCCAGAAGGAAAGCCAGACTCATGACTTAATTACTGGGTGAAATGTTTCCAGACCAACAAGTAACAACTCGTGGAAAATGAAACAAATTCTTGACATATCTGAAACATATCTGGCAGGGTGAATTTTTTTAAGTCTTACCTATTTATGAGCAAGAGAGGAGGAGAAATGGGTTCTTTTTTTTTGAGAAATGGGTTCTAAATAAAGCTTTGCTACTAAGCTTCAGTTTTCTCACCTCTAACATGGAATTTAAGCAGCTACTTCATACAGTCATCAAAAGAATTAAAGAAATAACGGCAGACCACAGAGGAAATGCTCCAGCACAATGATAATTTTTAGGAAACAGTTTCTGTGCAGGCGTTAAGTGGTGTGAGTGCTTTAATAGGAGTACAGTGTAAACATTTCCATATTTATACATTTCCTATCTGCCTGAATGGAAAGTCATCCAGCTATGGCTGCTTGGCTGAGCCTTAGAATAAAGGGGAGTTTGTGCTCAGTGTCTTCCTTTTGCTCTTGTTTTTGTGGTTTTTCCCTCTCCACAATCACTCCCTGGAGTTCAGTGTCTCCGAACATCTAACCACAGCCTTGCTCCCTGCATAGCCCCTGTTAGGTGCAGGGTCACAGTAGGGATCAGCAGAGAGCAGACAGGGACTGCCGGCTTGCATGTCCACTGGGTCCTCAGGAATGACCTCTGACCTCAGTAGGTGCTTCTCAATGGAGTCTAGATCTGAGTGGGGTCAGAGTCAGTTCACAGTGAGAGGGACTTTATTCATCAGAGGAGGCGCCCATGTCAAGGGGTAGAAGTGCAGAGGTTCTTCGGAAAAAAGAACAATGCTGTTAAAAACAGAAACGCTATGAATAATTTACAGAAGAATGAATTCAATTGGCAGATAAACATGGAATTATGTTCAATATAACTTCATAAATTAATGTATAAACTAAAATGTATGTATTTTAACTGCCATTTATAGCAGTGTGACTAGACCTAGAAAATATTATATTTAGTGAAATGTCAGACAAAAATACTATTTGAGATTACTTATATTTGGAATTGAAAAATAATACAAATGAATGTACCTACAAAACGGAAACAGACTCACAGACATAGAAATCAAATTTGGGATTACAAAGAGGAGAGAACAGAGGAGGGACAAAGTAGGGATACGGGATTAGTAGATACAAACTAAGTAAAGTAGATAAGCACCAAGGATTTGTTGTACAGCACAGGAAATTATACGCATGATCTTTAATCTGTTATGGAATACAATTTTTCAGAATACTGAATCACTATGCTGTACACCTGAAGCCAACACAATGTTGTAAAGCAGCTGTACTTCAGTTTTTAAAAATTTGCACTTCGCTCTCATCCCCCCACCCTGGGGCCATGGAAAAACTGTCTTCCATGAATCTGGTTCCAAAAAGGTTCAGGACTACTGCCCTAGCTGGTAATGTGGGTAGGCCTTATCTGATCAGTTGAAGGCCTTAAGGGGAAGACAGGTCTGAGGAAGAGTGAATTCTACTTTCAGACTGCCTTTGGACATAAGCTGCAATATCGTGTCTTCCTTAGGTATCCAACATGCAGCTCTGCCTTGCAGATTTGGGCTTGCCAGCTAATTCCTTAAAGTAAATCAATCTTACCCTGTATATATTCACTTATGCAGAGGAGTGTAATTGTCTTTTCATTGTTTTATGTTGTGCGCCATGTCTCCTATTAGACACACGCTCATTCCCTAGATCCTCACACAGTAAATTCTGGAGCTCTCTCTGACCCACTGTTGCTTGTTCTCACCTCAG
Seq C2 exon
GATCACACTCTCTGCAGTATTTCTACTCAGTTGTGTCTGAACCGGGTCCAGGAGTCCCTTCATTTATGGCTTTTGGCTTCGTGGACAACCAGCCCTTCATTCGCTATGACAGTGAAGAGATGAAGGCAAAGTCTTGTGTTCATTGGTTGAGGGAGGAGCCAAGTTACTTTGATGATGAGACCAAGATCTTCACAAGTCGGATGAAGATTTTCCACTTAAATCTGAGGAATGTACAGCAATATTACAACCAAACCAAGGAGGATGGTCTGAACAGAGCGCTGGCACAAAAGCAAACAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000038619:ENSBTAT00000052679:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.040
Domain overlap (PFAM):
C1:
PF0012913=MHC_I=PU(0.1=0.0)
A:
NA
C2:
PF0012913=MHC_I=PU(52.7=99.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Human
(hg38)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]