BtaINT0128994 @ bosTau6
Intron Retention
Gene
ENSBTAG00000021318 | SCAMP5
Description
Bos taurus secretory carrier membrane protein 5 (SCAMP5), mRNA. [Source:RefSeq mRNA;Acc:NM_001166565]
Coordinates
chr21:34092170-34093488:-
Coord C1 exon
chr21:34093332-34093488
Coord A exon
chr21:34092272-34093331
Coord C2 exon
chr21:34092170-34092271
Length
1060 bp
Sequences
Splice sites
5' ss Seq
CAAGTAAGT
5' ss Score
10.08
3' ss Seq
AGATGTCTCCTCTGTTGCAGGAC
3' ss Score
8.98
Exon sequences
Seq C1 exon
TGAATAGCGTCACGCTGGCCGTGAACCTGGTGGGCTGTCTCGCGTGGCTGATCGGAGGCGGGGGAGCCACCAACTTTGGCCTCGCCTTTCTCTGGCTCATCCTCTTCACACCCTGCTCCTACGTCTGCTGGTTTCGGCCCATTTACAAGGCCTTCAA
Seq A exon
GTAAGTGACGGGTGCTGAACCCAGCTCCTAACCCTGTATCTTTGTCCATCTCCCCTGTCTCTTCTCTACATATTTTTCTCTTTTTTTTTTTTTTGCTGTCCCCCAAGCTCACTTTCCCTTTATCCTCAGCTCAGACTGCCAGGTAGGATTTAGGCTTCCTGGGAACTCTAGGCTGGAGTGAGAGGGCTGGGAGTCAGAGCCTTCCTCTTAGGTCCTTCCTTCTTCACTCTACCCTTGGGTGGGACAACATAGAGACCAGACTTATTCTTGTTTTCCCTTCCCCAGGCAACTAGCTGCATGACAAATTTTGCCAGTGGGGCTATCTGTCTTGGTTTAGCTGCCCATGCCGGTACCCATGGGGCTGGCTAATTTGGTGCCAACTAGACCATCTACCCACATGCCAGTGGGACAAGCCATCCATGTGCCACTGACACTGTTTTTGTGCTAACGAGGGCATCCAACTCTGTGCCAAAGGGACTACCCATCCATGTATCAGTAGGGCTAACTCTCTTAGTGCCAGTGGGTGTCTGCCTTGTGTCAAGTGGGATTTTCAATCTTTGTGCCAATGGATTATCCCTCTCAGTGCCAATTGGGCCTCTAATATTAATGTTTGCCAATTGGATCCATCCGTTTATGTGCCAGTTAGGTTATAATCTTGGTGCCAGTCATGTGTCCATTATTGTGCCAACAGCACTTTCTATCTTGTGGGGCCCTCCCCTCATGTACCCCTGGAGCTTGATGTCTTGGAGCCAGTAGGGTTGTCCAACCCTTTGACATGGGCTGTTTATTCCTGCCACAACAGACCCATCTATTTCTGTGCCAGCCATCCATGTACCAGTGAGTGGTCCATTCATGAGGCGATCTCTCCCTGTGCAGTGTGGTACACACAGGTCCAACACATGGAAACTTACAAAGATCCATGGGTGAATGGCGTCCCATTTTGACCCCTTAACTAAGATCCACTGAGTACTCACCTACACTTGGAAGGACTTGGAAGTCTCGAAGGCAGGGAAGCCGTGTCCCTCCACCCAGGTGACAGGAGATGTCTCCTCTGTTGCAG
Seq C2 exon
GACCGACAGCTCCTTTAGCTTCATGGCATTCTTCTTCACCTTCATGGCCCAGCTGGTCATTAGCATCATCCAGGCCGTGGGCATCCCAGGCTGGGGTGTCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000021318:ENSBTAT00000065890:4
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(29.4=100)
A:
NA
C2:
PF041448=SCAMP=FE(19.2=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTGGCCGTGAACCTGGTG
R:
CACGGCCTGGATGATGCTAAT
Band lengths:
222-1282
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]