Special

MmuINT0128817 @ mm9

Intron Retention

Gene
Description
protein tyrosine phosphatase, non-receptor type 13 [Source:MGI Symbol;Acc:MGI:103293]
Coordinates
chr5:103969991-103970635:+
Coord C1 exon
chr5:103969991-103970405
Coord A exon
chr5:103970406-103970540
Coord C2 exon
chr5:103970541-103970635
Length
135 bp
Sequences
Splice sites
5' ss Seq
TAAGTAAGA
5' ss Score
5.17
3' ss Seq
CCTTCCTCTTCCCTCTGTAGTTC
3' ss Score
10.49
Exon sequences
Seq C1 exon
AGAGAGCTTCGTTTAGGAGCCTGAACCTGCAAGCAGAGTCTGTTAGAGGATTTAATATGGGCCGCGCAATCAGCACGGGCAGTCTGGCCAGCAGCACCATCAACAAACTTGCCGTCCGACCCCTGTCAGTTCAAGCTGAGATTCTGAAGAGGCTGTCCAGCTCAGAGTGGTCGCTTTACCAGCCCCTGCAGAACAGTTCAAAAGAGAAGACTGACAAAGCTTCCTGGGAGGAAAAGCCTAGAGGGATGAGCAAATCGTATCACGATCTCAGTCAGGCCTCTCTCTGTCCTCACCGGAAACAGGTCATTAACATGGAGGCCCTCCCACAAGCCTTTGCGGAGCTGGTGGGAAAACCCTTGTACCCGATGGCAAGATCTGACACAGAGTCACTGGCAGGACTCCCAAAGCTTGATAA
Seq A exon
GTAAGAGCACGATTGACTAACCCGGAGTAAAGCCTTTGCAGCCCCTCCTGTCATGCGTTTGTTTTCCTTTTATTATTTCCACCGTGTTCTTTTTGCATTGACACTCCCCCTCCTGCCTTCCTCTTCCCTCTGTAG
Seq C2 exon
TTCAAAGTCTGTTGCCAGTTTAAATAGAAGCCCCGAAAGGAGGAACCATGAATCAGACTCATCCACTGAAGACCCTGGCCAAGCATATGTTGTAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000034573-Ptpn13:NM_011204:18
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact

ORF disruption upon sequence inclusion

No structure available
Features
Disorder rate (Iupred):
  C1=0.309 A=NA C2=1.000
Domain overlap (PFAM):

C1:
NO
A:
NA
C2:
NO


Main Inclusion Isoform:


Main Skipping Isoform:


Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal4)
ALTERNATIVE
Zebrafish
(danRer10)
LOW PSI
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ACGATCTCAGTCAGGCCTCTC
R:
CAACATATGCTTGGCCAGGGT
Band lengths:
246-381
Functional annotations
There are 0 annotated functions for this event


GENOMIC CONTEXT[edit]

INCLUSION PATTERN[edit]


SPECIAL DATASETS

  • Pre-implantation embryo development
  • Muscular differentiation time course
  • Spermatogenesis cell types
  • Reprogramming of fibroblasts to iPSCs
  • Hematopoietic precursors and cell types