GgaINT0102985 @ galGal3
Intron Retention
Gene
ENSGALG00000016111 | CSMD3
Description
NA
Coordinates
chr2:139052306-139053680:-
Coord C1 exon
chr2:139053600-139053680
Coord A exon
chr2:139052420-139053599
Coord C2 exon
chr2:139052306-139052419
Length
1180 bp
Sequences
Splice sites
5' ss Seq
TAGGTAATG
5' ss Score
7.57
3' ss Seq
GTTTTCTTTTTATCATACAGGAG
3' ss Score
9.57
Exon sequences
Seq C1 exon
CCTATCAGCTTCGAGTTTGCCAGCCTCCAACAAGCATACCAAATGCTGAAATTCTAACTGAAGATGACGAGTTTGAAATAG
Seq A exon
GTAATGTGAAAGAAAATAAAACCAGTATTTGTTTAAAAACAAAACAAAACAACAAAAAATAGTGTTATGAACAGATCTTTACTATAGAATGCCTTAAATATATTTGAGAATTAAAAGTTTAAGAAGTCAGTCCTCTTCCTTATGCCTCCTGAATGGTGTTTCCGAGATCACATATGAGTATCACAGTAACAACCTTCCAAATAACTTTAACAATACCTTTTTCATAATATTAGTAATTATTGTTATTTATTAGAATTTAAATGATTTTTATTCCACTTCAAAAACATACAAGCAAATGAAGAAAAAAAAAAAAAGTTTCTAGACATCTGTACCAGAACTAATGTTCTAGAAGTGAAGGGTAACACCAAATTTGTAAAAACTAGGAATGACATGCTGACTTTTGAGACAGGTTAATAATATTAAATATTATTTTTAGAATGATCAATTACACGATTAGATGTCAGATGTCTCACCACCTAGTTTTGCTCAAATTTCCCCCTTGCCCAACCCGTGGTTTTCTTCTTACGTACTAATATACTGGACCAAAAAAAACTTCCAGGATACACTTTTTTTTTTTTTTTTTTTGTGACTTCATGAAGCTACATGAATCATTTCTTAATCAAGAAAATATAATTTTTTATTCCCACCATCAACTAAGATCCATTTCCTNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCATTTCCTATTTATTTCTTTTCCTTGTGGTTATATGAATTACTGTCTTTATACAATGTTTACCCAGTAAACTCAGGCTAATATTGTTGCACAGCAAGGAACTTCACTAATCAGTAATGTTTTCAAAGCTGAAAGTTTAAAATAATTAATATTTAATGGTATTGTTTTTCTTTGTTTTCTTTTTATCATACAG
Seq C2 exon
GAGACATAATAAGGTACCAGTGTCAACCAGGCTTTACATTGGTTGGTAATGAGATTCTGACATGCCGACTGGGTGAAAGGCTTCAGATGGATGGAGCACCACCTACTTGTCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000016111:ENSGALT00000036594:43
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.036 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0008415=Sushi=PU(36.2=75.0)
A:
NA
C2:
PF0008415=Sushi=PD(62.1=92.3)
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:
ATCAGCTTCGAGTTTGCCAGC
R:
TGACAAGTAGGTGGTGCTCCA
Band lengths:
190-1370
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]