BtaINT0119920 @ bosTau6
Intron Retention
Gene
ENSBTAG00000014947 | PTPN13
Description
Bos taurus protein tyrosine phosphatase, non-receptor type 13 (APO-1/CD95 (Fas)-associated phosphatase) (PTPN13), mRNA. [Source:RefSeq mRNA;Acc:NM_174590]
Coordinates
chr6:103498256-103500014:+
Coord C1 exon
chr6:103498256-103498409
Coord A exon
chr6:103498410-103499799
Coord C2 exon
chr6:103499800-103500014
Length
1390 bp
Sequences
Splice sites
5' ss Seq
AAGGTCAGA
5' ss Score
6.8
3' ss Seq
TTTGATACCTTTTTTTCCAGAGA
3' ss Score
6.96
Exon sequences
Seq C1 exon
GTGGTTCATCTGTTGTTAGAAAAAGGACAGTCTCCAGCATCCAAAGAACATGTCCTCCAGTGTACGGTCTCTGATCCAGACACCCAAGGTCAAGCCCCAGAAAAAATGATGACGAAAATGACTCATGTCAAAGACTACAGCTTTGTTACCGAAG
Seq A exon
GTCAGACCTTGGGAGGCTGTCATCTCACCTTAAACTTATTCCTGGATTATTCAAAATTTGATTTTTACATGTCGGATCATAATTCATCCTGAGTCTCTTGATTCTTGTCAAGTATAAATAAGAACCTGATGCAGCACTGTACTGAATTTGGGGAGGGCGGGGGGAACCACGCGTAGTTGTAGTTCTTGAAGTCTGAAAGGCTTTGACTAATGAAATCAGGCACAAAACAAATTATGGTCATTTAATGGTGCCTAAAATAGTTGTAAAATTCAAACTAAAATTTGTAAGAGAAAAAAATAAATATAAATAACTGCTGAGAATGACTTCAAACCCATATGAAACCTTGACTCTTACGTTTTCTATATATCTGTTTGATTTTACGAACTTGTGAAGCTAACTCTGATAGAAATTCACTAACAGTTCCCAGATACTTGTTTTCCTTACAAACGTTTCCAGCTAACTGGTAGTAAAATTGGACATGCCACTAACTCGCAATGAAAAAAGGAAATCAAGACTAATGTAGTGAGTTTTTCATAAGGTTAAATGTAGTCATAATACAGAAGTACTCTTCATTCTGAGTTTATCTGTCTTCCTTTTGATGGGTATAAATGTCCTTTACTTTATAAATGGTGGTGGTGGTACATAAGCATTGTTTTGTCTTTATTTTAGATTTTTCTTTGCTTATACAACTTTCATCAATTCTGAATTAGTCCCCAAAATAAGGAGAAAATATTAGCCCAACCTATATCATCTTTCCTGATTATGAAAATAAGATTAGCATGTCCACTTAATCCTACTGTCTTCTGTTCTTCCATTATTTCTTCTGTTACTATGTCTTTAAATATATTTCTTCATGCTTTCCTGATTATTATTCTTTTAATTTCTTCTGTTGATGAGAATTTTATCATCATGCGTTACAGTTTTACTGAATTAAATTATATCTCACCTAAATATTAAGTCACCTATCCACTTCCCCATAACCCTTCTCTGTTATTTGTTTTGTTCTTCTTACCATATCTGTCCCATTTATGTCTGAATTTCTTTCACTGTCTCCTTTCTTGGATTTTTCCCTCTTTTTCTCTGTCATTCTGCAGTTTATAAAACATGGAATTAAGACATAGTTTCCTTTTTAGAATCTTTTTTTCAGAACCCACTTTTCTGATCAGGCAGCCTATTAGTTCATGCAGCTCAGTTCAAGAAGTTAAATTTTCTTAATAACAGATTGTAAAGTGGGATTTGAGTATAGAATAAGCGTGCAATAAGTGCATATAAAGCTGTGAGCATGGTGGAAATGGGCTTTTTAATAATGTATTCAAAACTGTATATGTTTATACATGCATAGAGAGAGCCTGTTAAGAATATTCACATTTTTTGATACCTTTTTTTCCAG
Seq C2 exon
AGAATACATTTGAGGTGAAATTGCTGAAAAATAGCTCAGGCCTAGGATTCAGTTTTTCTCGAGAGGATAATGTTATACCCGAGCAAATGAACACCAGCATAGTAAGGGTTAAAAAGCTCTTTCCTGGACAGCCGGCTGCAGAAAGTGGACAAATTGATGTGGGAGATGTTATCTTAAAAGTGAATGGAGCCTCTTTGAAAGGATTGTCTCAACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000014947:ENSBTAT00000055276:27
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.558 A=NA C2=0.194
Domain overlap (PFAM):
C1:
PF0059519=PDZ=PD(7.2=11.5)
A:
NA
C2:
PF0059519=PDZ=PU(77.9=93.1)
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:
AGGACAGTCTCCAGCATCCAA
R:
TGAGACAATCCTTTCAAAGAGGCT
Band lengths:
342-1732
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]