MmuINT0036559 @ mm9
Intron Retention
Gene
ENSMUSG00000029516 | Cit
Description
citron [Source:MGI Symbol;Acc:MGI:105313]
Coordinates
chr5:116429771-116431821:+
Coord C1 exon
chr5:116429771-116429878
Coord A exon
chr5:116429879-116431703
Coord C2 exon
chr5:116431704-116431821
Length
1825 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGT
5' ss Score
10.47
3' ss Seq
ACCCTGCTTTGCCCACACAGGTT
3' ss Score
9.87
Exon sequences
Seq C1 exon
GTTCTCTACTCTCACGAGAAAGTGAAAATGGAAGGCACAATCTCTCAGCAAACCAAACTCATTGATTTCCTGCAAGCCAAAATGGACCAGCCTGCTAAAAAGAAAAAG
Seq A exon
GTGAGTTGTGATGCCCAACAGCCGGGGGCAGGCGATCTCGCTCTGCCTCCCGTGACTCAGTAGCTACCACTGTGACTAGTAACCTCACAAATGAAAAAAAAATGTACATTTTTGTTTGTTCTGGGTTGAGAACCCCGTCTAAGTCTAACCAGAGTGGCCTTTATCACGGGTGACCATTGATCAAGACCAGCAGATAACCGCTCTGTAAGGGAGTCTTGTGTTCTGCTCCTGCAGAGAAAGCTGGGCTGGAGCAGGGGGTCATCTGCCGAGGGAACGGGCTTCTGCACAGGTTGAATATTAGGTCTGAAGGTCACGTGTGTCTGAGAGTTTAGCAGGTCCCACTTCCTGGGACTCTAGGGCATGTGTCACCTACGTGGGTCTCCAGGAAGCACTCAGGATTGATCTAGTCCATTGCTTTTTATTTAGCTTCCTGCTTGGGTCCCTTTTGAGACACAGTTTTGCAGCGTAGCTCACGCTGGACTTAAAACTCATGATGTTGCCTTTGGAGCACTGGGATTGCAGGCGCGCCCTCCCATCATCCCGTGCAGTTAAATGGCTCACGGACACAGGAAGTTAAAATGGCCTGCTTTAAAACTTGACTAGACAGCTCTCTTCCCCAGCGCCATACTCTGCTTTAAACCATAACAACTGGTGAAAACCAGGATGAAAAGCCAGCTGTGACATATGAGGCCCTAGGCTCAGTCATATGAGGGGTGGTGGGGAGAGATTAGCTGTGGCCCAGGTCATATGAGGGTTCCTGTGAGGAGACTGCCCAGTCCGCAGGCTCCCCACCAGCTGCAGCTCTCGCCCTAAGTTGTTGGCCAGCTCCAACTGAGCGCCAGGAAGGTTTCAAAGGGCTTGGCATTTCCTCCCAAGGGTCTTAGCACACTGTAACAATCATGGCAGCAGTGTTAAAGGAGGTCAGAGGAAGGGACCAATGGACCAACACCCTCGGTTGGCCTCTTCGTTACCCGGTTCCTGTCTGCCGCACACAGTCCTCCAAGGCTGTGTCTCGCTGTGCTGGCCACGGGAGGGTCTTTTCATATGCCATGTTATCATATATTCTTGCTAAAGCTCACGATATTTAATCTTTTTTTTTTTTTTATTCTGGCAGCGGACTATTGTCTGGTTGTGTTGTTAATGTTAGGATGTTTTGCGTTCGTTTTCCTGTTAATTCTTTTTTTTTCTTTTGTCAGACACGTGATTCCATTTTTTTCTCTTCTGTGTACAGTAACTTTCTGTTGGTATTTTTTTTTAGTGAGCCCTTTGTTTTGATATCATCTTAGCATTTGTTTTTCAATTTTTGCTTTCTTTAAAAAAAAAAAAAACCAACCCATAACCCTCCCCCTCCCCGTGTCTTGTCACTAAGCACCATGAGACAAGTTCAAAGGCAAGACGGACCTCTGAACCATCACCACCTCTCCCAGCTCCATACTCCATCCACCCTCATTACATTTTTTGAGGGGCAAGGACTCTCGGGAAATGGCTCTCCAGTCTTGGGAATGCTAAAGGACGAGGTGGTGGCAGTTGAAGCATCTTTAACCTTCTCGGTGAAAACCTCTGCACCGCTCCTTTTGTTTTTTTCAGCTGACTGGAATGGGCTGAGGCTCAGCCTCCCCTCCCCCCTCCCCTTCATATGCCATTTTTTCCCCAAACACACTTACAGTGAGTATATGCCTGGCCTTGGTGGCTTGCTCCTCCCGAGTCAGCTCTCCTTTAGCCTGGGTCTCCTCGGTACCAGTTTCTAGGAGTTAGGAGATATCTCTGTTTCCATTGCTAGGGTTTATTTAGTCGACGGAAAGAGGACCCTGCTTTGCCCACACAG
Seq C2 exon
GTTCCTCTGCAGTACAATGAGCTGAAGCTAGCCCTGGAAAAGGAGAAAGCCCGATGCGCGGAGCTGGAGGAGGCCCTTCAGAAGACCCGCATCGAACTCCGCTCTGCGCGGGAGGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000029516-Cit:NM_007708:29
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.194 A=NA C2=0.389
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTTCTCTACTCTCACGAGAAAGTG
R:
CAGAGCGGAGTTCGATGCG
Band lengths:
214-2039
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: