BtaINT0038406 @ bosTau6
Intron Retention
Gene
ENSBTAG00000011390 | CHRND
Description
Bos taurus cholinergic receptor, nicotinic, delta (CHRND), mRNA. [Source:RefSeq mRNA;Acc:NM_174271]
Coordinates
chr2:120977908-120979291:+
Coord C1 exon
chr2:120977908-120978108
Coord A exon
chr2:120978109-120979179
Coord C2 exon
chr2:120979180-120979291
Length
1071 bp
Sequences
Splice sites
5' ss Seq
ACTGTGAGC
5' ss Score
4.2
3' ss Seq
CTAAGGACAGGCTCCCGCAGGTG
3' ss Score
-1.11
Exon sequences
Seq C1 exon
AGAACGGGGAATGGGAGATAGTGCACCGGCCAGCCAGGGTCAACGTGGACCCCAGTGTGCCGCTGGACAGTCCTAACCGCCAGGACGTCACCTTCTACCTCATTATCCGCCGCAAACCGCTCTTCTACGTCATCAACATCCTGGTGCCCTGTGTGCTCATCTCTTTCATGATCAACCTGGTCTTCTACTTGCCAGCCGACT
Seq A exon
GTGAGCCCAGCACCCGGCACCCCCTCTTCAAGGGCCCCTAAGCTTGGCCGCCCCAGCCCTGCCCCTCAATTTCCCCGGGAGCCACTTGGCTGGGGGGCGGTCACCACTCCTGGGGTTCCCTGCCCAGGGTCCTGCATGCAGAGCACGTGGCCTGTCAGCGGAAGGGCTCTGTGTCCCTGTGGGACATCCCTTAAGCAGACAAGGCCCCAGGGAGTCCCATCCCTCTTGGACCTCGCTTCTGCCTCTCATGCTGGGCTTCCCAAAGACCCTAGGAGAACACTAGAGTCTCCTTCTGCTGGGGAGAGATTGGCTGCAGAGCCAATGGGTGGATCACAGGGTCTCTAGGAAGCCAGGGCAGGGGGCATACAATCTATACTCACCTGATTCTAGAAGGTATCATGTCACATGTCATCTGTGGTCACTTGGCTCCAGAACATTTATTATGAGCAGGGCATGGTGAGTGCCAGAGACAAATATGATCCAGCCCTGACCCTGGCAGACAGGGTGGAAAATACAGGATTGGGAGTACAGCCTGGGGGTGGTGGGGTGGGAACCAGAGCCAGGCTGTGGGGCACACTGCAGATGAAGAAGGGGCAGTGGGGCGGGGGCCCAGGGGTCTGTGACCATGAGGCCCACGCCCAGCACTTCTCAGGGGATCAGATGGGCAGGGCAGGGCGGTGCTGGGCTGGGGTCTGGGAGGACATCCTGGGGCTTCTACGCGGGGCAGGACACAGCAGATCTGTGGTCTAGGAGAGCTGAGTGGCAGGCGATTGGCTGACGAGGATGGCAAGTGTTCCTTGAGCTCTCACCCACTGCCAGGCAGAGTCGGAGCATTTAAGACATACTCTCACTCTATCCTCCCAACATTTAACAGTTGAGGAATGTGAGGCACAGAGAGGTTAGGCCGCTTGTCCAAGGTCACCTAGCAATAAGGAGAAAGATGGATGGGAACCCAAGCGCTCTAGCTCCTGAGCCCTGGGCACCATGGCATTGTGGACAGTAGTGCAGGGGTCACCGTGCGACCCTCCAGGCTCCGGGCCAGAGGTCATAGCTAAGGACAGGCTCCCGCAG
Seq C2 exon
GTGGTGAGAAGACATCCATGGCCATCTCGGTGCTCCTGGCCCAGTCTGTCTTCCTGCTGCTCATCTCCAAGCGGCTGCCAGCCACGTCCATGGCCATCCCCCTCATCGGCAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000011390:ENSBTAT00000015135:7
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=PD(17.6=57.4),PF0293211=Neur_chan_memb=PU(8.9=30.9)
A:
NA
C2:
PF0293211=Neur_chan_memb=FE(15.6=100)
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:
ACGGGGAATGGGAGATAGTGC
R:
TTGCCGATGAGGGGGATGG
Band lengths:
310-1381
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]