BtaINT0038408 @ bosTau6
Intron Retention
Gene
ENSBTAG00000011390 | CHRND
Description
Bos taurus cholinergic receptor, nicotinic, delta (CHRND), mRNA. [Source:RefSeq mRNA;Acc:NM_174271]
Coordinates
chr2:120979381-120980747:+
Coord C1 exon
chr2:120979381-120979495
Coord A exon
chr2:120979496-120980542
Coord C2 exon
chr2:120980543-120980747
Length
1047 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGG
5' ss Score
9.16
3' ss Seq
GGCCCCTCTGACCTGCCCAGCTC
3' ss Score
4.32
Exon sequences
Seq C1 exon
GTTCCTGCTCTTTGGCATGGTGCTGGTGACCATGGTCGTGGTGATCTGTGTCATCGTGCTCAACATTCACTTCCGCACACCCAGCACCCACGTGCTGTCTGAGCCGGTGAAGAAG
Seq A exon
GTGAGGGCTCAGTAGCCAAAAGTTGGAATATTGTCCAGTGCCTTTCTGCAGCGGAATGCGCGAGGCGCATGCGTACACACGCACGGGCACGCGGGGGTGGTACCCGGGGGTGGTACCCGGCGGCGGTGGAGCGCATGCGTACATGCACTGCTTCTCGACTCGCCCCAGGCTGAATGTTACCCAGAAGTCAGACTTTAAAGAGACTGCAAGATTTCCTTTCTGTGAAGTTCAAGGACAGACAAAACCAGTCTTTAGTGCTAGAAGTCAGGGTGTGGTGATTCCCTCTGGGGCTGCGTAGGAATTGATGGCGGCCAGGCAGGAAAGAGGGGAGCTTCTCTGGTGGCTCAGATAAATAATCTGTGCCCACAGTGCAGGAGACCTAGGTTCGATCCCTGGGTCGGGAAGATCCCCTGGAGGAGGGCATGGCAACCCACTCCAGTATTATTGCCTGGAGAATGCCATGGACTGAGGAGCCTGGGGGGTTACAGCCCGTAGGGTCTCAAAGAGTCAAACAGGACTGAGCAGCTCACACACAACACAGGCAGGAGGGAACATCTTAGATACGTTCTTATCTGAGAGGTGTTTACACAGCGAAATGCTTCTGAAGAATTTCTCCCGGCTATACGAGGACAGTTTGTTGATTCTATTGTGTATTGGTATACCTCGATTCAAAACACAGTGAGAACTGTGGGGGCAGGGTCCCCAGGAGGGGTACTGTACTTGCCTCTTGGCCTCTGCAGGGCTGCCTGGTTGTTTGGGGACAGCTGAGGGGGGTCGTTTAGCAACTTTTCTGGTCTTAGCTCAGCAGTCAGGGCATTTTTCTGACTTTTTGTTTTTCACCCGGAATTCATTTTCAACCAATGAGTTAGTTCTTCTCTATGCTGAGTAATAAGGGAGAACTGGAAGCAACCTAAGTGTCCATCAGTTAGGGATCGGGGGGATAAATGATGGATTGGGGAACACCTTGTGGCAGCCGGGAGTGGAGCCCCGATATTTGGATGAGTGAAGGTGATCCACTTTGTATGATGGCCCCTCTGACCTGCCCAG
Seq C2 exon
CTCTTCCTGGAGACCCTTCCCGAGATCCTGCACATGTCCCGTCCGGCAGAGGACGGGCCCAGCCCCGGGACCCTGATCCGGAGAAGCAGCTCCCTGGGCTACATCTCCAAGGCAGAGGAGTACTTCTCGCTCAAGTCCCGAAGTGACCTCATGTTTGAGAAGCAATCAGAGCGGCATGGGCTGGCCCGGCGCCTCACCACGGCAC
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000011390:ENSBTAT00000015135:9
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=0.188
Domain overlap (PFAM):
C1:
PF0293211=Neur_chan_memb=FE(16.0=100)
A:
NA
C2:
PF0293211=Neur_chan_memb=FE(28.7=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:
GTTCCTGCTCTTTGGCATGGT
R:
CCATGCCGCTCTGATTGCTTC
Band lengths:
294-1341
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]