GgaINT0078167 @ galGal3
Intron Retention
Gene
ENSGALG00000016341 | CSMD1
Description
NA
Coordinates
chr3:92968337-92973062:+
Coord C1 exon
chr3:92968337-92968519
Coord A exon
chr3:92968520-92972885
Coord C2 exon
chr3:92972886-92973062
Length
4366 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAGT
5' ss Score
11
3' ss Seq
TTTTAAACTTTTTTTCACAGCTG
3' ss Score
8.82
Exon sequences
Seq C1 exon
GAAATAATCCTGGCTACTGTGATGATCCAGGAATACCAGCCCATGGGTCTAGATTAGGAGATGAGTTCAAAATAAAAAGTTTGCTTCGTTTCTCCTGTGAAATGGGTTATCAACTGAGAGGATCTTCAGAACGAACATGCCTGCTTAATGGGTCTTGGTCAGGTATACAGCCTGTGTGTGAAG
Seq A exon
GTAAGTATTGATGACACCATCAGTATTTATGGCACTATTGAATAGAATCATAGAATGGCCTGGGTTGAAAAGGACCACAATGATCATTGAGTTTCAACCCCCCTGCTATGTGCAGGGCCACCAACCACTAGACCAGGCTGCCCAGAATACCTTATAAATGGAATTGTATTGTTTTATTAAAAAGAAATATATGACAAAAATATGCTTTCAAATATTTCTGCAGAAATTTGATATAGTTTGCAAGCAATTAATATTTTGATTAAAAACAAAAGTACAAACATTTAAGGTTTTATAGTATGTGTTTATAAAAAAAGAAAATAATTCTAGTTCAACAACTAATGAGACTGGAAATAGAGAAGAGATACCTAAGTAAAATATGTAATTAAAAAAATGCTACTGCTTGAAAATATGATAACAGTGTTATAAATAAAGCCATCATCCATCTTCATTTCTTTCTGTGTAGTGTCTAGGCATCAAGGACTGAACAAATGACAAAATAATGTTGCTTTCTTAACTAAGAAGAAATTAATAAATATTTCTTCCACATAAGTTAATTTTTTTTAGAGACTTTATTTTATGAAAGACTAGTTTTATGTTAGGTTTTTCAGAAGAAAAACAGCAACAAATATTTCTGGAAAACACATGTAACAATGGAATGAAAAAAATAGTTTATGGATTCTGTAGTATCTCATGGCTGCTATACTGATCTATAAACTGGAAGATAGTATAAAAAAACATATTTTATTAATGATATCTTATTAGCATCTAACAATTATTATTTTTCAGTATTCCTCAGTACAGATTGATTGTCTAACCTGTATTAAAATTGCAGAAGGCACAGAATCAATATTTACAGGAGAAAATTGAAGTTCCTCAGTGTCCTTTCTTGTATTTTCTCTTAGAGACATTAAATATGGCAGCAGTCAGTGGCAATCAGTGGTATGTGAAGTGCTGCTGATTTTCGTATCTTTTTTTTTTTTTTCTTAAGCTTTATGTTTCCAGAAAAATCATGAAAAGAAACCTTTCTTTCAACTTTTCTTTCTGCTTGGATTGTTTTTTGTTTAGTATAAGTGACAATGAGATTATGAGGAAACCATTTTTTCAGCCCTGCACACACTGTGTAAAGCATGTCACAGTGACAAATCCTCAGAGTTTATAACTGTTTTTATCTCAGCTTGCTATTACACACATCTGGTATTTATTCCACCTATACAGAAGTCACACACTGCATAAAATTTTAGTATGTTAATCCCTTTGTTTGAACCTGTGATTGAGTGATTTAGCAATTGCTAAAGTAATTAATGCAGAACATCAGAGGCCCCAAAATGCTTATAAAACCCAAGAATATTTAAAAGGCTTCCTGCCAATGCATATATCCTCATAGGCAGAATTGCTGGAAGTTACTTCAGAATTGATAACACTTGCTCCATATCAGTTCTAACGTTCCTATCTTTGGAAAACATGCCATTAGTCCTCATTGTCTTTTTGGCTGAAGGTCTTGGTGTTAAATGTTTTCACACACAAATACTTGAGAAAATTTGAGATCTAAAGATGACAGAGAGAAGCCCAGTTATTCTCAGAAGCACTATAAACATCCCTTCATGCATAAATCTGAGAACTGCTGCTTCTTCTTGAAGATATTAAGGTGCTCTACTTGGAAGAATGTACATAAGATTTGCATCAGCACCTGCACTGAATATTGTGCATGGAACCATGAAGATTTGCATAACTAAAATAGAAGCTGGCAGTGCAAAATAAGACATAGCATTTCCATTAGTAACCTCTACCATCTTCAGGCTTCAAGATGAACATCTGTAACAAACTGTTACAGGATGTGTGAGCTATCTGATTCTATTTATTTATTTGTTTGTTTATTTGTTTATTTATTTATGGAGTTTATTATATCAGGGTTCTATCTGTAGACTGATTCCACTCATGTCCAGAAAGAGACAGAATCTCAAGCTATCACATCATGACTCTTCATCCTAAAAATTTGCAGTCAAATGCTGGGAATAATGGATAAACACCAGTACCTTTATTCTTCATTTCATTTTCTCACTTTTGTTTAAATTTCAATTTTATTTTTGTTGTACCAATTTTATCTATGCTATGTAGTAACCATTTTGCAATCTACTTTTGGTAGACTCAGAAGGAAAGTATACAATAATGGTCATCTACTCACCTGTAAAAGAAAAGCATTTGTGGCTATTTCTCTTTGGATTGGTTGATATGAAGCATATTTCATCTGAAAACTGGATTATTCCAGAATGCATTCTATTTTTATTTCTTCGGCTGAGGTTTTACTGGGCCACATGAGACCATTATCCACTGCATCATGAACAGCAGAGATTGTAAGATTTATGGTTCTCTCCCTACTCATAAAAGCAAAAGTCATTTAAAATGTTGCTGTGGCAAAGTTTGAGGTGAGCAGGTCAGTGTACGTATATTCTTTACAAAGCACCTCATACTATCCTTTTGAGTTCAGGTGCAGGTCATCCAAAACTCTAGAAAGATACAGGACAGTTCAAATACAGTGTCAACACATTGAATAATTAATGAATAGCATCCTGGCCTGTATCAGAAATAGTGTAGCCAGCAGAACTATGGAAGTGATTGTCTCCCTTTATTTGGCACTGGTGAGACTGCACCTTGAGTACTGTGTTCAGTTTTGGGCCCCTCACTGCAAGAAGGATGTTGAGGGCCTTGAGTGTGTCCACAGAAGGGCAACAAAGGTGCTGACGGATTTGGAGCACAGGCCTTATGGGGAGTGGCTGAGGGAGCTGGGATAGAGAAAGCTTAGGAAAGACCTTATTACTCTCTACAACTCCCTCAAAGGAGGTTGTGGCAAAGTGGAGGTCAGTCTGTTCTCCCAGATTGCTTTTCTATTTATTACAGTTTGCTATGTCAACACTATTTTTTTTTCTTTTTAGAGCTGAACAGCATATATTTCTTTATTACATAATATATGTATATGAATAATAAATAATTTCTATCCTCCTATTACATAATAGGAGGATAGAAAATGGCTTCAATTTATACCAGGGGAGGTTCAAGTTGAATATTGCGAAAAATTTCTTCTCTGAAAGAGTGGTCGAGTACTGGAACAGGTTGTCCAGGGAGATGGTTGAGTCAGTGTCCCTGGAGAAGTTCAAGGAATGTGTAGATATGGCACTGAGGGACCTGTTTTAGTGGGCATGGTGGCGACAGGTTGGTGGTCAGACTAGATGATCCTAGTGGTCTTTTCCAACGTTTCTATGATTCTATGAATGCCTTAAATAATCCAAAGCAATATAAAGACACATTCTTTTTATAGTTTTGTCTACACTAAAAATGATGATGATCTGAGAGCAGGCAGGGACTCCTGCAAAGAAGCCTGGAATATACAGAGACATCTGTAACAGTCCTAGAGCAGTGAAAAGGCAGGACTATTGTATTTCTATCTAACAGTGCAACGAAAGTAATAATGAGAAGTATACCTCATCCTTTTTCCTCCTGTCTGAAGGCCATAACTATAAAAAGGCATTTATGATACTAAACATCAGTAATATTCAGAGTAAGCCTGGAGCAGAGGAGATTTGGGGGAGGTCTTATCAGTGCCTATAAATACCTGAAGGGAGAGTGCAAAGACGTTCGAACTAGGTTCTTTTCATTGTTGCCCAGGGACAGGGCAACAGGCAAAACTGAAGCGTAGGAGTTCTCATCTGGGCACTGCCACAGGTTGCCCAGAGAGGTCATAGAATATATCTTTTTGGAGATATTCAAAATACCATATGGTCATGGTCCTGGGTAACTGGCTTTAACTGACCCTACTTGTAGTAGGGTATTGGACCAGGGATCCCTTCCAGCATAACCCATTCTGCAACTCTGTCATTCTGTTACTAACCGAAATAATAAGTCAATAAGTAAAATAAATATATGTATAGTGTGTGATTATTTTAAAGGCAATCACTATCAAACTGTTGTTTTGGCAAATGTTAAAAAGATCTTTGCATAAATTCCATAAGTACATTTAGTGTTACTGACAGTATCCAAGTTTTCCTAGTGCGTGTTGCGGGTGTGTTGCACCTTGACCAGTATCTGCAAATTGTCTTCAATTTGTTTTATTAGCATTATAAGTGAAATTCATCCAGTTCTCTAAGGAAGGTGGAGCTATTATCTCTACACTATACTTCTGTGTAATAACTGTAGCTTCCTAGTCAAAATTACACTCATTAAGCATTTTCTTAATAACATTTGCTATACCATTTTTAAAAGGCAAGCTGATTAAAAATAATTGATCACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTCCCCAGCTAATCACCTATCATGGAAGTATTTCATTTTTTAAACTTTTTTTCACAG
Seq C2 exon
CTGTATCTTGTGGAAACCCTGGCACTCCAGCCAATGGTATGATAATATACAGTGATGGAATATTATTCTCCAGCTCGGTTATTTATGCTTGCTGGGAAGGTTACAAAACTTCAGGGCTAACTACTCGACATTGTACTGCCAATGGGACATGGACTGGCACTGCTCCAGACTGCACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000016341:ENSGALT00000036950:50
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=0.000
Domain overlap (PFAM):
C1:
PF0008415=Sushi=WD(100=87.1)
A:
NA
C2:
PF0008415=Sushi=WD(100=91.7)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
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]