MmuINT0003934 @ mm9
Intron Retention
Gene
ENSMUSG00000051278 | 4930422G04Rik
Description
RIKEN cDNA 4930422G04 gene [Source:MGI Symbol;Acc:MGI:1918893]
Coordinates
chr3:127256407-127258303:+
Coord C1 exon
chr3:127256407-127256573
Coord A exon
chr3:127256574-127258213
Coord C2 exon
chr3:127258214-127258303
Length
1640 bp
Sequences
Splice sites
5' ss Seq
CGGGTGAGG
5' ss Score
8.48
3' ss Seq
TTTGCTGTTTTTCATTTTAGAGG
3' ss Score
9.6
Exon sequences
Seq C1 exon
ATTAGAAAGTGGAGTTTATGTCATTGAGCCGGTGAAGTGGAGACTTTTCTCTCCCGTGTTCTAGGCAAGAAGGGTGGACAGACCGGGCGACTTGGCGCGGTTGGGAGAGCACTGGACACTGACTCGCCTCCACGGAAGCGACCCACGAGGCGCCGTTAGAGTGCCGG
Seq A exon
GTGAGGCGGTCACCATAGCGGCCCATCCCGGTTGTGGGTGTTTTAGGGGCTGACATAGGACCAAGGGGGCCATTATTATTTAGTGATACAAAACCTTGAAGTGTCAAGGCTTGGCAAGTGAAGCTATGTTTCTTTTAGGGATCTGTACTGTTCCTTGTGGTTTAGCAGGCCGTTCGTGGTTTGGAAACTTTCCTGGTTTGAGCGGTGCTGTTCTGAGCTATTGTGACAGTTTTTCATCACTGCAGAGGGCCAGATAGAAACTGTTGTTGGGCTCCAGAGCTGGACTTCCTAACGTAATAGATCAAGAATAGGACCTAAAAGAATAGGACCTAAAATGTTCATTGCTAACTAATTGTCAGGTCATGTCCCTGGAACCACTTGAAGATATGTGTGCTTATGTGTGCTGCTTTTGCATCTGTATTCAGTTCACCATCGACGATTTCAAGATTTCAAAATTTGACCTTATAGTTAACATGGTAGTTACAGTGGCTGCTGCAGCACTGTCCAAGAGATTTTTCTTCCTGGGTGTGGTGGCATATTGCTTGTAATATCCCAGCTATTTCCAGAGGCTAGGACGGGATTGTGCAATATGGTCAGATCCTATTTTAAACAAACATAAAGGACTGGATGCATGTAAGCACTATTACCTAGTTTACATATAGTCCCTTTTGTCAGCCCCTAGCACTGGGTAAAAGAAAGAACAAAATTTTCCTTGCAGAGGAATTATATATTGTATATTTGGCTCTAGGATGTTGTGCTATATTGACTAGGGTATATAGTCAACCCTCTGTACCTGTAATTTCTGGATCTGTATTCAGCCAGTTATAGATGGGAAATAGAAAAAAGTTGTTAGTACTGAGCATACAGATTTTTAAATTATCATTTTTATTTCTTCCTTTTAGACAGTGTCTATCTATGTAGTTAGTCCTGACTGTCCTGGAGCCCTATAGGTAGACAGGCAACCAGGCTGCCTTGAAGTCACAGATCCACCTGACTGTGCATCCTGTGCACTGGAATCAAAGTTGTGTTCCACCAAGTCAGGCTTGTTACCATTTCTTGAACAATGCAGTTTAATCACTGTTTGCATATCATTTACAACCTACTAGGTACAAGTAATCTAGAGATAACTTATTTATGTTAGAAAATATGTGCATGCTCCTATTATATGCGAAACAACTATGACGTTTTATATGTGAACTCAAGTGGCTGGCGCCGGATGTTAATATTTGTGGTCCTGAAACTAGTTCTTGGATAACTAGGGATTACGCTAGCAGGAAAAATTTAAGACACAAGGGGGCCATCTTGTGGTAAGTATAATGATTTTGAAAAATAAAATTGAAGTTGGGTTCTAAGGAGCAGTACATGTTGAAGGGAAAACAATCCATTTTCTGGTATATAGCAAGCCACTGGAGAGATGTTTACAGATTTCTAGTAACTATGAGTTTTACCTTTATTTTCCTGTGTGGTGTCACGCAGTTCTGTCCTCCATGACAGATACAGTTTTGTTTCTCTTGGTGGCTTCATAGTCTTGGAATTGTTTGGTTTCTGTCTCCAGTCAGGATTTATTGAAAAAGTTTGTACTTGATATTTATTCTTTTTATCAGGGTCGATTGACCATTCTTTGCTGTTTTTCATTTTAG
Seq C2 exon
AGGATATAAATGCTGACTAAAAACTGATTGTTTTCTGGACCTGACTAGTTTATAATCTCAGAAGACACAATGGAATGTCAAGAGTTTATT
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000051278-4930422G04Rik:NM_197997:1
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
5' UTR
No structure available
Features
Disorder rate (Iupred):
C1=NA A=NA C2=0.000
Domain overlap (PFAM):
C1:
NA
A:
NA
C2:
PF103824=DUF2439=PU(5.0=57.1)
Main Inclusion Isoform:
NA
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGAAAGTGGAGTTTATGTCATTGAGC
R:
AATAAACTCTTGACATTCCATTGTGT
Band lengths:
254-1894
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
Other AS DBs: