BtaINT0002117 @ bosTau6
Intron Retention
Description
Bos taurus major histocompatibility class I related protein (MIC1), mRNA. [Source:RefSeq mRNA;Acc:NM_001127317]
Coordinates
chr23:27726748-27729750:-
Coord C1 exon
chr23:27729627-27729750
Coord A exon
chr23:27727009-27729626
Coord C2 exon
chr23:27726748-27727008
Length
2618 bp
Sequences
Splice sites
5' ss Seq
CCGGTGAGT
5' ss Score
10.9
3' ss Seq
TGTGGTTCCTCCTTCCCCAGGAT
3' ss Score
10.23
Exon sequences
Seq C1 exon
CCGCCAGCTTTTCTTCGGTCCCGGAGCCTCTGGCAGGGAAAGAAGATCTGGGCCATGGGGCTCTCTCATGTCTGGCTGTTTCTAGCCCACGCTGCCTTTTTTGTGCTCCTGGGTAACGCCGCCG
Seq A exon
GTGAGTGGGGTTCTTTGAGGTCTCAGTCCGGACGGAGCCCGGGGTGGTTTCAGGGGTTCGGGTGGTTAGTATTCTATGGGATTCGGTGAGCGTCGCGGGGATCGTCTCAATTGCGGCTGGGGGTGAGCGAATAGAGGAGTTGGGGGTGGAGATGGGAGGAAGGTGGGGGGCGGGGAGGTGTAAGGTCGAGGAGCGGACGGGAACTTCACACGCGTGTGGCGAGCACTGCATCCCGCGTTTCAGTCTCTGCCGTTCCTAGCCTCTGCTCTCCCTGCCCCACCTACCCTCCCCGATGTCCTCATCACATGCCTTAGTCCTCAGATTCTCCTGACTGGCAAGGCAGCCTGGTCCCCACCTCGCTCCCTGCCGCTTCCCGCCCCCGCCTCTCGCCCCAGCGCCCCACCTGCCAGCCTCCCCGCCCCGCCCCGTTGCTCTCTTGAATGGAGTTTCTTCCAGGTCCCAGGCTCAGGCGATCACTTCTTAGCCGTCTGTGGGGCGCCCTCTTATGCCCCTGAAAGCTGTCCTCTCCTATTCTTAGCTCTGCCGTCTCTTCTCATTTCTGGACGCCAGAAACAAGGAGTTTCCAGGTTGGCGGCGCTCAGGGGTCCTCAGCCCCGAGAGTTAGGGCTCTTTTTCTAGTGACCAGGGCCTCTGAGGAGGGGCAAGCTCTATGCACACTCTTCCTACTGCTATGAGCACTGTGGCGGCTCCTGAATCACTGACGGAGGTTGGGTCTGAGGGCTTTGGGACCAAAGGATTCTTCCTGCGATTTCCGTGGTCCCCCCTCCCCCACTAACGTGAACTCTAATTTTCCGCTGTGCCTGTGGTCCCACAACTGAATCTCTCCTTACCTCCTCCCTTGCTGGCCCTCGAGCCCCCTCAGGATTTGCCCTCCCCCCTCGGTGCTGCCCTCTCCCCTCCCTGCTGCCCCCTCCTCTCTACGGCTCTCTGATCTCTTCCTAAGGCGTCCCCACCCTCATCCCTTTTCCCACTACAGGTCCCTCCCCTCCCCTCATGGGTCTTTTCCTGCGAGGATCGGTCACCTGCAAGGCTCCTCCCTCCCCTCAGCTTTCACTAGCCTTACTTTTCTTGGGATGACTTTTACCCATGAATTTTCCTCTCCAGCCTCTGCGCTATTTCACCAGGGGGAGCTCTCCTGCCAATGATCCCTGGGCCTTGAGCACAGTGCCCAGCCCCTGGGGGAGGACCTGTCCCCCACTTGACACCCACCCTCCGCCCCCGTGCAGGCACCTGCTCTTGGCCCTCGTCCAAGAGGAGCCTTTCCCGCAACACGGCCCCTCCCCACTCCTGCATCCTAAACCTCACCCTCTGGATTCCTCCACTCCCCAGGCCACAGGTGCTGGACTCCACTTGCCCTGGTCCCTCTGCAGTTCCCCCCATGGCACCTTGCCCTGCTCCCACCCTTGTCCGACTGCCTTGGGCCCTCACAAAGTTCTCATCAATCACAGGCCCCATGGTGCCCAGAATCTCCACCTCACTCTCATCCTCCCTCACCCAGGGCATCCCTCCTCTTCTGTCTTTACCTTAACCCAAGGCGGGGGGTCACCCCTGAGCCATGCTCCCCCCTTGCCCCTCAATCCCAGGCCCTCACCATATCTTCTCTGCAGTCTCTTCCCTTCCCCCACAGTAGGAATACTGCCCGCGGTCCACTGCCCACCTCCTTAGCCTTCATCACCCTCTCTTTGGTTCCACGACCCCAGTGGACTCTCACTATCTCAATCTTGTATCCGAAATCCTTGTTTGTGCCACTTGGTCAGCAGGCTTTTCCTACAGGGAGTCTTCTCCCAGGCCCCCACCCCCTGCTTGCTGGCTGCCTGACCCGAACCCTCTGTGGAGGTGTGACCTCACTCCCTCCAGCCCCTCCCACCATGTAGGTGCTTCCCAGTGTGCACCTTGGCTTTCAGTTCTATCTTCCCTTGCCACTCCGATATTTTAATTCTCCATGACCCTTATGCACATGGCACTGACTCCTCTCCCAGGGGACACTGGCAGGTGCAGCCACCTCCCCACCTGGGGCCTCACCATGCCTCTTTGCACTCTGCGCCCAGACCCACTCCTTCACCTCCCCCAGGTTACTGGCCCACCTTCATCTCTCTTGGGGCCACAGCCCAGCCCCTCAGGCCCCTCTGCCTCCTACCTCACCCTCCCTGGAGCCCTCCTTGTCCATGATGAGCCTGCACCAGGGGCAGCAGCCCTCGCTCTCCATCTCACCTGGCCCCCCTCTGAGCAGGGATCCCTCTGGTCCTGGGTCTGACACTGCCCTCCCCTCCCTCTGACTCCACCTCCCCTCGCCCTGCTCTTCCTTCCTCTCCCCTTGCCCTCCTGCCTGGACCCTTAGGGAGCCGGTGCCTCCCTGTCCTGGCACTTGTCCTACACGTGTGTCCGTCTCCACCCTCTCCCTCCTCTCCTCGATTCCCCTCTCCCTCCTTCTCTTTCCCATTATCCCGTATGGAACTCCTCATTCTGGTCCCTTGTACACATGCATGTTCTGCATCCTCAGCACCTGGAGCAGGTCAGGACACAGAACTTGTCTGTTAAACATCTGATGTGCACTTGTCTCCAGAAAGCAGCTTCATCTGTGGTTCCTCCTTCCCCAG
Seq C2 exon
GATCCCACAGTCTTTTATACAACATGACTGTGCTTTCCCGGGATGGCTTTGTGCAGTCCAGGTTTTTTGCTGAAGGATACTTGGATCGTCAGGCCTTCCTGCACTATGATCACAAAAAAGGCAGGGCAGAGCCCTGGGGACGGTGGCCTGAAAAACTGGCAGCAGAGACGTGGGAGACAGAGACCATGGACTTGAATGAGAGCTGGAAGGAGCTCAGAAAACTTCTAGCAGAAATCCTGTCCCTGCAGGAGGAGAAAGGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000010166:ENSBTAT00000013413:1
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=0.000
Domain overlap (PFAM):
C1:
PF0012913=MHC_I=PU(0.1=0.0)
A:
NA
C2:
PF0012913=MHC_I=PU(51.8=98.9)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Human
(hg38)
No conservation detected
Mouse
(mm10)
No conservation detected
Rat
(rn6)
No conservation detected
Chicken
(galGal4)
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]