MmuINT0038667 @ mm9
Intron Retention
Gene
ENSMUSG00000020953 | Coch
Description
coagulation factor C homolog (Limulus polyphemus) [Source:MGI Symbol;Acc:MGI:1278313]
Coordinates
chr12:52704183-52706760:+
Coord C1 exon
chr12:52704183-52704699
Coord A exon
chr12:52704700-52705843
Coord C2 exon
chr12:52705844-52706760
Length
1144 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGA
5' ss Score
10.77
3' ss Seq
TTAAAATGTTTCCCCTTTAGGTA
3' ss Score
11.44
Exon sequences
Seq C1 exon
GCTGTGTGTCGGAATAATGGCTTCTTCTCTTATCACATGCCCAACTGGTTTGGCACTACAAAATATGTGAAGCCTCTGGTGCAGAAGCTCTGTACGCACGAACAGATGATGTGCAGCAAAACCTGCTACAACTCAGTGAACATTGCCTTTCTGATTGACGGCTCCAGCAGTGTTGGAGATAGCAATTTCCGCCTCATGCTAGAATTTGTTTCTAACATAGCGAAGACATTTGAAATCTCAGACATTGGAGCCAAGATAGCTGCTGTACAGTTCACTTATGACCAGCGCACCGAGTTCAGTTTCACTGACTATAATACCAAAGAGAACGTCCTAGCTGTCCTAGCGAACATCCGCTACATGAGTGGTGGCACAGCTACTGGTGATGCCATCGCCTTTACTGTTAGAAATGTATTTGGTCCCATAAGGGACAGCCCCAACAAAAACTTCCTGGTTATTGTCACAGATGGGCAGTCCTATGATGATGTCCGAGGCCCTGCTGCAGCTGCCCATGATGCAG
Seq A exon
GTAAGATGGCTGTCTTCCTTCGGATGAAGGAAGGGGTCCCGTGAATTCTAGGGGTCGGTCAGCATTTTGTAGAAAGGATCCTTGCGGTGTGAATTTATATAGTCTACCAGCTTTGGTGTCTAAGCGAACTGAAATTCTTCCAAGCTCCACTGAAATTCCATTGGGAGGTTTTGCTATTGTTTTTCAAGACAGGGTTTCTCTGTGTAACAGCTCTGGCTGTCCCAGAACTCACATTCTGGACTAGGCTGACATCAAACTCAGAGTTCCTCCTGCCTCTGCTGCCCAAGTGTTGGGATTAAAGGCATGTACACACAACACCCAGCTCAAGAAGGGGAGTGTTTTTTAATTCACCAGATTGCTTTAAAAACTTGCAATTTAAAAATAACAATATAATTTTTAAAAACATTTGAGCATTTTTCCTGTGTTTATTATGTATGTGCACCAGGTGTGTACCTAGTGCCCATGAAGGTCATGAGAGGGCATTGGCCCTGGAACTGGAGTTATAAATATTTGTGAACTATGTGGGTGCTGGAAACTGAACACAGGTCTGGTACAAGAGCAACAAATTACCTGCTGAGCCATCTCTCCCGCTCCCAGATCTACAAGTTTTGATTGTAAAATGGATTTGTCACTATAACTTCAAAGACTGAATTAGAACAAACAAAATTATTTCTAGCCCCCATTCCTCAGACAATGCAACCTTCCCATTTATCTGTCCTCTGTGCCAGTTTTACTTTAATGTGGTTATCAGGGTCCCCAAGATGATGTCTGAAAGTGACAATAGCAGGGAGTCCTTTCTCACTGCCAAACATGTGTGCCTGCTGCAGGGGCTTCATAAACTATCAACTTGATTTTCTTTCTCTTCCTCGTTTGTTCAGTGCAGTCTTGAATAGATTGACAATCTCAGTATTTTCATCGTTATTAATATGCAGTTGCTGGTGGCAAAGCTTTTGGTTTTGACCAATTATTTTTGATATAATCAAAATGACTGTGGTCTAACCTAAAAACTTAGCATAGATTTCACTTAAAAACGTATCAGGCAGTTTCCTCTGCAGCTATGTATTATATATATGGAATATATACATATTATATATATGGAATATATAACTACATTTTTAACTTATTTAAAATGTTTCCCCTTTAG
Seq C2 exon
GTATCACCATCTTCTCTGTTGGTGTGGCTTGGGCACCGCTGGATGACCTGAGAGATATGGCCTCTAAACCCAAAGAGTCACACGCTTTCTTTACCAGAGAGTTCACAGGGTTAGAACCAATTGTCTCTGACGTCATCAGAGGCATTTGTAGAGACTTCTTAGAATCCCAGCAATAACCGATACTCTGACAACTCAAGGAATACGTGCAAGGGGATCTAATGTGCAAATTATATTCTCAATGCCTATGTAACTTTATAGCTTACCAGTGTCAAAAAATGCGTCCACAGCTGTTTAAAGCAAATGAATATTCATGTGATGCTCACAATTTAGATTGGCCGAGACTTGATAATCAGGCCCTTAGAAACTCAGGAAAGAAGAGTTGTCATGGATTAACATTGGGAGTTCAAATATGCATTCAAGTGGATAGGTAAGCTACACAGCTCAATAAAAGAACCTGGCGCTTACACACAAAGCACTGTTCCCTCTTTAATCACTCTGCATTGACCATGCAAGGAAAACAGAACAGCTTTTAAACACAGATCAAGTATACATATTTTGACCCATGTGGATGTTTTCTTAAAACCAGCCAAGAACAGACAGCTGTTATTATGTGCACTAGCCATAACTACACATTATATGGAATCATATATCAAGCTTCTTTTGTAGTGTGTTTTCATAACTTGATGGCTGAAATACCACACTGAGTAAAGGTAGGATTGCCTGGTATTTTTCTATTTATATCCTTAATTTTATGTGTATAGACAGGCATGTACTCCGAGGACTAAGAAAATGTTTAAGCAGATAACTTTTTTTTTTTTGAAAAAAAAGATGTGTCAAGTATTGTAACCGAAAAAATACACAGCTTAATAGCTTGGCTGTCAGCAATAAAACTGCTAGTGACTAAGTGCCTATTTATT
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000020953-Coch:NM_007728:10
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0009223=VWA=PD(3.1=2.9),PF0009223=VWA=PU(72.8=72.8)
A:
NA
C2:
PF0009223=VWA=PD(26.6=78.0)
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:
CTATGATGATGTCCGAGGCCC
R:
GCTTTAAACAGCTGTGGACGC
Band lengths:
342-1486
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: