BtaINT0119916 @ 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
chr6:103493426-103495086:+
Coord C1 exon
chr6:103493426-103493889
Coord A exon
chr6:103493890-103494954
Coord C2 exon
chr6:103494955-103495086
Length
1065 bp
Sequences
Splice sites
5' ss Seq
AAGGCACCG
5' ss Score
1.92
3' ss Seq
GTTTGTTTTTCTTTGTTAAGGAA
3' ss Score
7.04
Exon sequences
Seq C1 exon
TGCCTTCTACTCCTGTGCACATGGCCAACGGCACGAAAAACTACATGAAAAAGCCTTCCCACCTGCAAGACGGCACTGTAAATTCTTCTGAGGACCACTGCTGGCCACGGGGCACCCCGAGGCACATCTCAGAGAGCTCTTTTGGGCTGTCTGGGGGCCTGCGGGAGGGCAGCCTGAGCTCTCAAGATTCCAGGACTGAGAGTGCCAGCTTGTCACAGAGCCAGGTCAACGGGTTCTTTGCCAGCCATGCAGCTGACCGCAGCTGGCAGGACTCACAGCGTGGCAGCCCTTCCCCATCTGTGATATCCAAAGCCACCGAGAAAAAGTGGACTTCTACTGATAGTAACCGAAGCAAAGCTAAAAATACAGGCATTTCTGATGCACCAGATTACTCTGACCGTGGAGATTCAGACATGGATGAAGCCACTTATTCCAGCAGTCAGGATCATCACATACCAAAAAAG
Seq A exon
GCACCGTTTAATTTGAATTTTGGTTTTTATTTTTTTCCCCCCCACTTAACAAAACAAACAACAGCAAATGTATTATAGAGCAGAATAATCTACTATGAACAGAGTACATTATTCTGGAAAGGAGAAATCGTTTATGTATAATGCTACTAACTGCTACTGCATTTGATGCTAACTTTCAGAGAAATTAGCAGCTTTGAATACTAATTCCAAAATGGCTATTATTCTGGGAACTTGCTACGTGATTACACAAAGGAATGAATAACCAGATTATGATTGTTTTCTATAAATTGTTTCTCTCTTGCATACTTAATATTTATATTAATAAGAGAATTTAATAGCTGAAAAAATTGTTCCTAAGTAATTCATATAATGGACAGGTGACTTTACTATTAACAGCCTAAATTACTCTGAAGTTCTGAATGTATGATAATAAGAACAATAACATAGAAAATTGACCATTTCCTAGAAATATTAGACATGATATAATTTAGACCCATTTTCACAAGTGGATTCAGAAAAGAACCTTAAGCCCTTTGTTCATTGAGAAACATTCCTCGTTAATGTCTCCAGCATTCCTCTTGAGAGAGTTCTGTCCTTATAGATTAGGCTTAGCTGTTGTGCCTCTGTTTATATTGGATTTAAACATTAGCAAAATAAACTTGAGGCCTACTCATCTTAAAGGCCCAAGTTAAAAGCTACTACATGATATATATGGATTTTTTTTTAAAGGAAATAGAAATGCTTCCTAAGTTTGAGTGTATAAAAAGCACTGGATAAGGATTATGTAAAAGCCAAGGTTTGAATTGGATTCTGGGCTTCCCTCAGTCATATCTTTTTACCTGAAGCAAGCCCTCTAGGCTCTAGATCTCAATTTCCTCAGTTTTAAACTCTGAAGGCCTTGGACTAGATAATCCTTAAGATCTTTTCCAGCCTTCATCATTTTTGAGTCTACTCTATCCTTTAATATCTTGCTTTTTCTTAATTTTTCAAAAAGAGAAAGATCTTCCATTAATAATTCTGTTTGATGCTAACAAGAAATGCTTTTGTTTGTTTTTCTTTGTTAAG
Seq C2 exon
GAATCTTCCTCCTCCATGAATACATCCAACAAAATGAATTTTAAAACTTTTCCTTCATCACCTCCTAAACCTGGAGATATCTTTGAGGTTGAACTGGCTAAAAATGATAACAGCTTGGGGATAAGTGTCACG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000014947:ENSBTAT00000055276:23
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.987 A=NA C2=0.864
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0059519=PDZ=PU(18.1=34.1)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Human
(hg38)
No conservation detected
Chicken
(galGal4)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GACTGAGAGTGCCAGCTTGTC
R:
CCAGGTTTAGGAGGTGATGAAGG
Band lengths:
345-1410
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]