BtaINT0038400 @ bosTau6
Intron Retention
Gene
ENSBTAG00000011390 | CHRND
Description
Bos taurus cholinergic receptor, nicotinic, delta (CHRND), mRNA. [Source:RefSeq mRNA;Acc:NM_174271]
Coordinates
chr2:120980837-120982350:+
Coord C1 exon
chr2:120980837-120980955
Coord A exon
chr2:120980956-120981883
Coord C2 exon
chr2:120981884-120982350
Length
928 bp
Sequences
Splice sites
5' ss Seq
GAGGTGAGT
5' ss Score
10.03
3' ss Seq
TCTCTTACCCTTGGCCCCAGGAG
3' ss Score
7.72
Exon sequences
Seq C1 exon
GCCGGCCTCCAGCAGGCTCGGAGCAGGCCCAGCAGGAGCTCTTCAGTGAGCTGAAGCCAGCTGTGGATGGGGCCAACTTCATTGTCAACCACATGAAGGACCAGAACAATTACAATGAG
Seq A exon
GTGAGTAGCCACGGTGTTGCCATGTACAGGTGTTCCAGTAGTGCACTAATCAAGCATATCCTATCTTAAGGGGGCACAGCTCCCCTCTGAGATACCTGCCAACTTAGATGAAGGAGTGAATGGTGAGTGCAGATTCCAGGGCTGTAAGGGAGTGGGAGCCCCTGCTTATAACCTCATAGCAGTGTGTGTGGCCAGGCACACACTCAGGTATACATGCAAATGCATAGCTCTGCCCTGTTGGGGCCATACTCTGGACCTCCCTTAAGGTCCCTTCTTTCTCCTAGCTGCCAATCACTTTCTGTCCCTGCTCAACTCCAAGCCTGAAACTCCAGACAAAGCCAGACACTTAAAAGGCTGCCTTATATGGTTGTTCAATATTGTATGTGTGCGTATGTGCTAAGTCACTTCAGTCATGTCCGACTCTGTGATCCTATGGACGGTAGCCCTCCACAGTCTCCTCTGTCCATAGGATTCTCCAGGCAAGAATACTGGAGTGGGCTGCCATGCCCTCCTCCAAGGGATCTTCCTGACCCAAGGATCGAACCCGGGTCTCTTAGGTCTCCTGCATTGGTAGGCAGGTTCTTTACCCCTAGTGTATACAACCTGTAAAAATTCTCTCTTGAGATAGGGGCACTTTTTTCAGTTCACATACAGGCTTGTGGCAGCACTGCGTGGCTGGGGGGAGGCCATGGCCCTGCTCTCTGTCTCCTGGACAGATAGGACAACCAGCCCTGCCAGTTGCTGGGGAGCAGGGGGAGGGGCCTGGGTATTTGCTGCAGACACGCCAGCATCTCCCATCTGCTGCAAGCCGGAGGTAGCCCCCACAGCTATGCCAAGGCCGTGCGTCTGTCACCAGGCCCCAGCTTGGGGTGGGAGTCTGTGGTCTGGGGGCCCTTCTCACCCCACTATCTCTTACCCTTGGCCCCAG
Seq C2 exon
GAGAAGGACTGCTGGAACCGGGTTGCTCGCACCGTGGACCGACTCTGCCTGTTCGTGGTGACACCCATCATGGTGGTGGGCACAGCCTGGATCTTCCTGCAGGGCGCCTACAACCAGCCTCCGCCCCAGCCTTTCCCTGGGGACCCCTTCTCCTACCTCGAGAAGGACAAGCGCTTCATCTAGAGCCCCTGGCCCAGCCCAGCAACCAAGGCCGTTTCTGGGCGTAGCGGGGAGGGGGTTGGCCTGAAAGGGATGGGCCTGCAGGGGGTCGGGGTGGGGCGGGTAGCTGTGTGGATAGGGGCCTCTGAGAGACCACCAGCTCTTCCTGGGGTGGCTGTATCTTGGCCCTGAGACCCGAGCCCAGTTGGTCCTTGCAAGGCTGGGGCAGAGACAGCTGAGGTCCAGGATTAGAGGGGAGCCCATGTCTCAACGGTGGTTCTTTTGCAAATAAAACCAGGACCCCCTGC
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000011390:ENSBTAT00000015135:11
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.425 A=NA C2=0.117
Domain overlap (PFAM):
C1:
PF0293211=Neur_chan_memb=FE(16.5=100)
A:
NA
C2:
PF0293211=Neur_chan_memb=PD(13.1=50.8)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGATGGGGCCAACTTCATTGT
R:
CCCCTATCCACACAGCTACCC
Band lengths:
356-1284
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]