MmuINT0164489 @ mm10
Intron Retention
Gene
ENSMUSG00000021277 | Traf3
Description
TNF receptor-associated factor 3 [Source:MGI Symbol;Acc:MGI:108041]
Coordinates
chr12:111260637-111267148:+
Coord C1 exon
chr12:111260637-111260811
Coord A exon
chr12:111260812-111261488
Coord C2 exon
chr12:111261489-111267148
Length
677 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGC
5' ss Score
9.6
3' ss Seq
TGTTTTCTTGCCTATGACAGGCT
3' ss Score
7.33
Exon sequences
Seq C1 exon
CGGGTAATCGACAGCCAAGCAGAGAAACTGAAAGAACTGGACAAGGAGATCCGTCCCTTCCGGCAGAACTGGGAGGAAGCGGACAGCATGAAGAGCAGTGTGGAGTCCCTCCAGAACCGAGTGACTGAGCTGGAGAGCGTAGACAAAAGTGCGGGGCAGGCGGCTCGCAACACAG
Seq A exon
GTGAGCGGGCCTGTGGTCGGGCAGCTGCTCCCAGGCACAGGTGGTGCATGCTGGGAGGCCTCTAGTAGGGGCAGTTTTCACTTAGATTTGTCCTTCTGCATGAGGCCCAGCTTGGCTAGACTACAGGTGACCCGCAGGACATGAGGATGTCAAGGTGTATTGGTCAGGGTACCACTGACACACCCTGAGAGCCTGGAGACAGGAGCAGACCAGGCAGGGGAAATAGGCAGCCTAGTGTTGCCCAAGTATTTCTGGCATTGCGAGCAGATGCGTACCTGTGGCTTTGAGCCTGAATGAGCAGTGATGGTTTGTTTTCATGGGAGGATTAGGGAGTAGGGGTGGATTAAACAGATGGAAGTGTGTGCTTAGGATAGAAGAGGAGACAGCGTGGATTCAGAGCCTTTGTCCCTGAGGAGGCCAGGACTATAGGGCAGGAAACACAGCAAGTAGGTAGTCAGACTCTGACAGCTGTGGCCTGGCGATTGGTACCTTGTGACGACCAGAGAAGAGGGGAGGAAAGATTCAACACAGATGCCCCACGCCGTGCCTGCTTTGCATATGCCCACCCTCTGCACTCACAGTGGTGTCTGTGGACTGGTGTTCCAGACACCGGTGCAGGTGTGCTCCGACGTTTTCATGTCTCGTTTGTTTGCCAAATGTTTTCTTGCCTATGACAG
Seq C2 exon
GCTTGCTGGAGTCCCAGCTGAGCCGGCATGACCAGATGTTGAGTGTTCATGACATCCGCTTGGCCGACATGGACCTGCGGTTCCAGGTCCTCGAGACCGCCAGCTACAACGGGGTGCTGATCTGGAAGATCCGTGACTACAAGCGCCGGAAGCAGGAGGCCGTCATGGGGAAGACCCTGTCTCTCTACAGCCAGCCTTTCTACACAGGTTATTTTGGCTATAAGATGTGTGCCAGGGTCTACCTGAATGGGGACGGAATGGGGAAAGGGACACACTTGTCGCTGTTTTTTGTCATTATGCGTGGAGAATATGATGCTCTGTTGCCATGGCCGTTCAAGCAGAAAGTGACACTTATGCTGATGGATCAGGGGTCCTCTCGCCGTCATCTGGGAGATGCGTTCAAGCCTGACCCCAACAGCAGCAGCTTCAAGAAACCCACCGGAGAGATGAATATCGCCTCTGGCTGCCCAGTCTTTGTCGCCCAAACTGTTCTAGAGAACGGGACGTATATTAAAGATGATACAATCTTTATTAAGGTCATAGTGGATACCTCGGATCTGCCTGACCCCTGACAAGAAAGCAGGGCGGTGGATTCAGCAGAAGGTAACTCCTCTGGGGGGGTGAGCTAGTGTCTTCACGGAGGTCCTCGCCCTCAGAAAGGACCTTGTGGGACAGAGGAAGCAGCCGGAGGAGGAGAAGGAGGTCGAGTGGCTGGCAGGAGAGCCACATGTGAAAACAGACCCCAACGGATTTTCTAATAGACTAGCCACACCCACTCTGAAGGATTATTTATCCATCAACAAGATAAATACTGCTGTCAGAGAAGGTTTTCATTTTCATTTTAAAAGATCTAGTTAATTAAGGTGGGAACATATATGCTAAAAAGAAACATGATTTTTCTTCCTTAACTTAAACACCAAAAAGAGAACACATGTGGGGGTAGCTGGATGTGTCAGCATGTTAACCTACGAGGAGAACTTATGAAATCATAACACAATCCCCATATACTCATCCTAAAATTCAAGAGTGCAATCTTGTTTCAAATATAGTATATTGTCTATTTTTAAGGCCTCATCTGGTCTCTGTTTTAATAATTTGTTTGTCAGAAGACCCTGAGTAGGCAGAAGGTCTCTAAATTCAGAAGTCATTTTTAATTTAAAGTTCTACAAATAATTGTTACTGCAAACATTTTGTTTTAAAACGTTGATAGACTGATATTTCTTGGAAGAAAATGTAAAATATCAAACACTGGTTATCACTTGTGATAGGAAAGAGAATATTGAACCTGCTGTTATTTCTCGTTAGAAATGTAACCCTTCGATATCTGTCGTAGTTAGTGACACTACTTCACAATGACTATGAGAGGGACAATGCTCATGGATGCTGTGCATCATTTCAGACTTAACAATTGTTTTCACCCTAAAATAGGGCATTAGTTGAACTTTGGAGTTCTAAACAAAATCCTATAGGTTTTTACAATTCTGCCCCATGTTTAGACAAGCTCTGTTGCTGACAGCACCAGCCTTGGTCTCCAGTGTCGGTGTCCGGGGATAGGCAGGTGACCCGTGCCGCAGGCAGGAGGCCCCAGCGAGCATCCCATCCTGTCATACTGCTGCATCCGGCTAGCGCGCTCCGAAAGCAACATCCGTGCTCAGAGATGGTGGCATACGGTACTTGTGCCTTAGATGTGACATGCTGCTTCTTGTCCCTGGGTTTGCGTTCACCATGGTTCTAGAAAGTGTCAGTTTAACCAGATCTCTCTCCACCACCAGAACTTTGTCTCTGCCAGGGCCCTCAGGCAACTCTGAACCTGCCTGGGGATGCCAGGCCTCCATTGGCAGCTCTTGAAGCCTCTGCTGCTAAATATTCACAGATTCCAACCGTAGGCCCCTAAGAGCAGCTCAGTCCCACTCCAAGGGAGGGAGGTGTGAGCAGAAGCCACACCCTTCCAGGTCTCTGCAAGGGCCCTGAAATCCCCACAGCATGAAGGAGAAGTGCCCTAGTCCCAAGCGTTCCCGAGACCACTGGTCTGGGGCCTGCCCGGGCTGGCAGCAGCAACCCTGGCCTCCCTGTGAGGAGGGCAGCCAGCTGATGCCCAGCCTGTGAGTGCAGAGGCCCGCCCTCTCAGCTCACTGTTCCCACTGTGATGAGAAGCCTGGAGCCCTGCCCCGGTGCCCCTTTTGCTATGCACCACACTTCACGGTGCTCTACACTGATGGGTGCTACACGCGACAGGTGCTTCTTAGGCAAAACCAATGTGTGCAAACCACCACATCTGTGCCACTTGCCCAAAAGGCGCGCCCACAATTGGCCAGCTGGGCCTGCGCTTCAGACTGCCTGCCTCTGGGCTCTCCCCATGGTCGCACGGGGACAGCTGGGTTGGTGCCCGGTAGCCCACCTTGTCTCTGGTGCTGCCATCTGTCCTGGGTGTGCCTTCGCCCCAGTGCCTGCTGGAAGTGCCCTCCTCTCGCACACCTGTCCCCGTGCTTCCATGAGCGACCTCTTGGTTTCGAGCACTCACCCTGCCCTTCCATGGCTGAAGCGTTTGGTTTGTCCTCTGCTCCCCGCTTCTCTCCATTATGCTGGGATTGCTTTGGGGTAAGTCAGCAACCTTGGTTCTGCCCACAAGGAAAGACCGCAGAGCTCAAGTTCTTTCAAAGGTGCCCTCCTCTTCCTCTAGGCCTGTCACCAGGGTTCCTCCCCCAAAGACCTGGAGTTGGGGGGAACACCCAGCAGTCCTTGGCTGGCTTCAGGAAGCTTTTCTGTGGCCAGATGTCAGCAACGGGGCCATCCCTGTAGCTCCCCCCTTCAGAGAAATCAGTGCAGTATCAACAGGTGTAGGCCAGCAGCATCGTGTCTGACAAAAAGCATGTCTGTCCTTAGTTTCAGACCCTTGTATGAGGGTGACCCTGACATGTCCTCGGGCCCGTCCTCCCTTTTAGTGAGACTTGGTCAAGGCTCCTTCCTATGCGAGGTGGCCCTCCTGGCTTCCCCCGTGCCTGTAGGGTGTGTGTAAAGTAAGTGACTGCTCCCCTGGGATGAGGGCCCTGAACAATGTCACAGCTTCCTGTAGTGTGTTGTGTCTATTGCATTTCTCGGTAACTGTAGAATAGTGGGCAAGCTTGCCCCTCTGTGCCCTGTCTCAGTGTGTGAAGGGCATCTCCTGGGAGGTGTGGAGCAGGCTGCGTCCTGCCTGGGTGTGCCTTGCTCTGCTCCATCTCAGCATTCCTTGGTGCTCACCACCCGGGGGTGTGGGGCATTGTTGGGCTGTGGTCTCAGCATAGCTGTGGCTACCAGTCCTAGCAGCTAGCCCTCACCATATCACAGGGTCCTGGCCATGAGAAGTATGGGGTGTCATGCGGCGTGTGTACCTGGCTGTGCAAAAGTGTCAAGTGCTCATCTTTTAAGAGGCCGGTAGTTGCATGGCCTCTGTGGGGAAATTGGATACAACTCCTGCTTGCCGGGGTGGTGTTTGTACCTGCTCACAGCTGACCCTGGGAAGATGGCAGCCACTAACTAGCAGTGTGTCCTGAGGCCCAGCCTGCAGTTTTTTGTGAATAGCTGAAAGCTTGTGTCAGTAACAACCCAGGGCCTTCCACCTTCGTTGGTCAGGGAGAAGAAGGTAGCCTGGGGTGCCCTGGCCGAGCCTCCTTCACCTCTTGGGGATAGACAGAGCCAGCGGAGGCCACACATGTAGGCCGCGTGTGAGAGGGATGGGTGAGACTGTGAATGAGTGTAACACACTGAGTGTGAGCTGGGCTCACACAGGAGAGCAGAGCCCATGCCCAGCATTCCAGGAAGCAAAGGGCTGTGAGAGGGTCCGCATCCTCTTCCTTTCTAAAGTAGCCTGTGCACAGATGGCGCCATGTCCCTAAGACAGCACAACAGTCAGACAGCACAGCCATGAGCTGAGGGAGGTGTCTGCTTACAGCCACCGTCCGCCTCCTTTCTTTCTCTGCTCTTTTCCCGTTTATTCCAAGGACTGGGCAGCCTCCAGCAGGGCCTTCAGACCCACCCCCACCAGATCCCTTTGAAATATGTGGTCAGCCTCATGAGAACCTAGCTGTCAGCCCCCTGTGGATAGCTAGCCACCTTCCCATCCCTCCTTAGTCAGCCCCTGTCCCACCAGGAGTTGGGACCTCATGCCTGCTATCTTGGGCCTGACATTAACTGAACAGTATACATAGCAGTCACCCACGGCAGACCTGGCAACCAGTGGACAGCATCCAGCAAAGATGAGGATGTCTGGGCACGCCAAGTAACGGGGTCCTAGGTGGACCACTCCTGCCGGCCCAAGAGGAGACCAGGGGGAGTGCCAGGGTCAGCAGCATGGCCCTTGCTGCCCCTCCCCCTGTGCACTGCCATGCATTGCAGGGACTTTTGTACCTGGCCAAGGCATTTCCCCCGACAGGTGACAGGGTTGGTCAGTCCTCACTCTCCCATACATCCCTCTGCTTGGGAGCATCAGTGAATAGAGAAGGGCTTGATGGTGCTTAGGGGACTATTTTTTTACTTTCAATCCAGAAGAGCTAGTGTGGGCTTCATGCCATCATGTCCTGAGTGTGTGTGACAAATGAGGGTCTGACTCTCGAATCTCCTCAGACCAAGACTCTATCTTCTATTTGCACACCCATAGCAGCTGTTTTCTCCAAGCTCAAATGTGCCCACGGGGGTCTGATCAGGTGAGGTGATCATTGGCAAGTGACCCAGCCGTTGCCAGCTCTCCCACCCCGGCTGCTGCTGCTAGCCACGAGGACTGTGGCGTCCAGGAGCCCATCCCCCAACCTGGACCTATCCTAGCCTGTTGTCTGCTTGGGCACCATTACTAGGTAGGCAGGCAAGGCAGTGACCCACACCAAAGCCAGCCCTACAGCTGAGCATGCCCCAGCACCCAAGCAGCGGGTATGATCCAATTCCCTAACCGCACCACGTCTGGAGTCTGTCCTGTGAGCTCACTGTGGAAAGGAGGTTACAAGCCCAGGTCACTGTGCCACTCCATAGTCAGTGGCGACCAGCGTGCACCCCTAATCCCCTTAGTCACTTAAGAAAACCTTCAAAGGCAAATAAATGACCTAATTGGAAAACACAAAAGCCGGCCTTCCTCCCAAGGATTCCCTAAGAATCTGTGGGCGCTCTGACTGAGTAGGTTGGGGTCAGTGCAGACAGCTGCAGACTGTTCTAAAGTTCCGTTCTTATCTCTGATGGCACACCTCTCGTGTTCAGTTCTATTACCCAAAAAACAAAGACCAAAGAAGGCCAATCTCTCATTTGACCGTATTTTTAATCTGCCTGTTTTGACACATGCCGTCTGTAGTAACCGCTCGCTGTGAGGCCCCATCTTGACAGTCCAAGTGATCGTGACCAGTGATTAGCGTCCCGTGTTCTAATGCTCTTCTAAGAAACTGAGACAGTGTGAATTATTGCTCAGCAATAATCATGTCACCAGGAGTTAGCAGCACGCCTCATCTCCTGATAGCATTATGATGTTTCGTGTTTTGTTTACCGTGTGTTACATGTAAGGTTTCATTTGGTATTTATTTGTGTTTTGAGGTCTTGCGATGTTTCTGTTCTGCTGCTAATAATAAAGTTTGTAAGACTGTAGAATGCAGAATTTTGTAATGCTCAAGTGTCTATTAGAGGAAAATAAAGCTGATTCAAGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000021277:ENSMUST00000021706:11
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.034 A=NA C2=0.037
Domain overlap (PFAM):
C1:
PF101744=Cast=FE(37.9=100),PF0205011=FliJ=FE(43.0=100),PF0149614=V_ATPase_I=FE(32.8=100)
A:
NA
C2:
PF101744=Cast=PD(9.2=7.3),PF0205011=FliJ=PD(7.4=5.2),PF0149614=V_ATPase_I=PD(35.0=32.5),PF0091721=MATH=WD(100=73.8)
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:
ACAGCATGAAGAGCAGTGTGG
R:
TCCGTCCCCATTCAGGTAGAC
Band lengths:
350-1027
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