MmuINT0160032 @ mm10
Intron Retention
Gene
ENSMUSG00000030942 | Thumpd1
Description
THUMP domain containing 1 [Source:MGI Symbol;Acc:MGI:2444479]
Coordinates
chr7:119715093-119718270:-
Coord C1 exon
chr7:119718022-119718270
Coord A exon
chr7:119717070-119718021
Coord C2 exon
chr7:119715093-119717069
Length
952 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGT
5' ss Score
10.86
3' ss Seq
CTTTCCTATTTTTGTTTCAGGAA
3' ss Score
12.38
Exon sequences
Seq C1 exon
AACCTGAGAAATTAGTGCATCATATTCTCCAGGATATGTACAAAACCAAGAAAAAGAAGACAAGGGTTATTCTACGAATGCTGCCCATCTCAGGCACATGTAAAGCTTTTTTAGAAGATATGAAAAAATATGCAGAAACATTTCTGGAACCCTGGTTTAAAGCCCCAAACAAAGGGACATTTCAGATTGTATACAAATCTCGAAACAATAGCCATATGAATAGAGAAGAAGTTATTAAAGAGTTGGCAG
Seq A exon
GTAAGTTCTCTTAGTAATTTTATATAGCCTGCTCTGGTTTATGCTTAAAAATTTTTAAGTTTAGTACATTTTTTTCTTCACCACATGTATCAGATCTAAGTAATACTGATATGTGAGGTAGATCCTCTGGTAGAATTCTTTGCAAATCAAAATTGACTATTTGGGAAGATACAGTGGCCTGCCTATACCCATGGGTGATTGGTCATTAGATCTCCTAGGGATACCAAACCTGTGAGTGCTCAGGTAAGTCTTATATAATGTTGGCTGCCTTGGTATAGTGTTTGCATATAACCTGCACATGTTCTCTTATATATTTTATACTATCTCTGGATTACTTAGAATACTAAGTCTGGTGGAACTTCTGTGAAAGTAGTTAAGTTCTCTTATGTAGAGATAATGAGAATTAAAATCTGTCTGTTCTTGTTAAGCGGAGATACCATTTTCTTTCCTAAGTATATTGATTCACACTTAAATGGGTTTGTGCACGTGAGTGCAGTGCCCACAGAGGCCAGAAGAGGCCGTCAGAGCTAACAGGTGATTGTTAGCTTCTTAGCATGAATGCTGGGAACAGGTGGGTCTTGGGCAAGAGCAGTGCTTGCACATTGCCTCTGAGTCATCTCTCTACTCTGCCAACTGTTGTCTAATTAAATGCCTCAAGGTTTCACGCATACTTATTTATTAAAAGCATTAATAGAGCTGCGTATGCATGCCCTTGATCCCACGGTTGGGAAGCACAGGCAGGCTGATTGCTATGAATTCCAGGTCAGCCAGTGCTGCATAGGGACCCGGTCTTGAAATAAAACAAAAAAGTATTAATGGAATTTGATTGTCAGTCACAAAGAACAGTGAATTTTTATAAACACTGTTTTAACAAATCCTGTAAGGAATGAAAGCCTTGTGTGGCTCCATCAGGCTTAATGTTATCCTTCCTTCTTTCCTATTTTTGTTTCAG
Seq C2 exon
GAATAGTGGGCAGCCTCAATTCAGAAAACAAAGTGGATCTCACTAATCCAGAATACACGGTGGTAGTGGAAATCATCAAAGCTGTGTGTTGCCTGAGTGTTGTGAAAGATTATGTGCTGTTCAGAAAATACAACCTCCAAGAAGTGGTGAAGAGTGCAAAAGACTCGCAGCCTCACCCAAAGCTGGGAAATGGCAAAGAAGCAAAATTGGAACCTGATAGCAAGTTGAGTCAGAGTGATCCCCCAGAAGGGAACCAGGTGGCACCAGAGAGTATCGAGGAGCTCGGGCAGACAGAGCCGGGGTCTGAAACCCAGGCGGGGAGTGAAGGAGACGCTAAACCTGAACCTGAAAGTCAAGTCTCAGAAGTACCCAAGACAAATGAAAATGAGCTCTCATAGGTCATTCTGTGGGAAGGTGGTCTCAGCTAGGGTTCCATATGAAATTGTGATAATATATTTTGACTTTTGTGTGCTGCTCAATGCTGATCCCACAGTCCCCGTTGTCAGTTTTGTTAGAGCCTTCCAGGCCTGTATGTCGGTATGCAGAAGCATACACTGTTTCTCAGGGGAGGGTGCTAGGAGGATGGTGTTGGCTTCTCCTCCTCTTTACTCTCTCTAGTTTCCTTTTAAACACTGCCAACTGATGGGACTGGACAGTCTCTGAGTGGGAAATGACAGGACATTCCCAGGAGGGTGTGTGCTATGGCTCAGCTGTCCCTGCTTGTTCTGTTGTACACATAGAGAAGCTGCATTGTGGATTATATGGGAATCACTTTGTGATGCTTTCTGCTGTTAGTTTTTCTTGGGTTTTTGTTTGTTTTGTTTGCAAATCTGATGTCTCATCACTGCAGGTGTTTTGAGAAGGTGTGAGTGAGAAGAGAACTGCTCTAGGTGTAGACCCAGGGGTGTTTCTGATAAGGTTAGGGATGAGGAATCACTGCCGGGCCACATATCCTAGTACCAAAACCAGGAAAGAAAGCTACTATCCCAGGGTTTCACTGGACTGCTGTCCAAGCTGGTCTGTCAGCTTGTGGTGCTTTCCAGTGTTCGTCACAGGCAGAGATTGGAAGGGTAGAAGGGAGCAGTGAATACTGTAAACCCAGCTGTCCAGGTGGGGACTGTAACATAGGTTGGGAACTGGGTTTGTGCTTAAATCTTAATGCACAGAGCTAGTGACGTGAGAATATATACTTCGCATCACACAGCTAGAGGCTTGCTTGGTAAGCCAGACCAAGAAGATATGGGAGAAGCAGAGAATAGGCAGTACCTTGCTAATGCAGACGGGGCTAGACCATCCTCAGGTGTTTGACATGCTACCTCGGGTCTGAGATTGAAACCATCTTGAAAGGATAGGCCTTAGGGTCACTTAGGGGAACGGGAGGAGAGGATCTTGGTGCCTTCTTGTGGCTTGCTCCAAGATAGAGGGACTTTTCTTTTAATAGTGTAGGACAGAGGGCCTGAGGACCAGTTACTCTTGGCTCAGACAGGTTGTTCTGGAGCAGGGCAGTTGCTGCACTTGGGATTTTGATCTATACTTTGCTTTTAACGGCCTTTTTATTTGTTTGTTTTGAACGAGTCCCTACTGGCTATTTGCCAGTTGTACAGTGCTGTGTGCTCTTGGGATCTAAATTCACTCACAGATTTTGCTCTGCCTTCAGATTTGCGGACTTTGTCTTCACTGCCTTTTCAGTGTGCTAGCGTACAGGTGATCCAGGGTAGGAACTTAGCAGTTAGTTTTAAACTATAGCAGTTAGGACAGAAAATAAAGAAGCAGAAACCAAATCCCCGTGCTGACGATCAGCATGCCTGTCCTGCTCTGCAGAGAGAGGAGTTAAGCCTGGGCCTGGAGGACACGTTTCTCCAAAGCTGAATACAGTTCTCAGATATTTTTACTGCATTTTGTTCTTGGTACAGCTGAACTTTCAAGTTTTCAAAGTTCCTGATATTTTAAAAAATAAAAATGAATTTGTTCTGTAAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000030942:ENSMUST00000033236:3
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.012 A=NA C2=0.621
Domain overlap (PFAM):
C1:
PF087955=DUF1796=PD(34.9=35.7),PF0292612=THUMP=FE(52.2=100)
A:
NA
C2:
PF0292612=THUMP=PD(22.0=26.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping 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:
GGAACCCTGGTTTAAAGCCCC
R:
CCTTCTGGGGGATCACTCTGA
Band lengths:
354-1306
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