MmuINT0023987 @ mm10
Intron Retention
Gene
ENSMUSG00000040225 | Prrc2c
Description
proline-rich coiled-coil 2C [Source:MGI Symbol;Acc:MGI:1913754]
Coordinates
chr1:162723110-162724869:-
Coord C1 exon
chr1:162724704-162724869
Coord A exon
chr1:162723288-162724703
Coord C2 exon
chr1:162723110-162723287
Length
1416 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGT
5' ss Score
10.67
3' ss Seq
TGATGTTACTGATCTTTTAGTTG
3' ss Score
5.85
Exon sequences
Seq C1 exon
ACTACTTTTAAGGGGTGTGTCAGGAGGTTTTGGACTAGATGAGTTTCCACCGAAATGTCGGAGAAGTCAGGCCAGAGCACAAAAGCCAAGGATGGGAAGAAGTATGCAACACTCAGTTTGTTTAACACTTACAAAGGAAAGTCCTTGGAAACACAGAAGACTACAG
Seq A exon
GTGAGTAGATGCAGTAGCCCACGTTATCTGGTTTGTGGGTTTGTTGATGCAAAGACACTGTGTCTAATGTGTATGATTAGAAGCTAGGGTGAACCCGTTTATTTTAGCCTTTTTGTATGTATTCACATTCTTTCCAGGGAATAAGAATTAAATATTTTACCTTTGAAAATTTGTTTTAATTTTTTAATGATACTTAGATGTTGTAGATGTGTGTGTTTGTGTGTGGATATGGGGAAGTGAGTGCAGGTGCCTGCAGAGGTCAGAGCTATGATATATCCCTTTGGAGCTGAAGTTACATAGAGATAGGTGTGACTTAGAACTTAACAGCTACTGTTCTTAACCTCACAGAACTTTGTATATATACACTTCTCTATACACTTGTGTCTATAGGAAAGAAACCATATAAGAGACGAAGAGGGGAGTGGGTGGGTGTGTTCGTGCTACAGGGGGAAAAAAGTCCTGTCTTTTTGACCTGGGTCCCTTGCACCACCAGTACATACAGTGAAAAGTAGAGCATTTGCTGCAGTATTGTGAACATTGTGGGCTTTGTTTGTGGGGTTAGGGGGTGATGAGACAAGGACTTGTTGCTGTGTATTTTAGTTAGGGTTTTATTTACTGCTATGAAGAGACACCATGACCAAGGCAAGGCAACTCTTCTAAGGAAAACATTTAATTGGGGCTGGCTTACAGGTTCAGAGGTTCAGTCCATTGTCAACAGGGTGGGATCATGGCAGCATCCAGGCAGGCATGGTGCAGGAAAGAGCTGAGAATTCTTATATCTTATTCTGAAGGCAGACAGGAGAAGACTGGCTTCCAGGCAGCTAGGACAAGGGTATTAAAGCCTGTATCCACAATGATAACACTTCCTCCAACAGGGCCACACCTCTTAATAGTGCCACTCCCTGGGGCCAAGCATATACAAGCCATCACACTGTGTAACCCTAAAGGGCTTAGAACTTAACAGTGGATCAGGCCAGCCTCCAACATGAAGCTATTTTCCCACTTTCACCTTCCAAGTTGTGTAGTTTGAACTTTCTTCTCTTAACATTTTAAGTTTTTTACTTAAAATAGATTGCCTGAAAACATTTCAAAACTAGCATTTCCCCTTCCCATATTCCCAGTATATAGTGTTCCATATTTAGAAGTTAAGGGGTTCTGGTGGGTGGGTTTGTTTTGTTTTTTGAGACAAATTTTGCTGGGGTCCCAAGATGGCTTAATATTTTGAGTGGATTGTTTACTTTTTACCTTCAATTAATGTTGTAGGTTATAAACTGAGTTTATAGAGCTCTACTTTAACATTGGGGACTAGTCAGAGATTGTTAACTCCTGTTCATGTATATTATTTGTTGAATAAAATGTATAATAGAGTGATGAACAGTAGATGTTCTAAGGAAATTGATGTTACTGATCTTTTAG
Seq C2 exon
TTGCAGCTCGACATGGGTTACAAAGTCTTGGAAAAGTTGGTATTTCACGGCGAATGCCCCCACCTGCTAACCTTCCAAGTCTCAAAGCAGAGAACAAAGGCAATGATCCTAATGTGAATATTGTGCCCAAAGATGGGACAGGATGGGCATCGAAACAAGAGCAACATGAAGAAGAAAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000040225:ENSMUST00000182149:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.878 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF070016=BAT2_N=PU(22.4=97.4)
A:
NA
C2:
PF070016=BAT2_N=FE(34.5=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ACTACTTTTAAGGGGTGTGTCAGG
R:
TTCTTCTTCATGTTGCTCTTGTTTCG
Band lengths:
342-1758
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- 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