GgaINT0078173 @ galGal4
Intron Retention
Gene
ENSGALG00000016341 | CSMD1
Description
CUB and Sushi multiple domains 1 [Source:HGNC Symbol;Acc:HGNC:14026]
Coordinates
chr3:89749060-89750408:+
Coord C1 exon
chr3:89749060-89749171
Coord A exon
chr3:89749172-89750228
Coord C2 exon
chr3:89750229-89750408
Length
1057 bp
Sequences
Splice sites
5' ss Seq
TTCGTAAGT
5' ss Score
9.77
3' ss Seq
CTCTTACAAACCCTTTGCAGCTC
3' ss Score
7.67
Exon sequences
Seq C1 exon
GTTGGAAGTACAGTCTTTTTCAGATGCAGAAAAGGTTATCATATTCAGGGATCTACAACCCGTTCTTGTCTTGCTAACTTAACTTGGAGTGGCATACAGTCTGAATGTATTC
Seq A exon
GTAAGTGCAGTTTCTTATCTAATGACTTTGTACACTGTGCAATTTTGAAAGAGTTACAGATTAATGCATGTGGAAATCATATTAAATAGCATGCTACAGAAAAATCAATTTTATTTAACAGTATTCTGTATGCTTTTCTTGTTGTTGTTTTGCTTTTGCTTTCTGTTCTAAGAACAAACATGTATGTAGGATATTACTTTTAAGTAAGATTTTTCAGATATTGTTTTCTTCTTGAATACACAATGCACAATAATTTACTCCTTAAAAAAATGTTTTTCCTCATTGACTTACTGCATTAAATGTTTTAGGTTAATCTTTTATCTTTGTGTGCGTCTGTGTATTGGATTAACAGAAAGAAAGAAAGTAGCCTGAAATTAGTTCTGGACTTTTTGTTTTGCTAGATTTCCTGAAGCATAAGTTAGAAATTTACTAAAATTCAACTTTTCTGGGCTACGCTTGTAAACAATTAGTGTCATTATAGCTTTACCTCTAATAAGTATTATCATTATAATAATGTGGATATCTAATAAGTATTGTATTAAAATATGGTGATCAAAGCTAAAAGATATTCCTTAGAATGACCTTATATTCTTATACCATTTCAGATTAACTATGGATATTTATAAATCAATATCATGTACAACAGACAAAGAAGCATAAAGCCTTCATATGGAAACTTTTGTTTGTTTGAAATTTATAATAAATTTATTTATCACAGTAACCACTCTGTATTAAGGTTCTTTACAATGGAAGTGATACCTAAAGCTGTGACAGTACAGTATTCAAAGGATATGAATTTACTTGTCCTTCCTCTCACTTCAATTATTTCCAGTCTTGCTATCATGAGCATATTGCTCAAAAATATCATTTTCATCTTCCTTCAAGCCATACATTCAGACTATTCCTGTTAGAAATACAAGCTATTGATGTTGCTAAAAGTGTACAAAGTTTACTTAATGACAGGGAATATGTTGGCATGCATTTGTTTTCAGTTAAGTAAGCTAATCCTGTGGATGCTTTTTGGTATCATTTTCTAACTCTTACAAACCCTTTGCAG
Seq C2 exon
CTCATGCATGCAGGCAGCCAGAGACACCAGCACATGTAGATGTGAAAGCAATAGATCTTCCTACTTTAGGGTATACTTTGGTGTATACCTGTCAGCCAGGATTTTTTCTTGCTGGTGGATCAGAGCATCGAACATGTAAGCCGGATATGAAATGGACAGGAAAATCACCTATTTGTAAAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000016341:ENSGALT00000026359:62
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=PD(63.6=92.1)
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:
TGGAAGTACAGTCTTTTTCAGATGCA
R:
ACAAATAGGTGATTTTCCTGTCCA
Band lengths:
286-1343
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]