DreINT0046736 @ danRer10
Intron Retention
Gene
ENSDARG00000003420 | chrna5
Description
cholinergic receptor, nicotinic, alpha 5 [Source:ZFIN;Acc:ZDB-GENE-050417-440]
Coordinates
chr18:40496265-40499667:-
Coord C1 exon
chr18:40499317-40499667
Coord A exon
chr18:40496627-40499316
Coord C2 exon
chr18:40496265-40496626
Length
2690 bp
Sequences
Splice sites
5' ss Seq
GAGGTAAGG
5' ss Score
10.28
3' ss Seq
AATGTAATATCTAATTTCAGGTT
3' ss Score
7.67
Exon sequences
Seq C1 exon
GTAATTCCTCTGATTGGAGAATATTTGGTCTTCACTATGATCTTCGTGACACTTTCCATTGTCATCACCGTCTTTGCTATTAACATCCACCATCGCTCCTCTTCCACCCATCATAGCATGGCTCCCTGGGTCCGCCGTATCTTTCTTCACCACTTGCCTAGACTGCTCTGCATGCGTAGCCACGTGGACCGTTACGCCACCAGCGCTGGGACTCGAACAGGAGGACTGGGCTATGGGAAGAGTTTGAGTCAGGATACCAACCAGCTCGATGCAGAACACAACCTGCAGGCGGCCTTAGAGTCTATACGCTACATCACACGCCATGTGGTGAAGGAGAATGAAGTCAGAGAG
Seq A exon
GTAAGGCTGATGTCTTTGATATACACAGTTAAAGGCTAAATTATTCGCCCTACTGTGAAATTTGAATTCTTTTTCAAATGTTTTCCAAGTGATGTTTAACGGAGAGGAGATTTAACACATTATAAACTAGTTATTAAATAATAAAACATGTAATAACTAAATTTCTTTTGTCTTTGCTATGCTGACATTACATATTGTTTTTCTAGTTAGTTTGCAAGATACTAGTATTCAGTTTAAAGAGCAAATTAAATACTTAAGTAGGTTAATTAGGGTAACTAGGAGAGTACTGTAGCCAGTAGAAATTTTTTTAAAATCTTAAAATTCTCAATGAAATCAACTGTACTTTCCAAATAGTAGTGTATATGTGCACTTCAGAGTGATGCAGTAGATATGCTGTCGCCTCCCAGCAAGAAGATCGCTGGTTTGAGCCTCGGCTGGGTCATTTGGCGCTTCTGTGTGGAGTTTGTATGTTCTTCCTGTGTTCGCGTGGGTTTCCTCCGGGTGCTACAGTTTACCCCACAGTCTAAAGACATGCGTACAGGTGAATTGGGTAGGCTAAATTGTCCGTATGAGTGTGAATGAGAGTGTATGGATGTTTCCCAGAGATGGGTTGCGGCTAGAAGGGCATCCGCTGCATAAAAACATAAATAAGTTGGCGGTTCATTCCACTGTGACAACGCCAGATTAATTAAGGGACTAAGCCAAAAAGAAAATGAATAAATTAATGAATGTGCACTTTGTTATTTAGTAAACAATCTCTCTCTAAAAATCCCTCTAAATGACTTTTCTTCACTTCTGGTCACATGGAATGCTTTTTGGGTGGGGCTATGAATCTATTCGTCCTCAAACCATTTATTATAATCTTCTAGAAATATATTCTTTTCTGCTTTGCATTACTGTGCGTTTTGGTTCTGTCGGTGTAATTTGCAAATGATCCCTAATATTGCGTGCGCGAATGTCTGGCAAATATCAAACTTAAAACCAACTTTACCGAGCTGTTTTTAGCCAAAGTAGCTGATAGATATCCTAAAAATGAATAATACTGATACTAACATCTAAAAAACTTTAATTTCATGGTGCCTTTAACAAGCACAAGTATAGATTTTAATAGTGCTTTAGTTAATGTTGAAATAAATAAATGCTTTACAAGAATTCATACTTAATGTAAGTAATTACATTAACTACAACTAATGGACCATTATCCTAAAGCGTTCCCATTTATTTTGCTAGCACACATTGTTATTGTCTATTTATTAATTAACAGTTTATCAAAACAATGTTTCTTTTGGTAACTTTTTAAATCAAATCTTACCATTTGCTTCCACTCTGGAATAGCAGTTCTTTATTGATGATGTCAGTTTGTGTGAAATTTTCTTAGCCACACCCCTTCCAACCATTAGTTTGCCATAAGTGAAAGATGAAAGAAGTGCAAAAATAAAACCCTGCCCACTACTCAGTGTTCCATTTAAATGGAAAATACTTTATCATGCTAAAATAGAAGTCTGTAGCAACTTGTTTTCATGCAGATTTTAACAACTTTAATTGTCATTCTGCAATTGTTGTGGGTGGCAGACTCTTTCGCTCTCTTTAGAAGTCAAAATACTAGTTTATTGAAACTTTACACAGCAGTTTGACTTTTTAGGCTTTTTTTCACAGGTTGTCAAAGTTAAAGTTGATCTAAAGCAATTTCCAAAAAATTACAATTCTGTCATCCTCATTCGAGACAACCCTACATTATTTTTTCAAAATTCAGGACCATTTCAAGTGGATGTACACCATGACAGAAAAAAAAGTAGGTGGATGATCTCATCCTTTTATCTGAACTTCTGTTCTAATGTCAGTTTTATTGCTGAAATTCAATTCAATTTATCTTTATTTCTATAGCGCTTTTACAATGTAGATTTTGTCAAAGCAGCTTAACTTAGAAGGTATAGTAAATTGAAACAGTGTCAGTCCAATTGTCAGAGTTGAAGTTCAGTTTAGTGTGGTTTAACTTCACAGCTGAAAGTCCAAACACTAAAGAGAAAATCCATCGATGCGAAGCTCCACAAGTGCCAAATAAAGCAAGCAAGTGGTGACAGTGGCAAGGAACAAAACTTTACCAATTGACGGAAGTGAAGGAGAAAAACTTAGAGAAAAACCAGGCTCAACTGGGCACAACTTGTGCAGAGCTGCAGTCTAGGCGCTGGAGGGCACTGCACGTCCATCGTCCACTTGAAATATATATATTGCAAATTTCTCCTCATTTAGGGTTATGATCATGCATGCAAAGTTTCAATTTGCTGATGTGTTTTAAAACAACCAAAAAAAAAAAAAACTGCTCGTAAACTGTTCGTGTTCTGTTCACCTATTGTAATGCTTTATAGCAACACTACATTACCCAAATAGTGACATATCTTGGTTATAACTTTGTTATTTTAGTTATTCACTAGCTTATGAAGCCAAAACAGGATATTTTCCCAACTTATTTTGAAGGTAAAGTATGTTTTGCTAGCCACAAATGATAAAAATGGCCTATCGGTTTTTTTTATCAAAATCAAACCACTGGCATATAATTTTGCAACATAATTTTGTAAATAATTTAAAAAAACGAATTCAAATTTCCCTGGGCAGCTGATAATTTCGCCTTCAACTGCATGTCTGCATGAGCTTTAATTTCTAATAAATTCTAATGTAATATCTAATTTCAG
Seq C2 exon
GTTGTTCAAGACTGGAAGTTTGTGGCCCAGGTTCTGGACCGGGTTTTCCTGTGGGCCTTTCTCTTAGTATCACTACTCGGCTCTGCTCTGCTTTTCATCCCTGTTATCTATAAATGGGCCAGCATCATTGTTCCCAGCTATGCTGAAATTACTAGCTAAACTACACGAATGTATACACTTCCAAACTTTTTGGCTTGAATAAAGTTTTTTGCATTATTATAGCATTTATTACTGTAGTCTTCAAAACATCTATGCAAATTGTGGCAATCATGCGCTGTCATTTAAGATGTAACATGCTGCATTCTATTCTCTGTTGTATGCTGATTTCATTATATTAAAGTTTACAATAAAAATATGTATTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000003420:ENSDART00000021372:8
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0293211=Neur_chan_memb=PD(57.6=61.5),PF0293211=Neur_chan_memb=PU(60.7=43.6)
A:
NA
C2:
PF0293211=Neur_chan_memb=PD(36.9=58.5)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]