DreINT0046707 @ danRer10
Intron Retention
Gene
ENSDARG00000011113 | chrna10a
Description
cholinergic receptor, nicotinic, alpha 10a [Source:ZFIN;Acc:ZDB-GENE-060503-725]
Coordinates
chr15:38278319-38281435:-
Coord C1 exon
chr15:38280903-38281435
Coord A exon
chr15:38279158-38280902
Coord C2 exon
chr15:38278319-38279157
Length
1745 bp
Sequences
Splice sites
5' ss Seq
TAGGTGAAT
5' ss Score
3.81
3' ss Seq
CTTTTATATGCATTCTACAGGGA
3' ss Score
7.23
Exon sequences
Seq C1 exon
TGCAGATGATCACTTTACCAGCACTATGGACACCAACGTGGTCATCAGGCATGATGGTCAGATCATGTGGGACGCCCCAGCCATCACCAAAAGCTCCTGTAAAGTGGACGTCTCCTTCTTCCCCTTTGATGCCCAGCAGTGCCGCCTGACCTACGGCTCGTGGACCTACAACGGCAACCAGCTGGACATTCTGAACGCCATGGAAAGTGCAGATCTCGCCGATTTGGTCGATAACGTAGAATGGGAGGTGTTGGGAATGCCGGCCAAGCGAAACATCATTCTGTATGGATGCTGTGCCGATCCGTATCCTGATGTGACGTACACCCTGAAGCTGAAGAGAAGAGCGTCGTTTTATGTGTTCAACCTGCTGATCCCCTGTGTGATGATCTCTTTCTTGGCTCCTCTGGGTTTCTATCTGCCGGCAGACTCGGGAGAGAAGGTGTCTCTGGGTGTTACGGTGATGCTGGCGCTCACTGTGTTTCAGCTGCTGGTGGCTGAGATCATGCCTCCATCTGAGAATGTGCCTCTTATAG
Seq A exon
GTGAATCATTTGTGCTGTGAAAGATATACAGTAGTCAACATTTGAGGGGAATCAGAATGTTTTTTATTTTTTTTCATTTTTGTCAATGAAGAGAAGATTTTTTTCAATATATATATATATATATATATATATATATATATATATATATATGTGTGTGTATATATGTGTATATATATATATTAGGGCTGTTAAAATTAGCGCGTTAACGCACATGATTCATTTGAAATATTTAAACTAACACAATCTCATGACAATTATTAACTTTTTGATTTAGTGGCTAATTCGTATGAATTCGTATGATCTAATTTGTACTATTTACTATGGTTTGTCCATCACCCAATGACAGTTGGGTTTAGGGGTGGGCTTGGGTGCCACGCCTCCTTTTTAAAATCGTACATTTTTGTACGACTCAACTCGTACAAATTCGTAAGAATTAGCCACTAAATTGACAAAACATAAAATACGTACGTTTCCTCATGAGATCAGGCTGATTTAAACTGTAAAAAAAACGCAAATAATGCAGTTGCAGTTTTTTTTTACCTCCTGTTGTGTCCGATGTGTGTATAGGGACGGCGCGTGCATAGAGGCGACCTAGGCTGCCGCCTTGGGCAGCAGAATAGTGAGCGAACCAAATTGTCCTTGCGTTTATCCGCTACACCCACCCCCTTCCTTACGGCCCTCACTTTCATCCGCAAACCGCTCACTTTAGAGTTGAGGGCAGTGTGATTGCCTTTTGCCTAGAGCACCAGTTAAGCTTGCTCCGGCCCTGCGTGTGTTTAACGTGCTAAACAATTTGGATAAGACTAAGAACGCGCTTCTAGAAGGAAAGTTTCAGTGTAAAACAATGTGGCATAACCAGGCGATACTGCGTTGTAATGGAATTTGTTACCTCATGGCTGACGGAAAGAAAAACCTCCACATTTCACGACTCGCATGATCCTGTAAGGTAATCAAAAATCACTGCGCACATATATATAAATGTACTCAGTGAAAGTGGCAGATGAAGTCGCAAGCTGTCAAGGACAGCCCTATTCCCTGCCGCTACTTCCATGAGCCCTCACATTTCCTAAATTTGACGTGTTTCCCCCTACACGCAACTTTTGTCGGTATCCTTGCTTGTAAAATACAGCCATAGTTTAGAACGCTTTGATGAATGTGATTGTGCGTGTTGATGAATCTGAAGGGATCCCTCGGTCACCGGGTTCGCTGTACTGCGCATGTTGTCTGTGTGTGTGTGCATGTGTGTGTTTGTAGTCCACTTAGAATCCAACATGGAAATAATTTTTGTTTGTTATTGGCATTGATTATTTTGAAATTCAAATGGCACTTAAATGCCTTTGTTTTTATTTCTGTAGTAAATACGGCAGTTTGTGATTAATCATGATTAATTAATCACACTTTTTTGTAATTATGTAAATTTTTAAAAATAATTTGACAGCCCCAATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATTTCCCAGTGTTGGGTTGCAGCTGGAAGGGCATCCGCTGCATAAAACATATGCTGGATAAGTTGGTGGTTCATTCAGCTGTAACTACCCCTGATTAATAAAGAAAAAAATAAAATGAAAGAATAAATATATAGTTATATTGTAAAAAAAAATGCAATATTTCCCAGTATTGTGCAGTCTTAATCATATCAGTGTCCTTTATTGTGTCTCTGCTTTTATATGCATTCTACAG
Seq C2 exon
GGAAATATTATATAGCCACGATGACCATGATCACTGCATCCACAGCCCTCACCATCTTCGTTATGAACATCCACCACTGTGGCCCAGATGCCAAACCTGTTCCAGACTGGGCCAAGAAATTCATCCTGCAGTATCTGGCCAGGATTTGCTTCGTCTACGAAGTGGGTGAAAACTGCATGACGCCGCAGCCAGAGAAACCAGATCCTCAACCGCAGAAGCCTCAGGACTGCAACTGCAACATGAACGGCCAAGCTGGAAAAGACGACTTTGTGTTTAAATTCGACAGAAATCAAGAAGCCACATCTCCGAAGCTGCTTGAGGACAGAGAAGATATGTCACAAATATTGAGCCCGGCGTGCTCACTAGGAAAACATCCCACCTGTCGGTATGGGGTGTGGAAGGAGGGAGTGTTCATGAGTATGGATTGCGGCGATGGAGCGGCTGAGACTGGAAAACCCATAGGAAGAGGACAGGAAGGGTGCAGAGATCATGACTCTGGGTTTAAATCACAGTGCAAGTGTGATCAGCAGCATCTCCTGAGGAATATTGAGTATGTGGCAAACTGTTACCGTGATCAGAGAGCTACGGCGAGACGAACAGGAGAGTGGAAGAAAGTCGCCAAAGTTCTGGACCGATTCTTCATGTGGCTGTTCTTCATTATGGTTTTCTTCATGAGCCTGCTTATAATGGGGAAAGCCATTTGACATGGAGGTGACTGAAAGAAGGACATGACTGAAATAATGCAAGTCTAGTAATATTTATTACAGCACTTCATACACACAAAATTTATTCAATTAAATTTATTCAATTTTTTGTAAGGTAAGTGGTTGCCAACAATT
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000011113:ENSDART00000152531:4
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.158
Domain overlap (PFAM):
C1:
PF0293118=Neur_chan_LBD=PD(55.6=64.2),PF0293211=Neur_chan_memb=PU(19.6=31.3)
A:
NA
C2:
PF0293211=Neur_chan_memb=PD(80.1=97.4)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCCTCCATCTGAGAATGTGCC
R:
CTCTGTCCTCAAGCAGCTTCG
Band lengths:
356-2101
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]