BtaINT0119925 @ 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
chr6:103502706-103504628:+
Coord C1 exon
chr6:103502706-103502889
Coord A exon
chr6:103502890-103504469
Coord C2 exon
chr6:103504470-103504628
Length
1580 bp
Sequences
Splice sites
5' ss Seq
CTGGTGAGT
5' ss Score
10.1
3' ss Seq
ATCACTGTTTCTTTCCTTAGGAG
3' ss Score
10.46
Exon sequences
Seq C1 exon
TAACCCTCTTCCCCCTCGACCACTGGATGTAACTCCTGGGCAGAGCTGTCAATCTCAATCAGAATCTGTTCCCATAAATGCAATGGATAAATATCATACACATCACACTTCTGAACCAACTAGACAAGAAAGCTTAACATCTTTGAAAAATGACTTGGAAAACCACCTTGAAGACTTTGAACTG
Seq A exon
GTGAGTTATTTCCTTTGTATGAAGAACATTCTATATTTTCTCAAGTAAAATGTAGTTCCTCAAATAAAATACACAGCTTCCCTTTAGGGAAATTGCTGTCCTTTAGATCAGCCTCATATCTATGCTCAGTAAATAGACAACACATCTGCCGTGTTTCTCTGCTAAGAATTCAGGGAAAAGACAAAAAGACTTGGGTACACGTCCTGACTCTCCCAGTGACTTGCTATAATTTGGCAGATGCTATGGATGAATTGCTTAATTCTTCTGAGTTTTAGCAATTTTAGCTGTAAAATGGGACTAGTAACCTCATGGTATTGTGGTAAGTATTAAATGAAATAACATATATAGAGCACCTAGCCCAGTACCTATAATTTCCCAAACTCGACGAGTTACCTGTTTACTCTTTAATCAAGTTTGAACGTAATTTCATTCTCTTCCACACTGTTTTATGGGTGCCTAAATGGAATCCTTTATACTAATAACCCTAGAACTTCTAAACTTACAAATTCACTTTGGAAGTCACATTTCTAATAGAAATAACATCCCTTGGACATACACAGTGATAGCACAATCATCTGAAGAAATAGAGAATCTGAGTTTTGTCATTTCTATCATTCTGTCTGACCACTTGGAGTTTTTAATTTCAAATGTAAAAGGTGAAAAAATTTGTTTGAAAAAAAATTTACAAAGTCTAAATTTTTTGGTAGTTCCAATTTTTGATAAATATAGTATTTTTTGAATTTGAAAAAAAAGAATAATATCCTTAACACTGATTCAAAGTCACCCTTTTAATACATTTTTTTGTTACCTAAGTAATAAATACTTATTATAGAAAAGTTAGAAAAGATTAAAACCATCACCAGTCAGAACCCATAAACACTTCAATCTTTCCAGGCACTTTGTTTCCCTATAATTGTGTGTGTGGATGTGTGTGTGGGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTAGCATCTACATCTTCAATTTCATTCTCAGCAGTAGAATGAAAATAATCTTTGGATGATTTCCTTAGAAATCTGTCATCACGCCTATAAGCCCTAAGCAACCCTTGTGCCACAGTTAAAATCTTAAAATAAAAATTTTTCATACAACTAAATATATCAAGTTGTGATATTTAATCACTCAGACTTCATGTTTTCACCCAAGAAAAGCTTTCTTCTTTTTTTTTTTTTTTTTATTTTTTTTTTTTTTAATTTTAATTTCAAATTTCAGGTATACACATGCTCCCTTTCCTAGCTTTCTTCTGTTGCTCTTGGCATGGGTGGTTTTTTTTTGTTTATTCTGAAAATATAAGAATTGAAGCTTGAGTAAGTTCTGGGTCAGCTATCTCCAGACAAGCACATAATGTTGAATTTAAACCTCAACTTTTATTTTGCATTGGCAGGCAAGAGGTTGGAGCAGTACCTTCTGTCTAGAACTAGACATACATACCTGCCTTCTTTACTTGGGCAAGTTAAGCAGCCTTTTAAGGTTTAGTTTTCTCCCGTGTTAATCAATGGAAAGAATAGTTGTCTTTCTCTTTGTACTGCAAAATAGAATCACTGTTTCTTTCCTTAG
Seq C2 exon
GAGGTGGAACTCCTGATTACCCTACATAAGTCGGAAAAAGGAAGCCTGGGCTTCACAGTAACCAAAGGCAATCAGAGCATTGGTTGTTACGTGCACGACGTCATTCAGGATCCAGCCAAAAGTGATGGGAGGCTGAGACCTGGGGACCGGCTCATCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000014947:ENSBTAT00000055276:31
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.855 A=NA C2=0.264
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0059519=PDZ=PU(60.8=90.6)
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:
TAACCCTCTTCCCCCTCGAC
R:
CTTGATGAGCCGGTCCCCAG
Band lengths:
343-1923
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]