GgaINT0063736 @ galGal3
Intron Retention
Gene
ENSGALG00000004425 | SCAMP3
Description
NA
Coordinates
chrZ:22162083-22164192:-
Coord C1 exon
chrZ:22164033-22164192
Coord A exon
chrZ:22162185-22164032
Coord C2 exon
chrZ:22162083-22162184
Length
1848 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAAA
5' ss Score
8.59
3' ss Seq
CTTTTTTTCCCCTCTTTCAGGAG
3' ss Score
12.74
Exon sequences
Seq C1 exon
TCCATACAGTGACACTGTTTCTTAATATCTTTGGATGTTTGGCCTGGTTTTATGTTGATGCTACACGAGGTGTTGATTTTGGATTGAGTATCCTCTGGTTCTTGCTTTTTACACCTTGTTCTTTTGTCTGCTGGTACAGACCACTTTATGGAGCCTTCAG
Seq A exon
GTAAAAACTTCATCTTGACTTGTAATACATTTCTTAAATATCCTACTTGTTGAAATGCATTAACCTGCTAGAATTTTTGTAATTAGGATGATCCATTAATCTGGTTTCATTAGAAACAAGTAGTATGTTTGCCATTAATTTAACTTCTGTATTTGAAGTATAAACAGCAGTAGTTATGAATATCATGAAACATCCTTTGAAATATTTACTGTTTCTACTTTTGACATAGTAATAACTTATTTCTATTGGGCTGGTAACAATTTTAAGAAAATTCTCATTATATTTCTATCCCTTTGCACCTGAGTATATTTACAGGTAAAGGTTCTTAAATTTTTGGTTTCCTAAGTGAAATTAATGAAACTTGCACTTCTTGTTTTATTGTCTAGTGGCCTGAAATGCCTGAAGTTGCTGTAGACAGAGATTCTTAAGCCTGAGTAAAGCTAGTATTTAATAGTCACGTTTGTGTACTTTTTCCCCAGCTTTAACCCATCTGTATTTGGTATGCTTCACAGTCTTGAAATCTGTCAGTGTTGAAAAACAAAATGGTTGCAAAACTGAACCTTGTTCCAATCAGCATGAGAAAATTTAAAATTTCTGTACTCTTAGAATATTTTTAATTGATTTTTACATTGAACTGGATCAGAATATTGTCAGATTAAATACACTTAATTTTTTTAGAGAAAAATTGCAGAAATTGCAGTCTAGCGTAATCTTTGGGCTACAAGTTTCTGTTACATGTTTCTTTTTGATAACCAAGGAGATGGTGTTGTATCCACGTATCTTTGAAGATTTGTGTAGCTTAAACTACATTTTCTCCTGTCAGCTTGTTTTTCACTAACAAACAGTAATGCCAGAATGCACGATGTAAATAACAGCTGGTTGGGTTTTTTTTTGTTGTTTTTATAGAAACTAGTCTTCTTGCGAGCATTAGAGAAGTGGTAGGTTTTACTGGTTATAAATCTGACATAATGTTGAATTATAAATAATCGTTACTCCTAATTTGCTGGAGGAGTTCAGTGTCACATTCTCCTTTAGGGTTTTAGATCTAGTAAATCTATAGCATTTCTTAGTTTCAACTTTCGTTTTGTGCTGAATAACTAAAGACAGTACTTACTGAACTGAAAGGATTGAATCAATAATAATGAAAAAAATTCCCTCCTCAAGAAGTATTACTACTAGCAAAACCTGATTCCATATTCTTAATTGGTATCTTAACTAAGTGACTTTTACTTTATTTGTAACTTTGGGATCAAGTATATTGATTAGTCACTAGTTTTGTGGTCTTCATTGAGGTTTTACCTGTTCATTTGTATTTGGATTTTTTTGGACAGGCTGTTGACACTTCAGTCCTTGTCAAGCTGGCATTTTAGTAATTTAAACAGATAGCATATTTTGTATGTTTTGCTTTTAAACAACAGATGCTTTGGTACTGTGATCTGCATTATGTTTCCATAATTAAAAATTTGATTTTATTTTCTTTTCAAGTAAAAGATTTTTGTGCAATACTGCCAGTACTGTAAATTTCAGACTTCTGTTCTACATTCACTGTGGCAGAACTTCTCTGTTTAGTCTAAGAGGCCCTGCTTTGTGCTGAACAAAACACAAAGGAGTAGCACCTTGCTGTTATTTTCACCTCTTGAAGAGATGCAAGAGGCAAAGATACTGTATTAGAGAGGAGAATACTTGTAAATAAACACAAATCACAGAATTACCAATACTTGAAGTCATCATCAATAATTCAAAACACTTTTCATCTACTAAATGTGGATTTTTTTTTCATAGTATAGTGGTTTGTCAAAACTCATTTATTTCCTGGCTGCATTACATTCTTTTTTTCCCCTCTTTCAG
Seq C2 exon
GAGTGACAGTTCATTCAGGTTCTTTGTGTTCTTCTTTGTGTATATCTGTCAGTTTGCTGTACATGTACTTCAAGCTGCAGGATTTCAAAGATGGGGAAACTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000004425:ENSGALT00000007047:6
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:
PF041448=SCAMP=FE(40.8=100),PF0309410=Mlo=PD(45.8=40.7)
A:
NA
C2:
PF041448=SCAMP=FE(19.1=100)
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:
ATATCTTTGGATGTTTGGCCTGGT
R:
CAGTTTCCCCATCTTTGAAATCCTG
Band lengths:
238-2086
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]