GgaINT0078168 @ galGal4
Intron Retention
Gene
ENSGALG00000016341 | CSMD1
Description
CUB and Sushi multiple domains 1 [Source:HGNC Symbol;Acc:HGNC:14026]
Coordinates
chr3:89738177-89740058:+
Coord C1 exon
chr3:89738177-89738353
Coord A exon
chr3:89738354-89739878
Coord C2 exon
chr3:89739879-89740058
Length
1525 bp
Sequences
Splice sites
5' ss Seq
CAGGTCAGA
5' ss Score
7.41
3' ss Seq
TTTTGTCTTTTCTTCACTAGTGA
3' ss Score
8.45
Exon sequences
Seq C1 exon
CTGTATCTTGTGGAAACCCTGGCACTCCAGCCAATGGTATGATAATATACAGTGATGGAATATTATTCTCCAGCTCGGTTATTTATGCTTGCTGGGAAGGTTACAAAACTTCAGGGCTAACTACTCGACATTGTACTGCCAATGGGACATGGACTGGCACTGCTCCAGACTGCACAG
Seq A exon
GTCAGAAATATATATATTTTTTCCCTCTAAAGCTTTAAAATATTAAGACAGCTAACGTTCCTTCTGAAATGATTATTTTGTTATGAAAAAAGAAGCACATTTTGTCCTATTTCTCTAATTTGAGATACATAAATATTTTATGTGCTTAAAGGTATATGTTTTTAACACATGCCAAAAGTTGCCAGAAATAACTTTTTAAGATGGATACATAGGTAACTTTTCTGTAGGTGAATCACAAGATTCACGTATCTTGTGAATACCTTATGAATTAAAAACATTACATTATCGCTTAGAATAAGTGTTCCTCTAAAATTTTCTTTAGCTTCTTTGTAATTTATGTACGCAGGTAGGTCTAAATCAGATTTTATCTAGTTGGATGCATTGTTGTGCCTGCTTATTTTGTGACACAACTGAGTCAGATCTGACTCACAGTCATTCTGTTCAGGACCAAGAGTCAGGGAGCAGTGAGTCTGAGCTGCTCCACCAGCGTGGAGAGGAACAGCCAGGCCAGCAGGTCCAGTGACCTTGCTGATGAGGCCAGGCCTACAGTACTGAGCAAAGAGAGCACAACAGGTTCAGTGACAGTAATGTGAGACCACCACAGCCCAGTGATCTCTAGGCAAGTCTGCAGTGACAAGGCAAATTCTGAACAAGCTGATAAGTCTAGTCAGTCTAGTCAGCAAGGTACATGGCCAGGCATAGACATACCTGCTGTGTAGCTCAGTCAAAGATCAAAGGCGAGGCTTTGAGCTTAAATATAGCTCTCAAACAAACGGAGAAGCCACAAAGCTGCTTTTTCCAATGCAGTCTGATCCTAGGTTACGTTTGCACTGAATCAGAGCTGGCCTTGAGCACAGGCTCACTGGGAAATGGGGAAAGGGCAGCAAAGTCAGTCGGTGCATACATAACCCTGGGAGGAAGTTACTCAAAATTATGGAATCTGTTAGAAAACCTACCTTTATCTCCTTTGATAGATGTAATGCCAGGTAAATAGTACTTAGTTTTATCATGTTGTACAAAATCTTCCTTCCAGGACTAAACAAGACAATTGTTAGAAATATGAATTAAATTCTGAGCTCAGTGGTACCAATTCAAAAAAATATCTCAAGAATTTCGTAACTGTTGGGATTACATCAAGTGATCTACATAAGATACACTGTTACAAATGTCCCTATCAAAACTACCACTAACATAACAATATTCTATGTCAGTAGAACATGCTAGTTTAAGCTAGTTTATTCAACTATGATTTTTAAGGTCCCTTCCAACCAAAACATTTCTATGATTCTATAGATTCTAAAATTGTTGATTCAAATAATATTTGAACTCAAAATTTGGCTCAGATTATTGCAATCCATCAAAATTTGATTTTTAACTAAGTTTTTGATTTTGTGTGAAATCTGTTTAAAATATTCTTACTTTCCACTTGAAACAAACAAACAAACCAACAAAGGTTAGCTATATATAGCTTAATGTTTCATTATGTTTATTGAAAAAAAAAGCCTTTTTGTCTTTTCTTCACTAG
Seq C2 exon
TGATCAGCTGTGGAGATCCAGGTGCATTAGCAAATGGCATTCAGTTTGGAAATGATTTCACCTTTAATAAGACAGTCAGCTATCAGTGCAATCCAGGATATGTGATGGAGCCTGCCAGTTCATCTACCATGCGTTGTATAAAAGACAGCACTTGGAACCAGAGTAAACCAATTTGCAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000016341:ENSGALT00000026359:57
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=91.8)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping 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:
343-1868
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]