BtaINT0128980 @ bosTau6
Intron Retention
Gene
ENSBTAG00000012094 | SCAMP3
Description
secretory carrier membrane protein 3 [Source:HGNC Symbol;Acc:HGNC:10565]
Coordinates
chr3:15433537-15434257:+
Coord C1 exon
chr3:15433537-15433657
Coord A exon
chr3:15433658-15434128
Coord C2 exon
chr3:15434129-15434257
Length
471 bp
Sequences
Splice sites
5' ss Seq
CTAGTAAGT
5' ss Score
8.78
3' ss Seq
GCTCTTTTTGTGCCTTACAGCTC
3' ss Score
10.19
Exon sequences
Seq C1 exon
GCTTCAACTGCAGCAGCCACAGCTGAGCTGCTAAAGAAACAGGAGGAGCTCAACCGAAAGGCAGAGGAGTTGGACCGAAGGGAGCGAGAACTCCAGCATGCTGCCCTGGGCAGCACAGCTA
Seq A exon
GTAAGTGGATCCTTGATGGGGTTGCGGAGGGCATCTGACAGCTTTGAAGTCTCAAAAAAGGAGCTCAGAGCATGGGCACTGGAGCCAGATTGCAGAGTTTGAATTTGGGTGCAGTGGCTTATTAAGGATGAGCTCTTAGGCAAGTTACTTAATCTTGAGTGCCTCAGGTTCCTTACTTGTAAAATGAGAATAATGTTTGTACCTGTTTAACAGGATTGTTGTGAGGTTAAAGTTACATAGATAACTATATAGTTATATAGATGCCCAAATCCTGGGCATAGTGGTTAGAAGTTATAAGCCATAGTAAACAAAAGTCATAATAAACACTACTAATATAATTTTTCCTATTTGCTCTTGTCTTCCTGAACTCTCGAATTGGAAATAGAAAATCCAGGGGTAAAAGGAAGGGGGAGTGATTTGTTGGTCTCTGTCTTACTAGTGGGACCCTCCTGCTCTTTTTGTGCCTTACAG
Seq C2 exon
CTCGACAGAACAATTGGCCTCCTCTACCTTCTTTTTGCCCGGTTCAGCCCTGCTTTTTCCAGGACATCTCCATGGAGATCCCCCAAGAATTTCAGAAGACAGTATCCACCATGTACTACCTCTGGATGT
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000012094:ENSBTAT00000046975:4
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.780 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF049918=LicD=FE(35.4=100)
A:
NA
C2:
PF049918=LicD=PD(34.5=88.6),PF041448=SCAMP=PU(23.6=95.5)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal4)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTTCAACTGCAGCAGCCACAG
R:
TCCAGAGGTAGTACATGGTGGA
Band lengths:
246-717
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]