BtaINT0119917 @ 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
chr6:103494955-103496412:+
Coord C1 exon
chr6:103494955-103495086
Coord A exon
chr6:103495087-103496318
Coord C2 exon
chr6:103496319-103496412
Length
1232 bp
Sequences
Splice sites
5' ss Seq
ACGGTACTG
5' ss Score
5.88
3' ss Seq
ATTTGTCTTTTTCCACTTAGGGA
3' ss Score
9.79
Exon sequences
Seq C1 exon
GAATCTTCCTCCTCCATGAATACATCCAACAAAATGAATTTTAAAACTTTTCCTTCATCACCTCCTAAACCTGGAGATATCTTTGAGGTTGAACTGGCTAAAAATGATAACAGCTTGGGGATAAGTGTCACG
Seq A exon
GTACTGTTCGACAAGGTTTTCAAATGTTTTCTCTTCTCCATTTCCAGCAGCCTATCATATGCCAATTTATTACTTGAATTATTTTGCTTCAAAAAGGAAATTTGTCAAATATTTGCAAAACTTTAAATTGGATTACATCTTAAGACTTTTTTTAAAAAACTTATGTTTTCTAGTCACTTTTTCCTGTGGTTTAAAAGAAAGTAGACAAATGCTGTTTTCCCCCAGAGATTTCATACTTGTTTAATCTGAATACAAGACTTGAAAAATATAAAATTGAGAAGTATGTCTTATATATATTTGGCAGCTTCTACATCAGCATGGAATAATTTTAACTTACATCATAAATAATTAAAGTCTAATATATATTTATATGCCCTTCACTTCATAATACATCTTGGCATGTAAATATGATTAGTAGCTTAATATTAGAAGTTCCCAAAAATATGTGTAATACTTCTAAAGAAGTTAAAATATGAGCATAGGCTATTTGATGAAACTGCTTTAGAATTCTATTAATGTACTATACCCTAAAGTATAATATTATCATTTATATTTGAAGGATGTTGTTTGTTAGGAAAAGCCATTTAGAAATAAGGTAGAAATAACACTCTTAACATATAGAGATCCAATTTTCTATCAGTCCTCAATACTGTAACCCTTTTTATCTTGTCCGTAACTTCTTTAGAATTTTATTATCTTCCTACTGTGAAGGGAAATAAAAGCTGAATATCCACAAGAGATGGAGCATCTACTCAGTAGATCTCATCTACTCTGTAGCACAACTTCTATGCCAAAACCTTTTAAAGTGAAAAGAAAATTTTCCATTGACTCATGAGATTTATTTTCAGATTAGCAAATATGATCTGAAGTGTATTACTCCATATGCTGTTTATTTCTGACAGTTATATTCTCACCCTAATATTTCATGGCTGGATTTTGCTTGCCATTTGTGCCTAATGCGTGGTATAGACTTCTGAAAGGAAGAGCACCCCCTCATCCAGGCAAAGATCTGGCATGTCGTTATTTTCTGAATAAAGAATGTTTCTAAAACATAGCTGCTTTTGCATTTGGAAAACTTACTAGAAATATTCTTGGGTATTGAAGTAATTGCATGTGCTAATGTGATGCTGCTGCTTTGGCTGATGAATGGAATGCTTTCTAGGTCTCAGACCTGAAAGATGGAGTGCAACATTTTTCATGTGACAAAACATTATTTGTCTTTTTCCACTTAG
Seq C2 exon
GGAGGTGTGAATACCAGTGTCAGACATGGTGGCATTTATGTGAAAGCCGTTATTCCCAAGGGAGCAGCAGAGTCTGATGGCAGAATTCACAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000014947:ENSBTAT00000055276:24
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.864 A=NA C2=0.406
Domain overlap (PFAM):
C1:
PF0059519=PDZ=PU(18.1=34.1)
A:
NA
C2:
PF0059519=PDZ=FE(37.3=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:
ATCTTCCTCCTCCATGAATACATCCA
R:
TCTGCCATCAGACTCTGCTGC
Band lengths:
214-1446
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]