GgaINT0046558 @ galGal3
Intron Retention
Gene
ENSGALG00000012513 | STAM2
Description
NA
Coordinates
chr7:37039090-37040935:-
Coord C1 exon
chr7:37040789-37040935
Coord A exon
chr7:37039160-37040788
Coord C2 exon
chr7:37039090-37039159
Length
1629 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAAA
5' ss Score
5.07
3' ss Seq
TATTGTTAATACATTTGCAGGCT
3' ss Score
5.62
Exon sequences
Seq C1 exon
GCTCATCCAAAAGTAAGTGAGAAGCTGAAAACTCTAATGGTGGAGTGGTCAGAAGAATTTCAGAAAGACCCACAATGTAGCTTAATATCTGCAACTATTAAATCTTTAAAAGAAGAAGGTGTCACTTTTCCTGCTGCTGGATCACAG
Seq A exon
GTGAAAGCTCAATTAGGAATACACAGTACCTCTCCTGTTAGACTTCTGTCAGTGAACGGCAGGAAAAAGCCGTGCACAGATCTTTTGATCAGAGGGAAGTAGGACCCTTGTTATAGTTTGGTTGCCTCCTGACACCGAGGTTCATTTCATTCTGCTTTTTAATTTCCTTGCCCACTGAGGAAAAGTGAGAACAGACTAAAGGTTATTTCTTACTGTCTTTGAGTTGTTTCATTTTAGATCTGTCTTTCCTTCAGATCATTTTTTTAGAGTTTCATCAACCTGTCATACCTTAAAAACCTAAGCAATCCTACACCCACGCCTTGTACTTGGTGTTTCATGGTTTTAATTGCTGACTTGGAGCACGTTTCTTCGTTATTTTTCCCTTCCAGAGCCTCACAAAACAATTGGCAGTATCTGAAACTGAGACATTTTTTGAAAATGATGTGCTATGCTTTCCTTTTCTAAGTCCCCTTTTCTTGTTCATGTTTTTTTGTCCATGTCAAGAGCTGTCCATCTCTGCAATGCTGCGGTGATGGATGCTCCAGTCCCTAACCTCACTTGCTCTTTTTATTTTACTTGTGGTGGTATTCTATGCCTGATCATCTAGCTGGTAGATATGGTGACAAGTTTTTTTTTAATGCTTTATTATTTATGCTTCTAAATATTCTTATGTTCAAAATGAGTTAGGTGAAGAACAGTCCTTAAACTTAGAAACATATTTTCTGTTATGTATCCCTTCCATGAAGTTCACTTTTCTCTGTATTAAACACAGGTGGTGGGTTTTTGTGTGTATTTTTTTTAAGTTCTACAGTCTTTCCTTCCTCCACCAAGATGTTTTCACCTCTAAATCTAGGATAAGTGTTAAAACATATGGCAGAAACATGGAAGATGGAGAGTGCTGGCAACCAGTTATGCTTTCTTCCTACAGATGCATATAAAAATGACATCTTGATGTCTCTGCATCATACGCTTCACTGCAAAAAAACAAAGCTGAAGTTTATTAGTATACTTGCACAGAATTGTTTCCTAGAACCATTGATAATTCCAGTATCTGAAACTGGTTTGTTTGTTCCTACAAGAAGACTTCCCTGTTGAAGTGAAGGTTTTCATTATGCTCTTGGGGAGACTCAAATTATTCAAATCAGAAGCTCCCAACTTGATATACCAAAAAACAGAGGAGGAGGGTAGCTATTAGCTGTCATGTGGAGAGAAATCTCCTTTTAGCAAGTCCAACTCCCAGTTAATAACTTCACAAACGTAGGACTCCAAAGAGCTTTTCTTCCCTTTTGAGAGGTGAGGTGGAGGACAAAGGTGGGAAGAGTAGTCTTTTAAATGCGAGTTGTTTCATCTAAGTAATGCTACTAGCATCATGATTTAAATGAAATCCTTAAATAAATGAGATCTGATTATTTATTTTACTTTGTTCCTTTCTGAAAACTAAATGTGGATGAGATTCCAGAGTGAAGTAATTTTTCTTTTCTAAAAGATCATCCTGGGCCAGTTCTGAAATGCTCAAAATAGGCAGCTAGCAGGGAACAGCTTCTTATTAATTTTTTTAAAGTATGTAATTATAGAGCTTTCTTCTTCCTTTGTTAGCATGAAGTTATTCTATTGTTAATACATTTGCAG
Seq C2 exon
GCTACCACAAATGCTGCTAAGAATGGTTCTTCATTAAGCAAAAACAAAGAGGATGAAGATATAGCTAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000012513:ENSGALT00000020440:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.082 A=NA C2=0.667
Domain overlap (PFAM):
C1:
PF0079014=VHS=PD(28.9=79.6)
A:
NA
C2:
PF0280915=UIM=PU(50.0=37.5)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Cow
(bosTau6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCTCATCCAAAAGTAAGTGAGAAGC
R:
TCTTCATCCTCTTTGTTTTTGCTT
Band lengths:
206-1835
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]