BtaINT0128973 @ bosTau6
Intron Retention
Gene
ENSBTAG00000005844 | SCAMP2
Description
Bos taurus secretory carrier membrane protein 2 (SCAMP2), mRNA. [Source:RefSeq mRNA;Acc:NM_001102170]
Coordinates
chr21:34221828-34222763:+
Coord C1 exon
chr21:34221828-34221956
Coord A exon
chr21:34221957-34222603
Coord C2 exon
chr21:34222604-34222763
Length
647 bp
Sequences
Splice sites
5' ss Seq
TGTGTGAGT
5' ss Score
5.84
3' ss Seq
CCCCACCTCCCCTTCCCCAGTGC
3' ss Score
8.29
Exon sequences
Seq C1 exon
TGAGAGAGAACAACTGGCCGCCCCTGCCCGTGTGGTGCCCTGTCAAGCCCTGCTTCTATCAGGACTTCTCCACAGAGATCCCTGCCGACTACCAGCGGATATGCAAGATGCTCTACTATCTCTGGATGT
Seq A exon
GTGAGTCTTGCTCTGCCCCTTCAAGCTCAGGGTGAAGTGGGCTGTGACTCGAGCGTGCTGGCTATGCTCTGGTTGCTCCTCTTGGCAGGCTGCAGCCTCTCTCTGGGCTGGGCTGAGGGGTGTCTCTGCCCACATAACTGGCTCCCCACAGTCTGCTGCCTGTCCTGGGAACCTCCCCACAAGGGCCTGTCCAGACCCCATATCAGGTAGGGTGGGACTAGCCGGAGGCTTCAGAGTTCCTACAGAGCTCTCTGCACTGAACAGCCCTCCTTAGGGGAAGGCCTCTCCTCCCCATGGTCCTCTCGGTTCCTAGGAATGAGGAGCAAGGAGAGAAGACTTCTTGTAGCTCCACTGGGGGCTGTCCACAACCAGGGGAAAGCCTGCTGAAAGACTTCATTCCCCAAAGCTCAGCCCTTGTATCTGTATCCGCCCCTCCACTGCCACTCCTCAGATACCTGAGTTTTAAGATTCCCTGGTTTTAAGGTCTCAGAACACCCTGCCTGTGTATACACCAAGGTCCTCTAGTATTTCTGCAGCTGCTCTCACAGCGTGGACCTCATTTCCTCTTCAGGGGATGGTTTGCCTCAGTGGGGAGGCCTTCGGTCCCCTTGGCACAAGCCTCTCTCTCCCCACCTCCCCTTCCCCAG
Seq C2 exon
TGCATTCAGTGACTCTGTTTCTGAACCTGCTTGCCTGCCTGGCCTGGTTCTTAGTCGACACCTCCAGGGGAGTAGACTTCGGCCTCTCCATCCTGTGGTTTGTGATCTTCACCCCCTGTGCCTTCCTTTGTTGGTATCGACCCATCTATAAGGCTTTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000005844:ENSBTAT00000007681:5
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=PU(23.6=95.5)
A:
NA
C2:
PF041448=SCAMP=FE(29.8=100)
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:
GAGAGAGAACAACTGGCCGC
R:
TGAAAGCCTTATAGATGGGTCGA
Band lengths:
287-934
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]