BtaINT0001476 @ bosTau6
Intron Retention
Description
Bos taurus major histocompatibility complex, class I, A-like (LOC616942), mRNA. [Source:RefSeq mRNA;Acc:NM_001206459]
Coordinates
chr23:27843203-27844987:+
Coord C1 exon
chr23:27843203-27843407
Coord A exon
chr23:27843408-27844711
Coord C2 exon
chr23:27844712-27844987
Length
1304 bp
Sequences
Splice sites
5' ss Seq
CAGGTACGA
5' ss Score
10.03
3' ss Seq
TTCTGATTCTTCTTCCTCAGACC
3' ss Score
8.81
Exon sequences
Seq C1 exon
CAGTTCGCCTACGATGGCAGAGATTACATCGCTCTGAACGAGGACCTGCGCTCCTGGACCGCGGCGGACCCGGCGGCTCAGGTCTCCAAACGCAAGATTGAGCAGAGTGGTGCTGCGAAGGGCGAGAGGAACTACCTGAACCGCGAGTGCGTGGAGGGGCTCCGCAGATACCTAGAGACCGGAAAGGACACGCTGCTGCGCACAG
Seq A exon
GTACGAAGGGCGCAGCGCCTCCCTGATCTCCCCTCAGGCTGGAGCTGGCTTCCCACGAGGAGAAGAAAGTGGTGTCCCTGTGGGAACAGCGCCCCAGGTTCTTGTCAGGAGAGGGAGGAATGCGCCCAGATTTTCAGTGAAAAAGTTGGCTTAAAGCTCAACATTCAGAAAACGAAGATCATGGCATCTGGTCCCATCACTTTATGTGAAATAGATGGGGAAACAGTGTCAGACTTTATTTTTGGGGGGCTCCAAAATCACTGCAGATGGTGACTGCAGCCATGAAATTAAAAGACGCTTACTCCTTGGAAGAAAAGTTATGACCAAACTAGATAGCATATTGAAAAGCAGAGACATTACTTTGCCAACAAAGGTCGGTCTAGTCAAGGCTATGGTTTTCCAGTGGACATGTATGGATGTGAGAGTTGGACTGTGAAGAAAGCTGAGCACTGAAGAATTGATGCTTTTGAACTGTGGTGTTGGAGAAGACTCTTTGAGAGTCCCTTGGACTGCAAGGAGATCCAACCAGTCCATTCTGAAGGAGATCAGCCCTGGGATTTCTTTGGAAGGAATGATGCTGAAGCTGAAACTCCAGTACTTTGGCCACCTCATGCGAAGAGTTGACTCACTGGAAAAGACTCTGATGCTGGGAGGGATTGGGGGCAGGAGGAGAAGGGGACGACAGAGGATGAGATGGCTGGATGGCATCACTGACTCGATGGACGTGAGTCTGAGTGAACTCCGGGAGTTGGTGATGGACAGGGAGGCCTGGCGTGCTGCGATTCATGGGGTCGCAAAGAGTCGGACATGACTGAGCGACTGAACTGAACTGAACTGAACAAGACGGTGACTCACCAGTAGCTTCATTTCTCTGAAGGACAATTAAGGAATCCAGTGTCTTTGGGAAGAAGCAGGAAACCATCCCTGAAATAACTGGTCAGTGGTGCCCTTTCACCCTGCCCGCCATCTTGTGACCCATGACTTTCTCAAGGCCTGTTCTCAGACCAAGAGCATCATAAAAGGCCAGACTCCAGCTTTTCTGAGTCATTCAGTTTCCAACAAAGTCAGGACCATTGCTCTGTATTCTCCCCCTTAAGGTGGAGCATCCTACCGTGGCTCTCACCCTGACTCCAGAACTTTACAAGGACTAGGAGATTTTCCCACACACCAGAGCCCAGGCTGGTGTTTGTGCTTTTTCTTTTCAAACTCATGCTCTCATCATTACTCAGAATGATTACGTGATGCTTCCTCCATGGCCCATGGGAGTAACATAAAGTGTGAATTTTCTGATTCTTCTTCCTCAG
Seq C2 exon
ACCCTCCAAAGACACATGTGACCTGTCACCCCATCTCTGGCCGTGAGGTCACCCTGAGGTGCTGGGCCCTGGGCTTCTACCCTGAGGAGATCTTACTGACCTGGCAGCGTGACGGGGAGGACCAGACCCAGGACATGGAGCTTGTGGAGACCAGGCCTTCAGGGGATGGAACCTTCCAGAAGTGGGCGGCCCTGGTGGTGCCTTCTGGAGAGGAGCAGAGACACACATGCCGTGTGCAGCATGAGGGACTTCAGGAGCCCCGCACCCTGAGATGGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000007075:ENSBTAT00000009299:4
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.261 A=NA C2=0.355
Domain overlap (PFAM):
C1:
PF0012913=MHC_I=PD(36.0=92.8)
A:
NA
C2:
PF0765410=C1-set=WD(100=93.5)
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
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CGCAAGATTGAGCAGAGTGGT
R:
GCATGTGTGTCTCTGCTCCTC
Band lengths:
345-1649
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]