BtaINT0128975 @ bosTau6
Intron Retention
Gene
ENSBTAG00000005844 | SCAMP2
Description
Bos taurus secretory carrier membrane protein 2 (SCAMP2), mRNA. [Source:RefSeq mRNA;Acc:NM_001102170]
Coordinates
chr21:34223915-34229099:+
Coord C1 exon
chr21:34223915-34224016
Coord A exon
chr21:34224017-34228981
Coord C2 exon
chr21:34228982-34229099
Length
4965 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGA
5' ss Score
9.22
3' ss Seq
GGCCTCCTCCGCCTTTGCAGTGG
3' ss Score
7.14
Exon sequences
Seq C1 exon
GTCTGACAACTCTTTCAGCTTCTTCGTGTTCTTCTTTGTATTTTTCTGTCAAATAGGGATCTACATCATCCAGTTGATCGGCATCCCTAGCCTTGGGGACAG
Seq A exon
GTGAGACGTGGGGCAGCACAGAGGGGACTAGGCCCTGTTCCCCTGCTCCCAGAAAGACCCCACCGATGACCCGTCTTCCACCATGGCTGGGAGAGGGGTGATGGGTCAGCGGGGGTCTGCCTTCTTCCGCTTCTTCCCCGGTAGCCACTCACTGTTTCGCCTTGCTCACCCCTTTCCAGAGTGCTGTGGGTGGAGTTGGCCTGAATCCTTAGGCTCTCAGGGCTGTGTCCTGCACTGCAGGGCGCCCTTGTCCTTTTCTCCTGCCGGGCCCTCCTAGAGCCTGCGGCTGCTCCCACAGGCCCCGGACGAGCCCCAAGGCTTGGGCGGCTGCCGATGGATGTCTTGGCCTTTACAAACTGTGAGCTGTGACTTTTTCTGGAGGCCCTGTAACCTCAGGAGGTGGAGCCCTCACCCCTGGAGGATCTGCTCCTTCAGGCTGCTCTCCTTGAGCATCCAGTTGGCTTGAGAGTCCCGGCTGCTGCAATTCTCAGCTCAGAATTAGTCTCAAAGAGCAAAGCTGATGGCTGATGTTTTCCTTTCTGCTCCAGTGCACAGGGAACATTACAGAAAGGTCAGGCTGGCACTTGGCTGAAAGCCTGAGCCTGGAAGGGCTGCACTATTTTGGTCCCCGCCCTCCAGTGGAGCTGGCAAGTCCAGAGTGGCGAGGAGGGGTGACTCACCTCACACTCAGTGCATGCTGCCTTCCTCCTCTCCTCTGCCTTCTTGCCTTGCTATTTCTAACCTGGCCCCTTTTCTGTTTGACTGGTGACCCAGTTTCATTACTCATTACCCTCAGTGAGATCCTGGTAGAAGACTGTGATTAACAATTGCTGTTTACACCCTGGACTGGGAGCCAGAAGGCTTGAGTTCTGGTCCTGCTCCGCCCCTCACTGCCCTGCCTGGGTCTGCCTGGTTGAGCTCCGAGGCCTCCAGCCTCCCGGTGACTTTCTCATCTCACCTCAGAACACCCACGATTGGGTGGAAGTCCTCCCGCCTCCCTTTTTTGTTACTGATTATAAAATACACATAACATAAAATCTGTCATTTTGTTTACCACTTAAACCACTTTGTATAATTGAGTGGCATTTAGTTCATTCACAGTGTCTTGCAGACATCAGCACTGTCTAATTCTGTATCACACTGTGACATTTGTATCACATTGTAAGGAAACTCCATGCCCATTAAGCAGTCACTCTTCATTCCCTCATTCACTGAGCCCATAGCAACCATTAAACTGTTTATGCATCTCTGGATTTGCCTATTCTGGACATTTCATTTTAATGAAATCATATGTGGCTTTAAACAAAAAAATTTATTTATTTATTTATTTTTGACTGTGCTGGGTCTTCATTGCTGCATGGGCTTTTCTCTAGTTGCAGCGTGTGTGGGCTTCTCGTTGCAGTGGCTTCTCTTGCTGCAGAGCATGGGCTAGACACACAGGCTTCAGTAGATGTGGCACCTGGACTCTAGAACACAGGCTCAGTAGTTGTGGCGCACACGGGCTTAGTTGCTCCTTAGCGTATGGAATCTTCTTGGACCAGGGATTGAACCTGCGTCCCCTGCATTGGCAGGCAGATTCTTTACCACTGAGCCTAACATTTGGCTTTTGGTGCCTGGCTTCTTTCAGATCAGATCAGTCTCTCAGTCGTGTCCGACTCTTTGCCACCCCATGAATCACAGCACGCCAGGCCTCCCTGTCCATCACCAACTCCCGGAGTTCACTCAGACTCACGTCCATAGAGTCAGCGATGCCATCCAGCCATCTCATCCTCTGTCGTCCCCTTCTCCTCCTGCCCCCAATCCCTCCCAGCATCAGAGTCTTTTCCAATGAGTCAACTCTTCACATGAGGTGGCCAAAGTACTGAAGTTTCAGCTTTAGCATCAGTCCTTCCAAAGAAATCCCAGGGCTGATCTCCTTCAGAATGGACTGGTTGGATCTCCTTGCAGTCCAAGGGACTCTCAAGAGTCTTCTCCAACACCACAGTTCAAAAGCATCAATTCTTTGGCACTCAGCCTTCTTCACAGTCCAACTCTCACATCCATACATGACCACAGGAAAAACCATAGCCTTGACTAGACGGACCTTTGTTGGCAAAGTAATGTCTCTGCTTTTGAATATGCTATCTAGGTTGGTCATAACTTTCCTTCCAAGGAGTAAGCGTCTTTTAATTTCATGGCTGCAGTCCCCATCTGTAGTGATTTTGGAGCCCAGAAAAATAAAGTCTGACGCTGTCTCCACTGTTTCCCCATCTGTTTCCCATAAAGTGGTGGGAGCGGATGCTATGATCTTTGTTTTCTGAATGTTGAGCTTTAAGCCAACTTTTTCACTCTCCACTTTAACTTTCATCAAGAGGCTTTTGAGTTCCTCTTTACTTTCTGCCATAAGGGTGGTGTCATCTGCATATCTGAGGTTATTGATATTTCTCCCGGCAATCTTGATTCCAGCTTGTGTTTCTTCCAATCCAGCGTTTCTCATGATGTACTCTGCATAGAAGTTAAATAAACAGGGTGACAATATACAGCCTTGACGAACTCCTTTTCCTATTTGGAACCAGTCTGTTGTTCCATGTCCAGTTCTAAGTGTTGCTTCCTGACCTGCATACACATTTCTCAAGAGGCAGATCAGGTGGTCTGGTATTCCCATCTCTTTCAGAATTTTCCACAGTTTCTTGTGATCCACACAGTCAAAGGCTTTGGCATAGTCAATAAAGCAGAAATAGATGTTTTTCTGGAACTCTCTTGCTTTTTCGATGATCCAGCAGATGTTGGCAATTTGATCTCTGGTTCCTCTGCCTTTTCTAAAACCAGCTTGAACATCAGGAAGTTCACGGTTCACGTATTGCTGAAGCCTGGCTTGGAGAATTTTGAGCATTACTTTACTAGCGTGTGAGATGAGTGCAATTGTGAGGTAGTTTGAGCATTCTTTGTCATTGCCTTTCTTTGGGATTGGAATGAAAACTGACCTTTTCCAGTTGTGTGGCCACTGCTGAGTTTTCCAAATTTGCTGGCATATTGAGTGCAGCACTTTCACAGCATCATCTTTCAGGATTTGAAATAGTTCAACTGGAATTCCATCACCTCCACTAGCTTTGTTCATAGTGATGCTTTCTAAGGCCCACTTGACTTCACATTCTTTCACATAGCATATTTTCAAGGTTCATGTTAGTACTTCATTACATTTTATGACTAAATAATATTCCATAGTTCTTGGAGATACTGCATGTTGTTTATCCACTCATCAGCTGATAGACATTTGGGTTTCCACCTTTTTGCTGTTGTGGATAGTGCTGCTGTGAACATTTGTGTATAGGTTTTTGAGTACCTGCTTTCAGTTCTTTAGGGTATGTATCCGAGGGTGGAATTGCTGGGTTGTATGGTGATTCTATGTATAATTTATTAAGGAACTGCCACACTGTCCTGCAGTGGCTGAACCATTGTATTTCTTTCTTTTTGGCTGTGCTGGGTCTTTGTTGCTGCAGGCATTCTCTAGTTGGGCCTGTTGGGGCTGCTCTCTAGTTATGGTGTGTGGACGTCTCATTGCAGTGGCTGTTTGTTGTGCAGCCTGGGCTCTAGGGCGCTCGGGCTTCAGTAGTTGTGGCGCATAGGCTTTGTTACCCCACAGCATGTGAAATCTTCCTGGACCAGGGATTGAACCTGTGTCCTCTGGGTTGGCAGGTGGATTCTTAACCACTGGACCACCAGGGAAGTGCAGGCCAAACTATTTTACATTCTCAATAGCAGTGTATGAGGATTCCAGTTCCTCCATATCCTCCCTAACACTTACTATTTTCCTTTCTTGTTTTTTTCCTTTTTTCTTTTATAGCCAATCTAGAAGTGTGGTAACTCGTGATTTTGATTGCTCTTTCCTGAACGATTATGATGTTGGCCATCTTTTATGTGCTTGCATATTTTCTTTGGAGAAATGTCTATTCAAATTGTTTTCTAATTTAGTATTTGGATTGTCTGTTGAATTCTTCATATATTCAGGATGCTGCATAGCTACTTGTCAGGTATATAATGTATAAAGTTTCTCCTTTCTGTGTGTTGTTTCTCACTTCTGATAATATCATTTGATGAACAAAGGTTCTTAATTGTAATGAGATCTAATAGTTTTCGTTCTTATTGTTAGGTTTGAGTTAGCTTTTCTATATGGTGGAAATAGGGTGCACCTTCATTGTGTTTTTTTTTTTCCTTTTAATTTTTTTAATGTAATTTTAATTGGAGGATAATTGCTTTACACTATTGTGTTGGTCACCTTCATTATTTTGTATGTGGATATCTAGCTGTCCTGCACCATTTGTTGAAGAGGCCATTCTTCAACATTCAGTGGTTTTGGCACACTTGTCTAAAATCAGTTGATGATAAATATATAGATTTGTTTCTGGACTCTCAGTTCTATTCCATTGATCTATAATATATGTCTATCCTGATGCCAGTACCATACTGTTTCGATAGCTATAGCTTTGTATTAATTTTTAAAATCAAAATGTGAGGCTGTCCCCTTGGTAGATGAGAACACTGGCTCAGGAAGGAGAGGTGACTGGCTGGAGGCAGCAGGGCTGTTCCTGGGCTGCAGGGTGGGGAGCTGAGGTGAGAGGATGAATGAAGTGGGTTGGCTAATGATCCTCCTTCCCAGAGGGACGGCCCTCTGCAGTGAGCAGCCCTAGGCTTTCCATGTCCCCTAAAGGGCTCTACCCACCGTCACTCTTAACAGTGAAAGCAGCAGCCACATCCTCCCTTCCAGGCCTCACATGGCCCATAGATTCCCTATGGGCATTATGGGGCCTGGTGGCCTTTACAGAGGCCTGGCCTCAGAGGCCAGGCTTTTGGCCCATAGGGCTCTGTGCTGCCCAGAGATGCCCGGGTGGTGTTCAGCACACAGTGGCCATTTGGAGAAGAGCCCCTCACAGGGAGCTCTGGGGCCCAATCCCACTGTGCTCTCCCCGGCCTCCTCCGCCTTTGCAG
Seq C2 exon
TGGTTGGATTGCAGCCCTGTCTACGATGAAGCACAACTTGGCTGTGTCGGTCATCATGATGGTGGTGGCTGGCTTCTTCACCCTCTGTGCCGTGCTCTCACTCTTCCTCCTGAAGCGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000005844:ENSBTAT00000007681:7
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(19.1=100)
A:
NA
C2:
PF041448=SCAMP=FE(21.9=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:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]