MmuINT0026557 @ mm9

Intron Retention

Gene

ENSMUSG00000042507 | C130039O16Rik

Description

RIKEN cDNA C130039O16 gene [Source:MGI Symbol;Acc:MGI:2685106]

Coordinates

chr12:85490123-85493981:-

Coord C1 exon

chr12:85493785-85493981

Coord A exon

chr12:85493512-85493784

Coord C2 exon

chr12:85490123-85493511

Length

273 bp

Sequences

Splice sites

5' ss Seq

CAGGTAAGA

5' ss Score

10.77

3' ss Seq

GCCCTTCCTGCCCGCCGCAGGGT

3' ss Score

9.13

Exon sequences

Seq C1 exon

GCCAATGACGTTCTCATTCTCCGGAGCCATGAGCCCAACGCCCCGGGGTCTGCAGGTATCCAGACCTCAGAGAAGCCGAGGGAGGGGCCGGGGAAGTCCCGAAGGGCACTGCCTTTCACAGAGAAGAAGAAAAAAGCCGAGGCATTTAATAAAACCCAGAACCAGGAGAACACCTTCCCTTGTAAAAAGTGCGGCAG

Seq A exon

GTAAGAAGTCCCTTCCTTGTCTTCAGAGGAACCCATTAATGTTAGGGCAGGGACTTTGACGCTGCTGGGGGCGGGGCCCCGGATCTGCTTTTTTTGATCAGCTCAGTGGGTTTCCAGGGTAATGGCGTCATGAGGCAGGCATGATATGAAGGGGCGGGGCGGGAACTTCCCGAGTGGGCGGGGCAAGGGTAGGGGCTAGGTGGACCGGCTGGGGTTTGAGGGAGGAGAGTGGAGGGGTGACTCTCTCATCGGAGCCCTTCCTGCCCGCCGCAG

Seq C2 exon

GGTGTTTTACAAGGTGAAGAGCCGCAGTGCTCACATGAAGAGTCACGCAGAGCAAGAGAAGAAGGCCGCAGCTCTGAGGCTGAAGGAGAAGGAGGCTGCAGCGGCCGCCGCACATCAGCAGGCGCTGAGAGAAGAGAGCGGCGAAGGGGAGAAGGGCTGAGGACCCTGCTGGATCCTATTGCCGGGCTCCCCAGCACCCCAGTCCCTGGAACCTCTAGAAGGGGCCAGGAGAGGGTCACTTGGACTTTGCTCTGCAGAACAAACCCGATAATGAAAAATAAACCGGCTCTTTTATTTACAAAGGCCAAGGACAGTGTTAAGGGCTGCAGGATCCAGTTCTCTCAGTATCTGGTTGGTCCCGAGTTCTGCTTTCCCGGAGCCTAGAGAGGCCGGGCCACTTGGAATGGGCTAGAGCTCTACAGCTGCTTCTCTGATCTCTGCTGTTGCATCTGTGCCTCTTTCATCCCAGGTCCTTAGTAAGCCACCACGGCAAGCCAAGCACAAGCTCGCCCCATGGCAGCATTGTTCCTCCTTCCGCAGAGGACCTGGAAGGCTGTGCAGACTTTTATCTAAGCCCCCAGAGGGACTCCTTAGAGAGCGGTGGCCTTAACACCTGTGTTGTCCTTGTGCTGTCATGCTCAGGCCGGAGTTGCTCCAACAATCCCGTCTGGAGGTCCCCACTTCCTTAGGCGTATCTCGGAGGGCTATTTTCAACCCCTTTGCTGCTTGTTAACAGCCCGTCTGGGGCTGTCAAAGTTTTCTCAGAAGTTTGGAGTTCGTGCCCTGCTCTCAGCCTACTACACGGAGAGGAACTGTTCAGAGGCCAGAAGATGCAGAGCTCTGCCCGAGAGATCTTTTGACAAACTCATGACTAGCATTTTATACCTTTGAGTCCCGGAGGCTGCTAAAGGAGCCTCAAGCAGGTCCTAGAGAGGCCTGGCCTGCTCTTTGGTGCCAGCTTCCTTCTTGCCTGTCGAGTTCTCAGTAGCTGCCAGCTGATCCCACCGCACCCCACTCAATGTTGATATTCACAGTCCTCCCTCCCCCCAATACGGCATGCTGGAGTTTGCTGGATTCTTCCCTGGGAGGGTGATGTCTCCTAACTAGATTAGACAGGAGCCTTCATTCTGTGGCTTGTTGTCATTTGGGAACTATTTATTTATTTTTTTTAATATTTAAGTTTTAACATCCTCAGGGACCAGGGGCCTCTTGCTTTCCAGAGGTCCAAGTGCATTTATCCCAAAATAAGGCACCTTTTTGGCATCCCCAAGCCCTCCCCCAGTTCCATGGCCCTGGGGTCCCTTACCTTGTGGCTCTTGGCCGCAGGAATGACAGAAACTGATCGGGCTGGGAAGGCGGGGAGTGTTATCAGTCACAGGAAGCCAGCAGATGTGGGTGAGGTCAAAGGCAGGTCTCTGTCCTGCCTTTTCTGTACTTTCAAATGCTCGAGGGAGTTGGCAAGAGGCCAGAATTCTAGTTTTGGTTATCAGCCTCGATTCTGGCTTGAAGAAACCATATTTGGCTTGGAATTACTGAAGGGTTGGAATGTTCTAGAGTCCCCTTCGCTTTCCAGTTCAGTAGGGGCCTAAAGCCACTTTTCTGATATCATCACTTAATTTTAGTTGTACAAAAGAGAGTCTTAAGTGACCGTGTGTCTGACTGTTTAGAATGTTAGTAAGGAGCGGAAATAGCCTACAGCCCGTTGGGAATTGGAAATAGAGATGGGGTTTTGTTTTGAAGCTGTAGACTATTGGGTATTTCTTACATTCATTTACACATTAGTATGGTTCTATGAGAGAGCTGCGGGTGGAAATAACAAACCTGTCCCCCTAGATACCTAGACAGTTACCTTAACCTTCAGTTTCCCCGGTTTGTTTCCTTCATAGGCTTCTATCAGCTCGAAGTCCCGGGATTACAAAAATGTGGTACCCTCTAGAAGCAGGAGGGCAACAAGTTTAGGATCTCTTCTAAATCACTTCTATAACGCGTGCCTTCACAGCTCAGCCCCAAAGTGCCACTTAGGTTTCCCAAGGTTCTTTTCTATTTAAACCATATCTGGCTCAGGCCCCTTGGTGGACAGGTGATAGCAGCCACATGAGATCCTTCAGCCACATGAGACTCCTCTGCTCAGTGGTACCAACTAATCCTTAGAAATCTTAATTAAAAACAGCAAAAAAGCAAGAACTTTTCTAAGTTCACAGAGACCAGATGACTATAGCCGGGGTGGGGGTGGGGGGATAAAGATGGTACCTTTAGGTAGTGATCCCACCAGACACTGTTTTAGAGGGGCCCATGCTCCAGCGCGCCCGTGTGGAAACTGAACTAGTTCAAAGCGGAGATGCACGTGCGGCCGGAGGCTGGCGCAGGCGCGTCCTTACTGGTGCTTTCTCGTACGAACACACTGGGCTTGGCTTTTGTTGTTCTTTCTATTCAGAGCTCCCTGTTTGACAATAACGTCCCTATACAGTGTCACCCTGCCTGTCCCCCAGCTTCCACCTGCATTCAGAGAAGGCCATGACACTGACCGTGCCTGTGTTCTGGGCCATCTCTGAGGTCTCTTGCCCTCACTGCTGTCCTCCAAGCCTTCAGCAGCCCCCTTAGAGCTAAAGTACCCACCCACCCACCGTCCTTGCCGCCCCACCTCCCACCCCGGCACAGAGGCCCTGTGCTCATGATGTCTAAAGGGATTGCCTATATTTAACTGCCTCAGTCACCCAACCTCTTTCTTCTCATGTGCCAGATGTTAAAGACAGAGGAGGAAGAGTGCAATAGTACTCAAGCCTCAGCTGTTGAAATGTTTTTATTGGGGCTCACTGTTCTGGGTTATTATTTATTACTAGACTGGCAAAGCCTAACCCCTTAGGTTTTTACAGGAAGTATGCATATTTTTATATAAAAACAGTTGTGTCTAACCCACATTTGGCTGTGTTTGTTGCCTCAAAAAAAAAAAAATTGCAGCTGTTAGAACTTTTCCTCATTTGTCTCTTACGTTAAAGGCCTTGCTGGAGAGGATGGAGCACAGAACAGCCTTGACAGTCTGTAATTAGTGTACAAATATTTTAATAGCATAAAGTAAGTATATTCCTTTTATTTTGAAACAAAATGGTCAGACACTGCCTTTCATGTGTTTGTTGCCTGTGGCACTCTTTTTAAAAAAGACTGTTACATATTAAAATAGTGTACATATATATATATATATAAATATAAATATTACCTCTTTGTGTACAGTTGTGATAGACCAGACTGAAAATTTTATTTTTTGTGTGCTTTTTATAAAAAAAAAATTAATACACTAAAGAGAATCTTGCTGTGATTGTAATGTACCTATGTAACTTATTTACTTTTGAATGTTCTGTATCTTAAGACCTTTTATTAAATAAGGTTTTAAA

VastDB Features

Vast-tools module Information

Secondary ID

ENSMUSG00000042507-C130039O16Rik:NM_001163502:12

Average complexity

IR-S

Mappability confidence:

NA

Protein Impact

Alternative protein isoforms

No structure available

Features

Disorder rate (Iupred):

C1=0.864 A=NA C2=0.887

Domain overlap (PFAM):

C1:

PF0214814=zf-UBP=PU(31.0=27.3)

A:

NA

C2:

PF0214814=zf-UBP=PD(67.2=72.2)

Main Inclusion Isoform:

NA

Main Skipping Isoform:

ENSMUSP00000048120

Other Inclusion Isoforms:

NA

Other Skipping Isoforms:

ENSMUSP00000105923

Associated events

Other assemblies

mm10

Conservation

Human

(hg38)

No conservation detected

Human

(hg19)

chr14:74185712-74186007

Rat

(rn6)

No conservation detected

Cow

(bosTau6)

chr10:85518179-85518636

LOW PSI

BtaINT0055757

(ELMSAN1)

Chicken

(galGal4)

chr5:25433017-25434006

ALTERNATIVE

GgaINT1012237

(ELMSAN1)

Chicken

(galGal3)

chr5:28318666-28319655

Zebrafish

(danRer10)

No conservation detected

Fruitfly

(dm6)

No conservation detected

Primers PCR

Suggestions for RT-PCR validation

F:

ACCAGGAGAACACCTTCCCTT

R:

ATCGGGTTTGTTCTGCAGAGC

Band lengths:

306-579

Functional annotations

(Submit an annotation)

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

Other AS DBs:

FasterDB (Includes CLIP-seq data)

AS-ALPS (AS-induced ALteration of Protein Structure, links to PINs)

APPRIS (Selection of principal isoform)

Special

MmuINT0026557 @ mm9

GENOMIC CONTEXT[edit]

INCLUSION PATTERN[edit]

SPECIAL DATASETS