GgaINT1009473 @ galGal4
Intron Retention
Gene
ENSGALG00000003005 | CHRNB4
Description
neuronal acetylcholine receptor subunit beta-4 precursor [Source:RefSeq peptide;Acc:NP_990150]
Coordinates
chr10:3112834-3116708:+
Coord C1 exon
chr10:3112834-3113806
Coord A exon
chr10:3113807-3115745
Coord C2 exon
chr10:3115746-3116708
Length
1939 bp
Sequences
Splice sites
5' ss Seq
AGTGTAAGT
5' ss Score
8.46
3' ss Seq
AATTGGCTTTTTTTTTCCAGGTC
3' ss Score
10.02
Exon sequences
Seq C1 exon
TGCGGATGGTACGTATGAAGTTTCGCTATACACAAACGCAATTGTACAGAACAATGGAAGCATTCGCTGGCTGCCTCCAGCAATTTACAAGAGTGCCTGCAAGATTGAGGTTAAGCATTTCCCATTTGATCAACAAAACTGCACCTTAAAGTTCCGGTCCTGGACATATGATCATACAGAAATTGATATGGTACTTAAAACTTCCATGGCAAGCATGGATGACTTCACGCCAAGTGGAGAATGGGACATTGTAGCACTCCCAGGAAGAAGAACTGTAAATCCTTTGGATCCCAATTACGTTGATGTGACATATGACTTCATTATTAAAAGGAAACCTCTTTTTTATACCATCAATCTTATAATTCCTTGTGTGCTAATTACATCCTTAGCCATCCTGGTGTTCTACTTGCCTTCAGACTGCGGTGAAAAAATGACCTTATGCATATCTGTGCTGCTTGCTTTGACCGTGTTCTTACTGCTGATCTCCAAAATTGTTCCTCCAACATCTCTAGATGTCCCACTGATTGGGAAGTATCTCATGTTTACAATGGTACTGGTGACCTTCTCGATAGTTACTAGTGTCTGCGTACTCAATGTCCACCATAGATCTCCAAGTACTCACACTATGCCTCCATGGGTAAAGCTGGTTTTCCTTGAAAGACTCCCAGCCTACCTGTTCATGAAGCGTCCAGAAAATAATTCTCCACGGCAAAAGCCGTGCAACTGCAAAAAGACAAGAGCAGAGAATCTCTGCATGGACCCAGCAGACTTCTACAAGAACTCTACTTACTTTGTGAACACAGCCTCTGCCAAAAAATACGACATGAAGATCACTGACACTCTTGACAATGTCAGCAGCCATCAAGATTTTAGGTTAAGAACAGGCACAAAATTTTCTCCTGAAGTCCAAGAAGCGATTGATGGAGTCAGTTTTATAGCAGAGCACATGAAAAGTGATGACAACGACCAGAGT
Seq A exon
GTAAGTAAATCTCCAAACTTCTTCCCTTGTCCCCCTCTGTAGCGTGTGTTCCTTCAGGAAGGAGATTTGTACTCTCTAGTTACCTTGAAGCTTTTAGAGATATTCTAGGTAAAGGTTAAAAACACTTAATGAATAGTAATTTGGTAAAGCCATCACCACACAAAAAGAGAATGCTGACCAGTAAGTCAGGAAACACCCTTGAAAAAGCTGTTGTCACCTTCAAGTAGTGTTTAGCAGGGAAAACAGTAATGCTGACTGCCAGGTCAGAGAGAACTCTATTTGAAAATATTTTTCCCCATCATATTCAGACAGACCGTAACACATCAGCTCATGTTAACCAGTGTACCTGCAGCTCAACCTCTGTGAACACCCTAAGACCTCTATACCTAGTTGAGCAAGATGAGCTGCTGTTTAAGTTGCTCTGTTACAGCAAACACAATGGGTAGAATTGAAATCCTAATGCCAGCAGAACTGATACTTCTTCCATTTGAGTTAAGTCACACTTGTTATTGGCTATGAGAAGTAGAGGGTTCAGGGCACACGTAAGCAGTGCTGCTGCTGTCCTGTTCACATGCCCTACCCGAGCTACTGGCCAGCACACTGCAGCTGGTACAAACACACCACAGATAATGCTCAGAAATACTCAGATGGTTCAGAGTTTTGTTTAGACCACAGTTAAGGAAAACTGCCAAGCATCCCTCTGTCATCCTGCTCAGTCCCAGATCCCAGTAGGACTATAGGTTCTTTATTCCTGCCCCCTCCTTCAGCCAAGCAGACTAAATGAAGCCTGGCTTCTGATACTGCAGAAGTCCCTTGAGGAGCATGCTGCTGAGTAGTTCATGTTTTCTATTAACTGAAATTACTGTCAATATAAATAAAGATCAGATGCTAACATTCAACATGACCCTACACGCACTGAAACTGACTGAACAGAAGCACACTTCACAGAGCAGGCAAAAAGTTTTCTAATAGCTCAGAAATCCTTGCAAGAATATGCTGCATTTTAAAAGATCCAACTTGAGACTAAGAGCAACTTTCAAGGGTATTTCATACATTAAAAATGAATAGAATGCTTTTCACACAGGGTCCTCTGATACTGCATATTACTGTTTTATGGACTCATAACCTTAATTCCTGCTATCTTCCTTCATCTGATAGCAACTGTTCGTGTGCATTTACTACAGCCTCATTTCAGAAGTGCAAAATTTCCATTAGCAGCAGTGGGAATTAGAAGTGTGTGCTGAAGGAAAAATATGTAATGTTCTAATCTAAGACAAGAGATAAATGACAAGCATGGTGAAGTCACTGAGGTGACAATGTCCCGCGTATAATGAGAATCAATGACAGAGGAAAAACAATCATTCTTGAGATGCAAATGAAGATTGATATATTCATCCTTTACAATGAAAGCCAGAAGGTCACTTCAGTTTGAGAAGAGAATCCAAGACTAGTCTTATGCTGTATGTTTCACACACAACACATGTAAGGCTGAGGGGATTTTAATAGAAGCAACAGTATTAATACGCATTAAACCACTTGATTAAGAAGACTGCTGATAAGAAAAGTCAGAGGCTAACCTTGTTTAACGGCAATAAATACTCTCTCTCTTTGTCCACAGAGATTAATAGCATCTGCAAATTAAAATTAAAGAAAAAAGATCCTTAATTGGATTACACCGTAGCTCCTTCCGGAACAGCACCAGGCAGCCATGCCCTGTACCTCACACATCAAAGACAGCTAAGAAATATTTACAGTATTTTTCTCCACTGCTCGGAATGGTTGCAGGAGAAAAATTCCTTCCTAAGTCTAAAGTCAATTTGTTCCCTGGACCTGGAGGTTTATTTCCTTTTATTTTCATAAACAAAGACTGCATCAGCAAGAGGAAGAGCAAAGTAACATGACAAATTGCTAATATCTTTAATTGGCTTTTTTTTTCCAG
Seq C2 exon
GTCATTGAAGACTGGAAGTATGTTGCCATGGTAGTGGACAGGCTGTTTCTCTGGATATTCGTCCTTGTTTGTGTTCTGGGCACTGTTGGATTATTTCTGCAGCCGCTCTTTCAGAACCACATTGCTGCCACGAACCCTTAGCTCTTATCTAAAATTGCCAATGCCTACATAGATGCTGGGTCTCATCCTGCTCTCAGTTGCCCTCTGCTAAATCCAGAGAGATGTCAAACGAGTTGCTCTCCCATCGGATTTATGGTAGGGATGTGGAAAGCAGCAACATTATTTTGATAGGAAAAAATGTTTAAAAAAGAAAAGGAATCATTTTTCCCAATGGGTTCAGTACTTCTGGTGATCTCATGGCTCTTCTTTCAACTCGTTGAAGCCTGAATATTAGAGAAAGACATTTCCCGTATAATATGCCAGCTTGGCTCACAAGGATTATTTATTAAAAGGGTATTTTATATACATTGCCTCAGGAAAGCCATTTTCTTTCCCTAGAATACTGCAGTTTCCATGCTCCAAAGAAGGCATTTATTTCCTCAAATGCATCAAAATGATTTGTGCCTGATTTATACAGAGCTTGATGGGTGGAATCATTGTTTAGCTGTGTTGGCTGTGATATTTAAGACTGAACTGAGAAACAGAGCCATACTTCTGGTTTCTCCTCGTGCTGTCCCTGTAGTAGGTTAATCAACCGAGGCCAAATTAATATGTAATATTAAACATTTATATGCTCTGTTCAGTGACAAAATGTAAATAAAATGTAAAAATTCTCCCTTATATATAGTCCTGAAACGTTCCTACAACTTTTAACAGCTCATGTAAGTGGCATTCATGTACACCTTCATGAATCTAAGGCTAAAAGTAGAAGAAAGCATCCTGGGGACAAACCAGCTGTGAAAGGTGGCTAGAACGTGGATAAGACACCTGAGAACAGACCTGCATGTTTTACTGAGGAGATGT
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000003005:ENSGALT00000039804:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.015 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0293118=Neur_chan_LBD=PD(54.4=34.5),PF103294=DUF2417=WD(100=42.2),PF0293211=Neur_chan_memb=PU(86.1=63.1)
A:
NA
C2:
PF0293211=Neur_chan_memb=PD(13.0=66.0)
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:
AGACTCCCAGCCTACCTGTTC
R:
CCTGTCCACTACCATGGCAAC
Band lengths:
357-2296
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]