GgaINT0078168 @ galGal3
Intron Retention
Gene
ENSGALG00000016341 | CSMD1
Description
NA
Coordinates
chr3:92972886-92974767:+
Coord C1 exon
chr3:92972886-92973062
Coord A exon
chr3:92973063-92974584
Coord C2 exon
chr3:92974585-92974767
Length
1522 bp
Sequences
Splice sites
5' ss Seq
CAGGTCAGA
5' ss Score
7.41
3' ss Seq
CCTTTTTGTCTTTTCTTCACTAG
3' ss Score
-0.38
Exon sequences
Seq C1 exon
CTGTATCTTGTGGAAACCCTGGCACTCCAGCCAATGGTATGATAATATACAGTGATGGAATATTATTCTCCAGCTCGGTTATTTATGCTTGCTGGGAAGGTTACAAAACTTCAGGGCTAACTACTCGACATTGTACTGCCAATGGGACATGGACTGGCACTGCTCCAGACTGCACAG
Seq A exon
GTCAGAAATATATATATTTTTTCCCTCTAAAGCTTTAAAATATTAAGACAGCTAACGTTCCTTCTGAAATGATTATTTTGTTATGAAAAAAGAAGCACATTTTGTCCTATTTCTCTAATTTGAGATACATAAATATTTTATGTGCTTAAAGGTATATGTTTTTAACACATGCCAAAAGTTGCCAGAAATAACTTTTTAAGATGGATACATAGGTAACTTTTCTGTAGGTGAATCACAAGATTCACGTATCTTGTGAATACCTTATGAATTAAAAACATTACATTATCGCTTAGAATAAGTGTTCCTCTAAAATTTTCTTTAGCTTCTTTGTAATTTATGTACGCAGGTAGGTCTAAATCAGATTTTATCTAGTTGGATGCATTGTTGTGCCTGCTTATTTTGTGACACAACTGAGTCAGATCTGACTCACAGTCATTCTGTTCAGGACCAAGAGTCAGGGAGCAGTGAGTCTGAGCTGCTCCACCAGCGTGGAGAGGAACAGCCAGGCCAGCAGGTCCAGTGACCTTGCTGATGAGGCCAGGCCTACAGTACTGAGCAAAGAGAGCACAACAGGTTCAGTGACAGTAATGTGAGACCACCACAGCCCAGTGATCTCTAGGCAAGTCTGCAGTGACAAGGCAAATTCTGAACAAGCTGATAAGTCTAGTCAGTCTAGTCAGCAAGGTACATGGCCAGGCATAGACATACCTGCTGTGTAGCTCAGTCAAAGATCAAAGGCGAGGCTTTGAGCTTAAATATAGCTCTCAAACAAACGGAGAAGCCACAAAGCTGCTTTTTCCAATGCAGTCTGATCCTAGGTTACGTTTGCACTGAATCAGAGCTGGCCTTGAGCACAGGCTCACTGGGAAATGGGGAAAGGGCAGCAAAGTCAGTCGGTGCATACATAACCCTGGGAGGAAGTTACTCAAAATTATGGAATCTGTTAGAAAACCTACCTTTATCTCCTTTGATAGATGTAATGCCAGGTAAATAGTACTTAGTTTTATCATGTTGTACAAAATCTTCCTTCCAGGACTAAACAAGACAATTGTTAGAAATATGAATTAAATTCTGAGCTCAGTGGTACCAATTCAAAAAAATATCTCAAGAATTTCGTAACTGTTGGGATTACATCAAGTGATCTACATAAGATACACTGTTACAAATGTCCCTATCAAAACTACCACTAACATAACAATATTCTATGTCAGTAGAACATGCTAGTTTAAGCTAGTTTATTCAACTATGATTTTTAAGGTCCCTTCCAACCAAAACATTTCTATGATTCTATAGATTCTAAAATTGTTGATTCAAATAATATTTGAACTCAAAATTTGGCTCAGATTATTGCAATCCATCAAAATTTGATTTTTAACTAAGTTTTTGATTTTGTGTGAAATCTGTTTAAAATATTCTTACTTTCCACTTGAAACAAACAAACAAACCAACAAAGGTTAGCTATATATAGCTTAATGTTTCATTATGTTTATTGAAAAAAAAAGCCTTTTTGTCTTTTCTTCAC
Seq C2 exon
TAGTGATCAGCTGTGGAGATCCAGGTGCATTAGCAAATGGCATTCAGTTTGGAAATGATTTCACCTTTAATAAGACAGTCAGCTATCAGTGCAATCCAGGATATGTGATGGAGCCTGCCAGTTCATCTACCATGCGTTGTATAAAAGACAGCACTTGGAACCAGAGTAAACCAATTTGCAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000016341:ENSGALT00000036950:51
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=91.7)
A:
NA
C2:
PF0008415=Sushi=WD(100=90.3)
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:
ATCTTGTGGAAACCCTGGCAC
R:
TGGTTTACTCTGGTTCCAAGTGC
Band lengths:
346-1868
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]