MmuINT0036567 @ mm10
Intron Retention
Gene
ENSMUSG00000029516 | Cit
Description
citron [Source:MGI Symbol;Acc:MGI:105313]
Coordinates
chr5:115986894-115988236:+
Coord C1 exon
chr5:115986894-115987063
Coord A exon
chr5:115987064-115988155
Coord C2 exon
chr5:115988156-115988236
Length
1092 bp
Sequences
Splice sites
5' ss Seq
GCTGTGAGT
5' ss Score
7.39
3' ss Seq
CTGCTTTCACACATGGAAAGAAA
3' ss Score
-1.01
Exon sequences
Seq C1 exon
ATGTCCCATACATCCTGAAGATGGAGTCTCACCCACACACCACCTGCTGGCCTGGGAGAACCCTCTACTTGCTAGCACCCAGCTTCCCCGACAAGCAGCGCTGGGTCACCGCCTTAGAATCTGTCGTCGCAGGTGGGAGAGTTTCTAGGGAAAAGGCCGAAGCCGATGCT
Seq A exon
GTGAGTATGGGACCCTTGATGTGGGTTGGGGCTTCTCTGTAGGGTGCATGGCCGTGGGCACTGACTTTATCTGCGGGGGGTGGGGGTGGGGGTCCCCTACTCTGAAGGCTGTGGTGAGGGTCCTGACTCGCTTTGTGGTGCAGAGCAGGGGCAGGGGAAGCTGCCTTGTCTGCCTGGAGCAACCTCACAGCAGCCTTGGCCTTTATAAGGAAGCCCCTCCTCCTGTTTACCCCCTGGGGTCCTCGAGTTATAAGTACTTTGACTGGAAACCCCTGAAGGAGATGCCAGTGTGCCGGTGAGCACCTGTGTTCAGGGAAGCTGCACACAGTCTGTCCAGATGTCCCTGCAGTGTCTGCTCTCCGCAGGCAGGTCTGAAATCCCACGCGTCCTTAAGATGTGACAAACATTGCTGCTATGCCTCCATCGGCACCGCTCCCCCTGGGAATATCCCCGGGTGCAGACCGTGCTCATCACTCACTGGCGTTGGCTTCACTGAAGACGAAGCAGCACTTTCTAGACACTTAGCAATAGGAGGGTTCTTGACTGTGAGCCTCGGGAAGAATTGTGTCCTGTTCCACACATGAGCCTTTTTTTCTGAAATGTGCCTTAATGTGTGTACAATAGGCACGTGACCATACTTCGAGTGAGCATCAGCCAGTGTGGGTTGAGGTAAAGAGAACTAGAGGCTTGGCTTGCTCAGGACTCCCGAGCTTGTGTGTTCTTGTCGCAGCTGGAGGTGGGGAAGGGGCCTTCCTAACAGCTTGTTACCGCTCCGCACCTTTATCTTACCATTTCCTGTCACGGCATAGCATCTGTGCCTAGGTCACCCACTTGTGTGTGTCTGCACCAAGCTAATTTAGGGCTGCACTGGAGGAGCCATTAACAGTGACCTGGGGTTTCAGTCAGAAGTTGTGGCCAGAGCCCGGGGTCACAGTTGAGAGGGCTGAGCACTTGGCCTGGTGTCTGTGAGGGTGTGGTCCAATGTGTGCCTCTGAGCGTGACTTTAGGTTACTGATCCTCGGGAGGGCTTGGTCACAGATAGTTTGAATTTACTCCGCCCCGTCTTTTCTGTCTGCTTTCACACATGGAAAG
Seq C2 exon
AAATTACTTGGAAACTCTCTGCTGAAACTGGAGGGCGATGACCGGCTTGACATGAACTGCACCCTGCCCTTCAGTGACCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000029516:ENSMUST00000051704:36
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.013 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0016924=PH=PD(35.8=75.4)
A:
NA
C2:
PF0078017=CNH=PU(2.2=22.2)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TCCTGAAGATGGAGTCTCACCC
R:
AGGGTGCAGTTCATGTCAAGC
Band lengths:
223-1315
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
- Ribosome-engaged transcriptomes of neuronal types
- Neural differentiation time course
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types