MmuINT0074998 @ mm9
Intron Retention
Gene
ENSMUSG00000035666 | Gtf3c4
Description
general transcription factor IIIC, polypeptide 4 [Source:MGI Symbol;Acc:MGI:2138937]
Coordinates
chr2:28677820-28683086:-
Coord C1 exon
chr2:28682998-28683086
Coord A exon
chr2:28682318-28682997
Coord C2 exon
chr2:28677820-28682317
Length
680 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGT
5' ss Score
10.47
3' ss Seq
CTGCTGGCTTTCCTTTGCAGATC
3' ss Score
12.15
Exon sequences
Seq C1 exon
GTGCTTTCTAACCTACCAGTCCTGCCAGAGCTTGATATACAGACGGTGTTTGCTCCATGACAGCATCGCCAGGCATCCTGTTCCAGAAG
Seq A exon
GTGAGTGCTGGCCTAGCCTTGGGGTGGGGTGGAGTCACTTAGTGTCCTGCTCTTGGTTGGGAACAGAATGAGTGTGCTCTCTGCAGTTAGGGTGAAGCCAGAACCAGTTAATGCATGCTACCTGTTGTGTGTGTCCTATGTCAGCTGACAGTGGGATGGGGCTTCAGTCCAGTGTTAGGGCTGACTCAAGGGAGCGTGTAGGGATTGTATTTGGGAGGCAGCTCTGCAAGAGATGCTGTATACAGAAACACCTGGTGCAGGTATGGCTCTTCTAGAAGCCTCTGAGGGCTACTTCCTGGCTGGTCTGTGTGCTCTTTAGCACATTGCTGTTTCTGAGAGCACTAACTAGAAATAAGATCTTAGGTGTGAGCAAGAGATCAGGCATCTAATAGTCCTGAGAATGCCAGTTGTTGGTGTGAGCTTCACTGACCCTACACTGCGAACAAACAGGCCAGTGAGACAAGTATATAGAATCAAACACAGTAAACAGAAAACAAGAGTATTCTATTTAAAACTTGGTCTGTACTGATTTTTGCTAATTTTCTCAAGGTTACATGTTAGCAGCATGTTAGCATTCTGTTTCTGCTTTTAGTTGACCTCACTTCTCTGTCTGTCATCCATACCTTGTCCTGTCAGCCTTTTCTGATACTGATGTTGGTCCTGCTGGCTTTCCTTTGCAG
Seq C2 exon
ATCCTGACTGGATTAAGAGGTTGCTGCAGAGTCCTTGTCCTTTCTGTGATTCTCCTGTCTTCTGAGTTCAGTGAGGAGGATGGAGGATATGAAGTTGGCTATAGAGAGTGCCCTGAAGCCTGAAGAGCAGGTGTGCTGGAGGGAGCCGGGCACTGCTCGGTGGAGACACTCTTCTAGCTGGAAGGAGGAGCTCATTGCACCAGCACACTCCGACTTCAAGGACTGAAGGCTATCTTTTAAATGACTCCATTCAGAGAGTCTGAGTCATTTAAAGGGGAACAGAAGCCATCCCAAGCTCCTCACCAATGAGGACCACTTGTTTCCCAAGTGTCTTGCCTAAAGCAGTTTGAGCAGAAGCCTTCTGCTTCTAGAAACATAATGGTCTCTTCTAGAGAATCTAAGGACCTTCTTGTGAGTTTGGTTTTCGTCCTTGCTTTGGTCGGGGACTGTCTCTGGCTCCAGAGGGCTGAAGTGGTTGGTACATGACACTGCATGTGCCAGTACACCTTAAAGTGTGTAATGCTGGCTGGCTGCGGCTGGGGCTTGCTCAGCAGACTCAGCTGCCCATTGACTCATTCATATGGAGACATTTTCCTAAAACTATATTTTTGAAGCCAAGAATAAAATCATCTTAATGTATCAAATGATCAGGTGACTATTAGAAGTAAATAATTGTCATTTATTTTTATCTCCTGTCATCAGATTTTCTGGCCCAGCTCTTTAATATGTAAGAAGAGATTAAGTATCCCTACTCTTCACAGCCCCACTTGATGACCATGTGGTAACCTAGATATTTGTACATCCAGGGGAAGTATTGTCTTCCTTTAGTATTAAAGTGAAGCCTCAGTATTTCTAACATTGGCTTATCCGGACATCTCCCTGAGCATTTGGAGGGAAAGCTGGTCTAGAGACTTGTGGAGAAAGATGGAGTTGGACGTCCTTGAGCTCTGTGCTCCAAGCATGTGCAGCTCAAGTGGAAAACCTAAGAGTTTCCTCTCCTGCCAAAGGTCCTTAATCTTTGGAACACAGGTATTCTTCTGTGGGCTTAAAGAGGAGATGTGCACTGTCAATTGACTGCTCGCTCTTAACCCAGCCCTGAAGCATTCTGGAGTCACAGTCGGGGTATTAGAGTAAGTTTCCTGGGATTGGTGCTAATGAACTGGACACATTTTGAAACTGTGCAATTGGAAATGAGATAGGAAATACAGAACATGAAATGCTTTACTCCTTGATGATTCTGTTTTATCATGAGTATTATTTTAACACACTTTCCCACTTTGATTTTATATCTTTAGCAAAAGAAATAATGTCTTAGTACTTGGGTACCACGGCGAGAGACAGGTCACCTGCCACCCTGCCACACTTCTGCACTCTGGGCACAGACCCTGAGAGGCACTTCCAGAAGCTGCTCTGAATTGTCCTGTTAAGACTGTTGCCCTGTGCTGTGTGTTTAATGGATTGTTTGTTGGGGTTGTTAATGTCCTGACGTAGGGTTGTTTCAAGAACAGCATCTCTCCAGACTTGAGGGGCAGCAAGGAAAGAGCCCCGAGTGACCCAGTTCAGAGTCTGCATGGCTGCAGCAGAGCCTGCCGCTGTTACTCCTCAGAGGGAGATGACAGGAGTGGAGATGGTACCGATAGTCGTTGCTAGTCTGTCTACCGTGCGTGCCAAGCTTCCTTTCTCTTGCTCTTTGGAATCAATCTCCCTAGGTGTTCTCACAGGGAATTCGGGGGAACTTAAAACTTGGTTGTTTAAAGCAGTTTGCATTTCTGTGAAATTTTATCATTTAGAAGTAACAAAAGAATTTCTAGGATCTGTACTTGTGTAAAGGAAGAAACGTGACAACTGGAACACAAGTTTTCAGCAAGAAGCCTAGCCCTGCAAAATTTTTGGACTCTGAGATCCAGCCACAGCCAAGTGTTTCCACAGCCAGTAGAGATGTCCCCCTCCCCTCACAAACACCACACTGATGTTAATCTTCAGAGCTGGGTGAATGAGAGAATTTGGGGTTGATGGCAGCCTCCTGTGTGCAACCTGTGCACTTCTGAATCGCTCTCCAAGGGTCAGCATATAGGCCCACAGAGGGTTGATGGAGAGACCTTGGAAAAGTGGGAGTGGCGCCAGAGTCTTGCGCTATGCCTCTTGCAGCTTGAACTCACCTGTGCTGCTTGAGGGAGGAGTTCAGTAGCTTCCAGTTGCAGCTATAGTAGCTGTTTCTGCAGGGGGAAGAAGAGTAGCCATCAAATTGCTGCCCTGCATTTAGAAGACTGGAGCAGACTCTACAGAGAACTTACACGCTGCAGCACTGCTGTGTACCAGGTTCCATGCCTAGATGGTTTCTGTTACTCTAGGTAGGAATGGGTAGCTTGTTGTGGTTGGCATTCAAACCAATGTCCTGATATGTTCACCCCCAGACTTGAAGCTGTCTCTGCTCCTACCAGATCTGCCAGAAGCTGTCAATGAGTACCAGCAAAGTTTATGATGGGATGTAACAATTGTTCTGCTTGTCCCTCTGGGGTCTAGCAAGTTTTTAAGAACATCTGTGTGGGCACAGGTAGGCTGAACCTAGCAATAAGTTTAACAAATGAATTGCATTGGGAAAGTTTTGTTTTCTGTTTGTTTTGTTCTGTTTTTTGGAATGGGGTCTCACTATGCTATAGCTCTGGCTGCCCTGAAACTCTTGTAGACCAGACTGCCATTGAACTCAAATATCTGCCTGCCTCTGCCTCCAATATTGGGAAAGTTTTAAGGGTTAATTATTAAGTCACTTGATTGGTTATATTGGTATCAAATAAGGTGCAGATGGTGGAACACAGCCCTAGCCTGGGAGCCCTGCATCCCTGGCAGCAGCTAAATGGCCTGGGTAAATGACCTGTTAAGCAGCTGCAGTTTCTGAAGTAGAACAGACTCAGCTTCTGGCCATCCCCTTCTTACTTTACCTTCCCCAAGAAGTGGCTCCCAGCATTAGGATGCATTCAAGGCCAGGAAAATATATAATGATAAGCATTTCTAAAGGCTAAGTCATGTGGGTCTTCCTAAAAAAAACCAGTGTCTCATGGTAAGAGGGCCAAGGTACTCAAGGCTGACTGCCGGCTCCTTGCCACCACAGTGTTGGCTGTTGATGCTGAGCTGAATGGGGTACATTCCAAGTCGGTCTGGACCCTCAACAGTCAGACACACACAGGGCTCTTTGACCACAGCACACCTTGGACTTGAGTAACCACAGCTAGGCTTTGCGGTCACTCATGGTATGGTAGACTGCAAAATCTCAACAGCCTTCCCTCTCCCCCCCCCCCAAGTATCGGCTTGGAAGGACACCCTGCTGGGTACAAGAAAGTGGATAATCTGGAGATTATGGAAAAGCACCAGTGTCCCCTAAAGTGTCACACTTTAGAATGTGCCTCAGATTGGTGTGGCCATTTCTTGTCTGCTCTTTCTTGAAGCTAAGACGTTATTGAAGGTAAATCTGCTTTGAGTCTGCTGCTCAACTAAGTGCTCAGTAGGTAAGATGTCCTTAAGTGGAACTAAGCTGTGCTCATGGTAGCCTCGTTTCTAGCTTCCACAGACATGGCAGCTCTGTCCACAGAACAGGCAGGAGGCAGTGTTCTTGGATTGTTTTCTTCAAGGTCATGTTTATATCGAGGGGAGAGACCCTGATGCAGTCAACAGGTTCTAGTCATGAATTTATTTAGAGCCAGATGGTGTGGTTCACTAACAAGGCCTAAGTCTTCCTTCCTTGTGATTAAGTGAAGCAGAAAAGGAAGCGGTGTACATCTGAATTACACTGTAGGCTCACAAGCAAAAACGTGGTCCTATGGTGAACAGATGACATCTCAGAGTTCTAAATCTCCACTTTATTTTTAAGATTAGAAGTTCTCAAAGCTGAGGCTGTAGCTTGGTGGATAGAGAGAGCACTTGCCTAGCATTGACAAGACCTCAAGTTCCATCCTCAGCACTTGGGGTGGGGTTATTATTTATATCACTACCATGAAATTATATTGTTTTCATAAAGAAAAATACTCTAAAATAGACTGGGTAAGGCATTGTGGCACACTGTGTTCTAAGCACCCAGGAGTCTGTGAGGCAGGAGACTCAAGTTGAAGGCCAGCCTGAGCTGTGTGGAGAGAGCACGTCTCAGAAAACCAGTGCTCAGGTTGGGCAGCATCAGAGGCAGTGATGGCGTAGTGACATTTTCAGACCAGGTGTACATTTGGCTGACGCGCTAGGGTGAGTGCTGGTGTTCTCGCTGTCTCTGTAAGGTACTAATATAAAGTCCCACACCAGTGTCCCATGAACTGTCTTTTCCAAGGCTTCGTTTCACAGTTGTATTTTGATACAACATGGATGTGAGCATCACACTTGTTTAAACAGATGTCTGCTGTGCTTAGTGGTTTTACCTCTGTTTACCTGATGCCTGTGTAAAGTCTGTGCTTGGCTTTGAATTGTGTGTTTACACCTTACTGTCTCTAAATAAAGAGAAAATTTTATGGTTATGCAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000035666-Gtf3c4:NM_172977:4
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:
PF126602=zf-TFIIIC=FE(33.3=100)
A:
NA
C2:
PF126602=zf-TFIIIC=PD(22.2=90.9)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGACGGTGTTTGCTCCATGAC
R:
CTTGGGATGGCTTCTGTTCCC
Band lengths:
344-1024
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: