MmuINT0105104 @ mm9
Intron Retention
Gene
ENSMUSG00000036062 | N28178
Description
expressed sequence N28178 [Source:MGI Symbol;Acc:MGI:2140712]
Coordinates
chr4:42951958-42954479:+
Coord C1 exon
chr4:42951958-42952053
Coord A exon
chr4:42952054-42952376
Coord C2 exon
chr4:42952377-42954479
Length
323 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGC
5' ss Score
9.6
3' ss Seq
CCTGTTCTCTCCCTCTGCAGATA
3' ss Score
13.86
Exon sequences
Seq C1 exon
CATCAGCCATGTTGGGCCTATAGCAGACAGCAGCCCAGCTGCCAGCAGCAGCAAGAGTCAGGAGAAGGCCCTGCTGCCCACAGAGCAGGAGTCCAG
Seq A exon
GTGAGCTGAACCTCATTTCTGCTGCTGTCTATAGCTTCCACTGCCGTCGCACCCATGTAAATAAAGGAAGGCATTACTACTTCTACCCCAGAACAGTAAATGCTCATCCTAGAAACCAGGCTCCAGACACATTTGACCCCAGGTCTCCAGGGCAAAAACAACTGGTTTGCTAGCTTTTTAGCAGAGCCGACCCTAACTGTATTAGTCATGAGGCAAGCCCCACTGAGTTTTGTCCAGTCCAAGGCAAGCTGCCACTGGGATTGGGCCTTCTGGGCCTTCCGCATCTGTGCCCCGCCTTGCAAACCTGTTCTCTCCCTCTGCAG
Seq C2 exon
ATACGTGGATTGGCCCACCTTCCTAAGAGAGAACGTCATCTACATCTTGGCTGCTCGTCCTAACAGCGGAGCGATCCACCTGAAGCCCCCAGGATAGGTGGGACAGAGAAGCTCAGTTCTGGGACGGTGGCATCCTCTCTCTCTCTCTCTCTTTCCTTTCTTTTTCCTTTACCAACCTCTGGCACTGAGACTCATGGGAATGGGACACTGCCAACATCTTAATTTGTCATTAAGCTTTATGGCACTGAAGCCACCGTTCCCCTCACAACCGAGGCAGTATTGCCATAGTGAGAGGCCCCAAGAGCTGTGGCATTACCTGCTATGGATCACCTCCTGCCCGCACATCATAAAACTACCTGCCACCTCACGCATACGTGTGTGCACATGCGCATACAACCACATACATGCCTAGACATCCATGCCTTCAAACTCCTTTGGTTCTTTCTTTGATGAAAAAGGACCAAAAGCCTTTTGTTGAGCCCCCCTGGTTTAGATAAGAGGGTCTCTTCTCACTCTTTTTATTGGTCAGTTCTGATTCCCAGGAGAAAGAAGGGGACAATTTAAATTCACTTCCCCTCCAGGAGATGCCGAGAGGCCCCCCTGCCCACATGGAAACGCCCTTCGGTGATGACCACTGTTATTTGTGAGTGTCTGTATGTCCCTCAGGTATGCCATGGTGGGAGAACAGTTCAAAACCATCCCGAAGTTTGTGTTTAAATTCTGATTCCTTGTGATAGAGAAGGAACCTAGTTTGTGGATTTCTGCCTGGAGAAAGTGGAGACAGTCTCTCCCAGAGAGCCAGAAGTCTAGGAACTTTTCAGCCAGGTCATCCAACTTCACAAGTCCTTAGCAGAACAGGAAAACCAAGATGAGACCCCTGGTCCCTAGTCTTCAAGTGGTCCAAAGCTCTAGGGACCCAAGAAGAACAGATACACTGGCAGGAATCACTGTGTGTGAGGTGCTTTAGCCTAGGTGGCGGCCTCAGAGGCCGATGAGGATGCAGAAAAGAAAGCCCGGGCTTTTCCTACTTTCCAGCCCAACTCAGCCACAGACATAGAACTGTGGCATCATATGGAGGGCAAGCCACCCTCTTACATAGCCAGAGGAGCTCTGCAGAATGCCTACGCAGTTGTGCTTTTTAAGAAGAGACAACAAAGGCTCGAGAAGATTTGTATCTCAACTGTCAAGAAGTCCTAGTCAGCGTCAGAAGGGGGACAGTGTGTCCTTCTCCCGTCTCCCCAGTCGCTGCTTCTCCCTGATGCTCACTCCGTGTCTTCCCCTCACCTGAGAGGACCTTGTGGACAAGTGGAGAACGAACGCCATGGGTGTAGCAAGCTTGGCCTCCAGGCTTTGTGTAACCCATCACCCAGTTCTGAAGCTCTGGAGTCAGAACATGGTGTGGGTCAGCCCTAAGACCTAGGGATCCAGGTTCTGGATTTCTGTTTTCAACCAGATGACTTGGGTATGGGCAGTTCTGACAACTAGTTCTTCATGAGAGAACTGAGCAAAGTCCCGCAGAAAGCTTGCATTGTCTCCACTGCTGAAAGCACTTGTACTAAAGTGGATGGTTTCAGGAGAAGGAGCATGCTGCTCAGTGTTGAGAGGCTCAGATGCCATGGGCACCTCCAGCCAAGCCTTGCTAAGAACCCTGCATGCTCTCCTTCTGTAGGACCTGCCTTACCTAGAAGCAGGGTAGTATACTGCTGGAGACAGATTATTTAGGACTGAAATGAAGCAGGCAGGAGATACATGTGGGTTCATTTTGAAACCCACAGCTTTTAAAAACTATTACTTAAAGCTGGGCATGGTGGTACATACCCTTAATCCCAGCCCTTGAGGGACAGAGGCAGGTGGATCTCTATGAGTTGAAGGCCAGACTGGTCTAAATAGCAAGTTCTAGGCCAGCCAGGATTACACAAGTGAGACTTGGTCTCAATAACAACAATGAAAATGACTCGGCCATGTTCCCAGGACTGATCAGTAAGATGGCCCATTATTGAATCGAGTCGAAAACAAAGCACAAACCTGCTGGGCTCAAGGACTGCATCTGTAGCAGCCAGCCCTGGGGTTTTCCATTGAGAAGATTAAAGCATGCTAAATTCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000036062-N28178:NM_172690:9
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.473 A=NA C2=0.182
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AAGAGTCAGGAGAAGGCCCTG
R:
TCTTGGGGCCTCTCACTATGG
Band lengths:
347-670
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: