DreINT0156940 @ danRer10
Intron Retention
Gene
ENSDARG00000005318 | stam2
Description
signal transducing adaptor molecule (SH3 domain and ITAM motif) 2 [Source:ZFIN;Acc:ZDB-GENE-041114-64]
Coordinates
chr9:38247258-38248898:+
Coord C1 exon
chr9:38247258-38247450
Coord A exon
chr9:38247451-38248803
Coord C2 exon
chr9:38248804-38248898
Length
1353 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAAC
5' ss Score
7.82
3' ss Seq
ATTTGGCTGTTATCCAACAGTGA
3' ss Score
6.08
Exon sequences
Seq C1 exon
CCATTGAGCTGTCCTTACAGGAACAGAAACAGCAGACAGAGACACGACCCCTCACAGTGATTGCCGATCCACCCTACAACACCAATGGAGGGAAAGAGTCACGTAAAGTACGCGCGCTCTACGATTTTGAGGCGGCTGAAGACAATGAGCTCACTTTTAAGGCTGGAGAGCTCGTGATCATCCTAGACGACAG
Seq A exon
GTAAACTGATTGTTTACGGAACATTATTTTATTACGTCGATGGCAACCGGAAGTTGCTGAGATTTTAATTTCAGTATATTGATGTACTTTTAACTGAAATGGAGTATTAAGTAGGGGGCGGGGCTTTCTTTTTGTGCATCATTCCTTTATCCGCTTGTTAAGTGTGACGTCACGCGAAGCGGCTTCCCGGTCCAAGCGCTCTATTCAACTGAATGGGGAGACTCATGAAATGGTAATAATAAACGTTTACAAAGCGATTTAATGCTTTCGAAAATCACGATGGCAGTATATATGTCCATGCCTAATATCCGATGGCCAGAAAGTGATTGTTTTTTATAAATTGTAAAATATTTGGTATTTGTTATGCAGCAAGCCCAGAGATTGTTGTGCACACTATGATTTTATGTAAAATTAACTTTAATGTGTGATAGGAATAAAACGTGATCATAAACGAATGATTTCTCCACTCAAATGAATGGCAGCTTGGACCCGGAAACAGTTTTACATACATCACAAACACGTCACCACTTAACAAGCGAATAGCAAACCAACGGGAAAAGGGGCGTGGTTAAGAATATTGTGGTTGAAGCTATTGACCTTATTCTAAATTGCGGAAGTGCGCCTGTTTTTGCGATTGTTTTAGAACTTCTGATTCAGTCGCCTATGGGAGAAATGACTAGGAATAATAAACGGCAGAAAACGGTCAAACTACTTGCTCTACAAACAAATGTTTGCATGACTGTACAGACCAAGTAGAATAATGTAATAAGAAAATGTCAGTTTGCAACATCAAACAGTGAAACGAGCAGTTTTTAATGTCTAAAAATGAATGGAAGTGAATGAGACCGGAAGTCTCGAGCCAAAAAGATTAAAATGGCTGCTCACGCTCGTCGGCAAAGAATAAGGTGAATAAAACTGATGTCAACAGAGAAGGATCACTACTCCTAACATGGAGAAAATTGGTCAGATTTGATTGAAGATTACCCAAACAATGTTATTTGAGTGGATTAACTTGCACAAATGAATTGTTCCCCCAAAGAATAAAAATGTGCACTAGCAAAATAAACATTGCATATTTGGATTCTACACAGACTTTAGCTAATTTTAAATAAATAAATATCAAAAAATCAACCTTTTTCTTTTTTATCTTATTAAATAATAATAAAAAACATTTCAAATCCATTCATTAAAATCTTGCATCTAAAATCTCATAAAATGAGGGTTTAAAGAAAGTTTTAATAAATTAACAAATTAAATACAAATATTTAAAATATTGTTTATGCTGTTTTCAAATATCCCATAACCTAAATTAAATGTTCATTATTCAACAATAATTTGGCTGTTATCCAACAG
Seq C2 exon
TGATCCAAATTGGTGGAAAGGCGAGAACCATAGAGGAGTAGGTCTCTTCCCATCAAACTTTGTCACCACCAACCTGAATGCTGAACCAGATCCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000005318:ENSDART00000022574:7
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.538 A=NA C2=0.333
Domain overlap (PFAM):
C1:
PF0280915=UIM=PD(44.4=12.3),PF0001823=SH3_1=PU(58.7=41.5)
A:
NA
C2:
PF0001823=SH3_1=PD(39.1=54.5)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ACAGGAACAGAAACAGCAGACA
R:
GGATCTGGTTCAGCATTCAGGT
Band lengths:
270-1623
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]