HsaINT0073479 @ hg19
Intron Retention
Gene
ENSG00000125484 | GTF3C4
Description
general transcription factor IIIC, polypeptide 4, 90kDa [Source:HGNC Symbol;Acc:4667]
Coordinates
chr9:135562626-135565470:+
Coord C1 exon
chr9:135562626-135562714
Coord A exon
chr9:135562715-135564267
Coord C2 exon
chr9:135564268-135565470
Length
1553 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGT
5' ss Score
10.47
3' ss Seq
CACTTGTCCTCCTTTTGCAGATC
3' ss Score
11.81
Exon sequences
Seq C1 exon
GTGCTTCTTAACCTACCAGTCCTGCCAGAGTTTGATATATAGAAGGTGTTTGCTCCATGACAGCATTGCCCGGCATCCAGCTCCAGAAG
Seq A exon
GTGAGTGCTTTCCCTTACTTGGGAGGGTGGGTGGGTGGAACATGCTGGCAGAGGGCCAGCGCCCCAGAATAACAGTTCTAGTCACGCTCTACACTTCTTGGTATTGTGTTGTCGGGGGTGGGGGGTGGGGAGTAGGCCCCTGCTGCTCTTTACGGTGTTACTGTGAAGCCACAGCTAACTAAAACATGGCCATTGGAATATGTCATATTGAAGTGCTTACTGCATTTAGTATGTAAGTTTGTCTGCGTTGCTATTCTGTCACTGCAAACAAATTATTCATTCCAAAAAATGTCAGAGCTTGTTTCAGTAGATGACATAGATAGATTATATTTGAATGTAAACTCTGTGGATGATACTTTATACGAAGACATTATTGAACCAGTAATAGGATATTCACTTGGAGTCATTCTTCCAGTAGCCATGATGGGTTTTTTTCCTGGTTGGTCTATGTGCTCTTTCCTGATAGTTCTAATGTCATCCGTTTCTGAGATAACTACCTGGAAATAAGATTGTAGAGTGGGCAGGAATTAGTGATTTAATAATGACGCAAATGTCAGATTTTGTCCTGACGTTAATAATGCACTCTAACCAAGTGAGCTAACTAGGTACAGAATATACAATTTTATATGTATTTTGAGGGGAATATTCTATTCTCAGCTGAAACAAACAGCATTCTATATAAAACTACATAAATTCTTGAGCTTTGCTCTAAACTGGCAGAAGCTCTCTAATTCTCATAAGTTGGTATGTTGATACCTTGTGTTCTGTTGTAGCTTTTTATTAGGGAAACAACAATCATACACAAAAGGAAAGAGAAGGGTATAATAAACCACTGTGTGCCCATCACTTCAGAAATTATTGACTCATGGCCTTTTCTGTTTCATGTGTAGTTCCCTCACCCACCTCCCTCCTCCTGATGGATTATTTTGAAACACATTTTTGGGAACTTTTAAATTTTTACTGCAATTGATAATGGATATGCTGCTTAGGCAGGAAATCTGGAAGAGATTGAAACTTTAAAAATCTTACCCATTGACTTTGAGTCTAGCCATTTAAAGCTTTTGAGAAGAATGAGAAGCTACTGGATCTAAGAAGAGCACTGGAGTAGAGTTTTTCATAGATGAAAGACGAGGAGGATTTGACCAGTGTTGCCGCATTTTTATTTCTCAAGGGCATAGCATTTTTTAAAAATTCCTATTACTGTAATTTTATGAGAGAATATTTTAACATTAACAATGTATGAAGAACACATTCTCGGAATATACTCCTTTCTTTAAATTGAATAAATTTAGCTTTATGAAACATTCTTCATTACCCTTATTTTCCTGTTTCATTACATTTAACTTTGTGAACCACAAGTTTAGTCCAGCCTCATTTGGAATGATAGAAACCGAAGCCCAAAGAAGTGAAGTGCTTTGTCTAGGGATATGTAGCTGGTTTATTGCAGAGGTGGGACCAGAATGCCCGTCTCTCAACGCTACAGTCCGGTATTCATCCCTTTTGACTGTCTTTTCCGAAGCTAACAGTTGATACCACTTGTCCTCCTTTTGCAG
Seq C2 exon
ATCCCGACTGGATTAAGAGGTTACTGCAAAGCCCCTGCCCTTTCTGTGATTCTCCTGTCTTCTAAATAATCAGTGACGGGAAGATGGAAGGGCATGATGAACTCTGCCATAGAAAACTTCCTCCAGCCTGAAGAGAAGGATGCACTGGAGGAAGCCGGACCCTCACGAGTGGAGAGAAGTCCTTGGTGATTGTAAAGAGGGCCCCTGGAGCTCATTTCTGAATCGCACTCTCCATTTCCAGAGACTAAAGGATGTCCTTTGAAATGGCTGGACTCAGAGAGTTGGAGTCGTTTTGAGATGAGCATTAGCCCCAGCTTTGTAACCAATGAGGAACACTTACTTATTTTTAAGTATCTTGACAGAAGCAATTTGAACACAGTGTCCCGTCATTTCTAGAAACAGAATGGTCTCTTCTAGAGAGCTTGGATAAGGACCTTGCTGGGTTGAGTTAGGTTTTAATCCTTGCTTTGGTTTGGAACTGCCTTCGGGCTCCAGAACTTAAATTGCTTGGTCCGTGGCATCTGATGTACCAACAGAGATTAAAAGTGTAAAGCAACACATGGGCTGATGTTTTGTTCTCAGAAAATAGCTGCTGGTCTGCATCCCTCCATTCTTGTTTTTTATGCATATGGAAAACATTTTCCTAAAACTCTATATTCTTAAGTTGAAGCCAAGACTAAAATTTAATGTGTCAAATGATCTGGTGACTATTATAATGAATAATTGTGACTTATTTTTCATTCTCTCCTGGGTCATCAGGTTTCCTGACCCAACTCCTTAATCCGTATAAAGATGTCAAATACTGTAGTTCACCCACGCCACAGCCCTGCTTCAGACTTAACTGTGGTAGCCTAGATGAGCTATTTGTACACAGAGGAAAAAAAGATATTTTCCTCTTTTAGTAATAAGACTTTCAGTATTTTTAATGTTGACATTTCCAGATGTTTCATTTAGTATCCAGGGGTCTGTCTGGAGACTTCTAGAGAGGGACAGCTCAGAAGTGAGACCCTTGAGCTCTGGTGCTGTAAGCTTGTGCAATTAAGTTGAACAGAGCCTGGGAATTTCTTTCCTCTGCACAGTCCCTTGATATTTGGAATCCAGGTTCTGCCCCCAACCCCTACCCACCCAGTGGTCTGTTAAGATGTCTCAGATGGGGCTGGGCTTGGTGGCTCATGCCTGTACTCTCAACACTTTGGGAAGCAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000125484-GTF3C4:NM_012204:4
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
Other Skipping 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:
TTGCTCCATGACAGCATTGCC
R:
GCTGGGGCTAATGCTCATCTC
Band lengths:
355-1908
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains
- Pre-implantation embryo development
Other AS DBs:
FasterDB (Includes CLIP-seq data)
AS-ALPS (AS-induced ALteration of Protein Structure, links to PINs)
APPRIS (Selection of principal isoform)
DEU primates (Only for human)