BtaINT0119915 @ 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
chr6:103492275-103493889:+
Coord C1 exon
chr6:103492275-103492406
Coord A exon
chr6:103492407-103493425
Coord C2 exon
chr6:103493426-103493889
Length
1019 bp
Sequences
Splice sites
5' ss Seq
AAGGTAACA
5' ss Score
8.92
3' ss Seq
GGCTGATTTTGACTTTGCAGTGC
3' ss Score
6
Exon sequences
Seq C1 exon
GAGACCGTTTGATATCTGTGAATAGTGTCAGTCTGGAGGGGGTCAGCCACCATGCCGCAGTTGAAATTTTGCAAAATGCACCTGAAGATGTGACCCTGGTTATCTCTCAGCCAAAAGAAAAGCTATCCAAAG
Seq A exon
GTAACACTGTGGACGTCTCTGAGCTGTGGATTCTGTTCCAGTTCCCACAAAAATTTCATTACCTTGACACATAAATTAGATTTAAACTTTTATTTCCTTTCTGGAAATCTAATATGTGTAGTTCTGATTGCTTTAATTTTATGCATCAGTACAAGTCTTTCATTCATCACTTCCAAGATTTCCTTTCTCATTCCTCTTTACGTGCATAAAAATTATTTGTTGTGCAAAATCAGTATCACTTGAGTAAATTCCAAGTACTTGGTGTGTTCTTTCACATCTTAGGCCAAATTAGAAATAAAATTCTTAATCATTGCCCAATTAATATAGTTATATAACAGTTATCTATGAAGTCCTGTCTTGAACCTGTTTATAAAAGGGAAAGGATGCCAACATACCAGAAATATAAAAGACATATATATATAAAAGACTTATATATGTAAAAGACCATATTTTTGCACCATTTTTCTAGATTCCACATACATGTAGTATCTATAATTCTTTTACACATGTCACCTGTGATTTTCATCTTAGGAAAGCTTTCCTAAGTGGCTTTTAAAAAGAACTAGATATGTAAGGAGGATGGAATTACCTTCTTTGATAATTACTTAGAGTCTAAAACATGCAGTTTGTTAAGACAATATAAAACAAGTATATAAATAACCATTCAACAAAGATCTTTGGAGATTCAAGTTATCTCTGGATAGGGAATTAAGAAAGTCTTCACAGAGGACTTACTTGAAACAGGTCTTGGGGAATGGAAATGAGGAGTTCAGGTGAGGCGGGTACACATTCCCATAGAAGTTGCCCAAAGAATGACCAAAAGAAGAGGCAAAGGAAACAGAAAGCATCTTCAGTGTTTATTGGGACCTTGTCATGGTTCCAAGCCCCGGTCAGGTGTTGTGCACATGTTATCCTGCGTAAAATCCTCGCAGCAGCTACCAGGGAACATTGTGCATGGGTGTGAGCCCAGGCGTGTGTCACTAACCTGTCATCCTCACGGGCTGATTTTGACTTTGCAG
Seq C2 exon
TGCCTTCTACTCCTGTGCACATGGCCAACGGCACGAAAAACTACATGAAAAAGCCTTCCCACCTGCAAGACGGCACTGTAAATTCTTCTGAGGACCACTGCTGGCCACGGGGCACCCCGAGGCACATCTCAGAGAGCTCTTTTGGGCTGTCTGGGGGCCTGCGGGAGGGCAGCCTGAGCTCTCAAGATTCCAGGACTGAGAGTGCCAGCTTGTCACAGAGCCAGGTCAACGGGTTCTTTGCCAGCCATGCAGCTGACCGCAGCTGGCAGGACTCACAGCGTGGCAGCCCTTCCCCATCTGTGATATCCAAAGCCACCGAGAAAAAGTGGACTTCTACTGATAGTAACCGAAGCAAAGCTAAAAATACAGGCATTTCTGATGCACCAGATTACTCTGACCGTGGAGATTCAGACATGGATGAAGCCACTTATTCCAGCAGTCAGGATCATCACATACCAAAAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000014947:ENSBTAT00000055276:22
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.222 A=NA C2=0.987
Domain overlap (PFAM):
C1:
PF0059519=PDZ=PD(41.7=77.8)
A:
NA
C2:
NO
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:
ACCTGAAGATGTGACCCTGGT
R:
TATCACAGATGGGGAAGGGCT
Band lengths:
358-1377
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]