MmuINT0160031 @ mm9
Intron Retention
Gene
ENSMUSG00000030942 | Thumpd1
Description
THUMP domain containing 1 [Source:MGI Symbol;Acc:MGI:2444479]
Coordinates
chr7:126861536-126862815:-
Coord C1 exon
chr7:126862641-126862815
Coord A exon
chr7:126861785-126862640
Coord C2 exon
chr7:126861536-126861784
Length
856 bp
Sequences
Splice sites
5' ss Seq
TAGGTATGT
5' ss Score
7.76
3' ss Seq
TTTTCCCCTTTTTCTCTTAGAAC
3' ss Score
10.35
Exon sequences
Seq C1 exon
TTTATAGACAAGGACCAGCAGCCCTCTGGAAGTGAGGGAGAAGACGATGATGCAGAGGCTGCCTTGAAGAAAGAAGTTGGTGACATTAAGGCTTCTACAGAGAAGAGGCTGAGAAGATTCCAGTCAGTGGAGAGTGGAGCGAATAATGTAGTCTTCATCAGGACGCTTGGGATAG
Seq A exon
GTATGTCTGACTGACAGCCCTAAGATCATCAATCCCATAGTATCTGGGCATTTCTGTCTTAGCAGATGCTGCCTAGACAACGGCTCCCCAGGTATAGCTGTTAATTATTCTGTGGAACGTTTCCACATTCCATCAACAGTATATCAGTTTCCGAAGGTTTTGGAAAGGTTTTCAGATGACACATACCACACTCAGGGAATTTGCTTCTTACTCCACACTGTGGAAGGGGTGCCATTTTAGTTTCCTAACAATGTAGAGTGGTGGAGGGTGGTGAGCATTGGGTAAGGGTAGGGACCTGGCTGTGCTGCATCCTTCCTTTAGTAACTCAAGGCAGAGTGAAAGCGTGTATTCTGTCTCAAAAGAGCAGCTGCTACTTAGTTCCAGGTAGTTACCATTTAGGAATAGAGGGCCTGATCCACTTAAAACCTGGAAATAGAATTCCTTTGACTTTCAAATGTGGTCACTAATTTGGAAATATTAGCACTGTTGTCTTGGGCAGATGTGTTAGTTGGGAAGTAGCCAGTGAATCACCGTGTCACACGGTGCTCTGTGTGCTGGGATTCTTTCCCAACTGAGAGCTGGACTTCTGTACTCCTTAACTAATGAATTAGGGCTTTAAGTTACAGATTTTGTTTTTGTAAAAATATGCTGTGTAATGCTTGTTACTCTAATTTGTATTACAAGAAGACAACAGTAAGGTGTTGTGGTTTAAGTTTGATTCCGAGACTATCAACATTTATATTTGGTAGGATCTTGAGAAATACTAGATGGATGGAAAATAAAAACAAAAAAGTCTTGTTTTTTCTTTTCTTTTTTTTCTTGTGTTTCTTCTTTTTTTTTCCCCTTTTTCTCTTAG
Seq C2 exon
AACCTGAGAAATTAGTGCATCATATTCTCCAGGATATGTACAAAACCAAGAAAAAGAAGACAAGGGTTATTCTACGAATGCTGCCCATCTCAGGCACATGTAAAGCTTTTTTAGAAGATATGAAAAAATATGCAGAAACATTTCTGGAACCCTGGTTTAAAGCCCCAAACAAAGGGACATTTCAGATTGTATACAAATCTCGAAACAATAGCCATATGAATAGAGAAGAAGTTATTAAAGAGTTGGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000030942-Thumpd1:NM_145585:2
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.441 A=NA C2=0.012
Domain overlap (PFAM):
C1:
PF087955=DUF1796=PU(64.0=93.2),PF0292612=THUMP=PU(25.2=67.8)
A:
NA
C2:
PF087955=DUF1796=PD(34.9=35.7),PF0292612=THUMP=FE(52.2=100)
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:
ATAGACAAGGACCAGCAGCCC
R:
TGTTTGGGGCTTTAAACCAGGG
Band lengths:
343-1199
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: