DreINT0046717 @ danRer10
Intron Retention
Gene
ENSDARG00000057025 | chrna2b
Description
cholinergic receptor, nicotinic, alpha 2b (neuronal) [Source:ZFIN;Acc:ZDB-GENE-041001-99]
Coordinates
chr20:19921949-19924932:+
Coord C1 exon
chr20:19921949-19923098
Coord A exon
chr20:19923099-19923731
Coord C2 exon
chr20:19923732-19924932
Length
633 bp
Sequences
Splice sites
5' ss Seq
AGTGTAAGT
5' ss Score
8.46
3' ss Seq
TACTGTATGTCTTCACACAGGTA
3' ss Score
7.81
Exon sequences
Seq C1 exon
TGCAGATGGGGAGTTTGCGGTGACCCACATGACCAAAGCCCACCTCTTCCACACAGGTAAAGTGCGCTGGGTTCCACCTGCCATCTACAAGAGCTCATGCAGCATCGATGTCACCTTCTTCCCCTTTGACCAGCAGAACTGCAAGATGAAATTCGGCTCGTGGACTTACGACAAAGCCAAGATTGACCTAGAGCGAATCGAGAACACAGTGGACTTGAAAGATTACTGGGAGAGTGGAGAGTGGGCCATTATCAATGCTGTAGGCACATACAACACCAAGAAGTATGACTGCTGCCACGAGATCTACCCAGACATCACCTACTTCTTCATCATTCGCCGTCTGCCGCTCTTCTACACCATCAACCTCATCATCCCCTGCCTGCTCATCTCCTGCTTGACTGTACTGGTCTTCTACCTTCCGTCTGACTGTGGTGAAAAGATCACTCTGTGTATTTCAGTCCTCCTCTCACTCACTGTCTTCCTCCTGCTTATTACAGAAATCATCCCATCCACTTCGCTCGTGATCCCACTCATTGGTGAATATCTGCTTTTCACTATGATCTTCGTCACTCTGTCCATTGTCATCACCGTTTTTGTGCTCAACGTCCATCATCGATCACCGAGCACTCATAAGATGCCCTGTTGGGTTCATTCGGTCTTCTTGGATTTGATCCCCCGATGGCTGTTTATGCGCAGACCAGCACCTGACAGCCGTCGCAGACAGAAACTCTTGCTTCTGCAGCGACAGGTGCCAGGAATGACAGCACGACCCGCAAACGCTTCCCTCAGTACATCTACTAGCTGGTTCAGAGGGCAGAACTCTGGGGAGGATGAGTCCTGTAGGCACTTCAGTTATAAGGACTTAGAACTAGGGACACTATCTTCGGCCATCTCACTTTCGCTCCAAGCCAGCTCGCCATGTCCTCTTGGCTTAACTCCGCCTCCTCTACAGAAATTTGGCCCAGCCCCTAGACTTGAGGTGGGCACGGCTTCCAGGCAGCTCAGTGGAAGAGCTAATGTTACAAAGAGGCTTGACAACATGATACCCCATGACAACCCAGGGTTCCCTCTGTCCCCCAGCGTCCTTCAAGCTTTGGAGGGGGTTCACTATATTGCAGACCACCTGAGAGCCGAAGATGCTGATTTTAGT
Seq A exon
GTAAGTTTCTTTCAGAGTCTTTAGCACAGCTGTAGACAAGTTCAGTCCTGGAGACCTGCAGTCCTGCAGAGTTGTAATCTAAGGTTTGATTGAAAAGTCACTTGCACCAACCAGTGACTTTTCATCAATTGATAGTAAGAGTGTTACTGATATCTCGGGATCTGCACACCGGTGGTTCAACTCATACCTCTCAGGTAGGTCTTTCAGGGTATCTAAAAGAGGTGAAGTTTCCAAGCTGCAAAATCTTGCTACTGGGGTGCTTTAGGGTTCTGTCCTGGGACCACTTCCCTTCTCTATCTACATGACATCAATTGGGTCTGTCATTTAGAAACTTGTAATTTCCTAACATTGCTATGCTGATAGGAGCAAAACTCTGCAGGACTACTCAACTCTGTAGGTCTGAATTTGCCTACCGCTTACCTTGCATGAAAAACATGTATATAAACATTTTTATATAGCCACAGTAGATCCATCAAGCTTGCCACCGACCTACATCTTGTTCAGTTCTATTTGAAACCTTGAAACAAGGAGTTGTCAAGTCAAATTCAAACTGTCCTTTACTAGTTACACATCATGCTATACATGTACTATATAATAATCCACTAATTCATCTTACTGTATGTCTTCACACAG
Seq C2 exon
GTAAAAGAAGACTGGAAGTATGTTGCTATGGTAATAGACAGAATCTTCTTATGGATGTTCATCATAGTATGTTTGCTGGGCACAATTGGTCTCTTTCTCCCACCATGGCTCGCAGGGATGATCTAGAAACACAGCACTAAATATCTTTTAAGAACATCGAGGACTTTTAATTTATGGGCTTCCACAGTAAGAACCAGCATGGGAACACAAATGACCCTCCTTGCAGCGATCGTCATGCAGTAATAGTGAAATTTCTCCTGCATTTGGGGTAATATGCATGAACTGGAATGTGGCACCAATCACCAGACCTGTCCTCCAATCTATACAACCATATAGGTTCTTTGTCCTTTTCCTGACATATGACCCATAGAAGCATTTACTAAAATAGTGCTCCTACTGCGAGTGAGACACGGGATCCATGGTGAAACTTTATCTATGTAAAACTCAGAACTGATAGAGAATTGCATTATGGTCGCGGAACAAACTTTGATTCAATACCAGAGAACAAACACGTTGTTAAAATATGTACCTAAAACTAAATTGTATTCCATTTGCCAAATTTTGGTCACTGAAAAGACGTAACGTACAAATATTGGGTAACACAAGGGATAGAGCTATGGTACATTTTTTGAGAAATTCTTTCAGAAAATTCATCACTATTCCCGATTAAATCGATTCTCAGTTTAGATGTTCACAGCAGATGGCACTCTCGGCTTTACAAATAGCAGTACGCTGCTTCCAACTCATTTCTTACAAATGCTACTTGAAGCTAAGATAATCTTTAATAAAATTAGTGTTCACACTTTGCACATTATCTACATTAATCTTGTGATATAGAGGCCAACTTACATGAGGCTCTTCCTCATGAGTGTTTAGGTGCACAGTTAAAAATTAGAATAGAGCGCCATCTGCTGTTGAAAACTAAGCTCAGAATCAATTCAAAAGAGAATAGCGATGCATTTGTAAAATATTAGTATTGATACAGAATCCATTTCTCAAATTATTTTTCACCTTTTGCTTTAGTATGGGACCATCTAAAAAGTCCACATGCTACATTTTAAAGAGCTTGTATTTTGATTGGTAATTTTGATTGGATTATTGACAATAATCTAGTTGGCACTCTAGGTCGTAAAACTTTGCTTGCACAAATAACCTATTTGGTTTTTAGGGCGCACTCACACTATGCAATCTGAATCGGGCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000057025:ENSDART00000136317:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.013 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0293118=Neur_chan_LBD=PD(55.6=29.9),PF0293211=Neur_chan_memb=PU(88.8=68.0)
A:
NA
C2:
PF0293211=Neur_chan_memb=PD(10.5=73.8)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Chicken
(galGal4)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCCATCTCACTTTCGCTCCAA
R:
AGACCAATTGTGCCCAGCAAA
Band lengths:
356-989
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]