BtaINT0038405 @ bosTau6
Intron Retention
Gene
ENSBTAG00000011390 | CHRND
Description
Bos taurus cholinergic receptor, nicotinic, delta (CHRND), mRNA. [Source:RefSeq mRNA;Acc:NM_174271]
Coordinates
chr2:120977036-120978108:+
Coord C1 exon
chr2:120977036-120977145
Coord A exon
chr2:120977146-120977907
Coord C2 exon
chr2:120977908-120978108
Length
762 bp
Sequences
Splice sites
5' ss Seq
CAGGTGCCA
5' ss Score
3.75
3' ss Seq
CGTCCACATGTCTCCCTCAGAGA
3' ss Score
8.28
Exon sequences
Seq C1 exon
TTCGCTCAAGTACACGACCAAGGAGATCACCCTGAGCCTGAAGCAGGCTGAAGAAGATGGCCGCTCTTACCCCGTGGAGTGGATCATCATCGATCCCGAGGGCTTCACAG
Seq A exon
GTGCCAGGAGCAGCAGCTCCTGGGTGGCCAGGCTCCCCTGGACACCCGCCCACAGATATAGTCACAGAGCTGCACGTGTGTGTACATACACGGGGACATGGTCACACCGGTACACAGACGTGCAGGTGGACACAGACCCTTCCCAGTCTGGACAGGGTCCCTGGGGTCGATCTGGCCGACGGATGAGGGGGTGGTTTAGTTTTCCCATCCCCAGAGGGCCCAGGGGGTGGTTGGGGCTTTGGCTGTCATCTGATGTGTGTGCCGCGTGTCTTCCACTTGGTGTGTATGCCGCCCCCTCCCAACGCCCGCCCGCCCCCATCTGTGACCAGGCTCAGACCTTTTATGGGGCCCAACCACTTGCCCCTGTCTGTCAGAAGAGACCCGCATCCAGCTCGTCCCAAGGCTGGTATATCATGGCAGGGGTAGTGATTCCTCTGACTGCTTTGTTATTCCCCAAGGCTCTTATTTGAACCACATATGGCCTCAGCTTTTATTTTTCCCAAGGAGAAAAAAAATCCATCCCAGAGGAAAACTTTGCCCTTGTAGCGTGAAATGTTCATCCCAAGCCCCAGGGAAAGACACCCACAAACAGAACATGACCCCTCCTCTGTGTCCCCACCCCTATCCCCCTTAGGACACTGCAGACAGGCCTGGCTAAGCCCCTGGGCCGGCTCAGTCCCTGCTAGCCCCCCATCCTGCACCAAGCCTCTCCTTGGCCACCTTGCCCAGCCTGACCCCAAGGCGTCCACATGTCTCCCTCAG
Seq C2 exon
AGAACGGGGAATGGGAGATAGTGCACCGGCCAGCCAGGGTCAACGTGGACCCCAGTGTGCCGCTGGACAGTCCTAACCGCCAGGACGTCACCTTCTACCTCATTATCCGCCGCAAACCGCTCTTCTACGTCATCAACATCCTGGTGCCCTGTGTGCTCATCTCTTTCATGATCAACCTGGTCTTCTACTTGCCAGCCGACT
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000011390:ENSBTAT00000015135:6
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:
PF0293118=Neur_chan_LBD=FE(16.7=100)
A:
NA
C2:
PF0293118=Neur_chan_LBD=PD(17.6=57.4),PF0293211=Neur_chan_memb=PU(8.9=30.9)
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:
TCGCTCAAGTACACGACCAAG
R:
AGTCGGCTGGCAAGTAGAAGA
Band lengths:
310-1072
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]