GgaINT0078174 @ galGal4
Intron Retention
Gene
ENSGALG00000016341 | CSMD1
Description
CUB and Sushi multiple domains 1 [Source:HGNC Symbol;Acc:HGNC:14026]
Coordinates
chr3:89750229-89752149:+
Coord C1 exon
chr3:89750229-89750408
Coord A exon
chr3:89750409-89752036
Coord C2 exon
chr3:89752037-89752149
Length
1628 bp
Sequences
Splice sites
5' ss Seq
AAAGTAAGT
5' ss Score
9.72
3' ss Seq
ATTTGTCTTTTTACTTGTAGGTA
3' ss Score
10.42
Exon sequences
Seq C1 exon
CTCATGCATGCAGGCAGCCAGAGACACCAGCACATGTAGATGTGAAAGCAATAGATCTTCCTACTTTAGGGTATACTTTGGTGTATACCTGTCAGCCAGGATTTTTTCTTGCTGGTGGATCAGAGCATCGAACATGTAAGCCGGATATGAAATGGACAGGAAAATCACCTATTTGTAAAA
Seq A exon
GTAAGTCATTATTGAGTGATATGCTGTGCCCTACTTGGATGGATTTCATTTTCCCCAACATTTGCTCTTTATATACTAGGACTGAATTTTCCTGATTACTATTTAAATATGAATATTACACAATAGTTTTTTTTTTAAATTATTTTGTGAAAGAAACCATTTTAAAGTTAAAATAAGCACAGCATCTACAATTAATCAAACAGACAATAGAGGTATGTGTATGTATATATATATGTATGCACATATACATGATTTTACTCCTTACCAGCAAACAAGAACAACAAAAACCAACACAATACAAAGTATTACTCTTAGCTATATTTCTCCTAATGCTTATGACATAGTTTTAAAGAGTATTTAAATGTCTTCAGTGTTTAATATATGATTTTCTAGAAGTAAGAAAAAATTATTTTACTTCAGTTGTCTTTTCAATTCATTCAGGAATGCTCTTTGTCTAAGAAAAACATCCATAATAAAAAAGAACAGCAAACTAATAAATAAATAAAATGTTTGCACCTGATTCCGCTTTTATTTATGTTCATGTAAATTTCCTATCATTTTCTTAGAATAACTCTGAGTATGTAATTGTGGGGGCTAAATTTGGCCTCTACATGTGAATAAACATGGATGAGTACCTAATCTAGCAAACTTAAAAAATTAATTTTTGTAACATGAGCAAAAGAAAGGCAATCAGATGCCATGGGAAAGACAGTTGCAACACTATATGTAGTTCTAATGTGTGAAAGAACTCTAAATAGATTTAAGGTTAGAATTGTAGTTCATTTTAAAGTTCTTTGTTTCAACAAGAGAAGTATAATCTGTACATAAAAATTAATCTTATTCTAGATGTGTAATGGATGATTTTTCATGGGTAATATGTAATTAATACATTGAGGTAAGAGTTCTTGTATGCTTTTAGTTGATTTTCCTTTTTATTGGCATGCAGTCTTGAGATATAATTCTCTTTGTGCACTCCACGCTTTTTGTCCTATTTTATCACTTAAACGGTCTAACCTGTGTATTTCTGCTCCTAAAGAGAAAGAAAAGGAACCAGAAATTATATAAGACAAAATATACAACCAGACAGTGATTTTTAAGTGTCTAACAATATGAAGCCACAGCTTTAGCTGAAATCAATAGGCATAGCTCCTGAGAACATCAGAAGCATAGCACATGATACTTCTAACGATTCTTTCCCATGATATCTGATCCTATCTTCTTAATCCAGATGTTTTTTGCTAATCTGTAGCAAACTTTATTAATGCAGTTTATTTATTTAGCATTTAGCATAATATTATGCATAATTAGATATAGTATTTGTCCCCTAAATAAGGCTCTCTTTTATAGCAGAGACTGATATAAAATTATGGGCCTAAGTGTATAAAATAATTATATAACTGGACAACTTTTCACAGTAAAAATGTTGCTTTCCTAAATTATTTTCTGATGGCTTTTGTTTAAGTGGATAGGTTTGAACATGTTAAGTATTCAAGACATCAGTTACTTCTGTTTTAAATATAACTTTATTGCATAAGGGTTAATTGCATCAATCAGGCATTGTTTTAACATTCTATTAAAAAAATAACAAATATGTTCATGAAAATGATAATTTGTCTTTTTACTTGTAG
Seq C2 exon
GTAAAGGAGTGAGAGAAGTTAATGAAACAATAACTAAAACTCCAGGTTTGTATACAAGAAGAGTTTTAGATCTAAATAAATAAATCAATTCACACTCTAGATTGCTATGGATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000016341:ENSGALT00000026359:63
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:
PF0008415=Sushi=WD(100=91.8)
A:
NA
C2:
NO
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:
CATGCAGGCAGCCAGAGAC
R:
CATCCATAGCAATCTAGAGTGTGA
Band lengths:
287-1915
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]