HsaINT0073483 @ hg19
Intron Retention
Gene
ENSG00000148308 | GTF3C5
Description
general transcription factor IIIC, polypeptide 5, 63kDa [Source:HGNC Symbol;Acc:4668]
Coordinates
chr9:135932153-135933890:+
Coord C1 exon
chr9:135932153-135932295
Coord A exon
chr9:135932296-135933200
Coord C2 exon
chr9:135933201-135933890
Length
905 bp
Sequences
Splice sites
5' ss Seq
CTGGTAAGA
5' ss Score
9.45
3' ss Seq
CTTGTCTCCTCCGGCCCCAGCTC
3' ss Score
7.39
Exon sequences
Seq C1 exon
GTTGCAGAAGATCATTCACCGCAATGACGGGGCAGAGAATTCCTGCACAGAACGGGATGGGTGGTGCCTCCCCAAGACCAGCGACGAGCTCAGGGACACCATGTCCCTCATGATCCGGCAGACCATCCGCTCCAAGAGGCCTG
Seq A exon
GTAAGAGCCGCTTGGGGTAAAGGGGGTCCAGGATGCCTGGTGATCTCCTTTGAGACAGAGGTGTCCCTAAGGGGACCCATTCCTGGGAAATGGCACCCAGGTGGCATCATCTTGCCCCTGGCCCTGGTGGGAGGAGGACATTGTGAGCCAGAGCCCAGCCCAGGTGCTGGCATCACCCCAGCTGCCCAGAGGCTGCCTCAGCCGAGGCCCTCAGCCCTGCGGTCCGGGGCAGGAGACAAGCCCAGAGGGGCTGGGTGCAGCAGCCTGGCACTGCCATCGGGGCCTCCACCTGACGCCCTCACACCAGCCCATGTCTTTCAGCTGTGCATGCGCAGGCTCTGCCTCTGTCTTCTTCCTGTTCTGTGTGGCCCAGCCCCTTCCTGGAACCAGGCAGCCCTGGCAGGAGTGAGGGCCAGCTGCAGGGAAAGTGAAGGGGGCAACACCTGCCAGGCTGTGGGTCTCACGAGGCTCGGGGGAGTTATAAGAGGCCCCCTCTCTCAGGGAACTCCTCCCAGGCTTGGGGAGGAGGCATCCTGGACCCAGCCACGCCCCACAGATCTGACCGAAGCAGGGGTTCTTGGTCTTGCTTGGAACCCAGATTCAGCCCCCTTTGGGAATCTAATCAAGGGTGTGGACCCTTTCCCAGAGAAAATGGTGTGTTCACTCCTGAGGGTCCATGGGCCCTTGAAGCTGCTCATGGCTCCCCTGCTGCAGGATTCCCCTGGGTGCCCGTCAAACTACAGCTTCCCTGGGGGGCCTCCACCCCATACTTACCCACCAGCTTCTTAAGAGCTCGAGCTCGGACCCTTATAGTAGTAAACAGGCTCCCCAGAGCCTGGTGGCCTTTCTGGGGCCACCCGGCAGCCTGCATGGGACACCCATGGCCTTGTCTCCTCCGGCCCCAG
Seq C2 exon
CTCTCTTTTCCAGCTCAGCCAAGGCTGATGGCGGAAAAGAGCAGCTGACGTACGAGTCTGGGGAAGACGAGGAGGATGAGGAGGAGGAGGAAGAGGAGGAGGAGGACTTCAAGCCATCCGACGGCAGTGAAAACGAAATGGAGACAGAGATTCTGGACTACGTGTGACAGGGCCCAAGGCTGGGCCTCCCTGACCCGGCCAGACTGGTGTCTGGCCTAATGAGGGAGCCGGGGCTCCCCATTGCCACCCACAGTGCCCGGAATGGCCCTAGGAGGCCCTCTGAGGAGAGCTAGAGTCCCAGCAAAGGGTGCAGCTGACCCTAGCACTGGCTGTGACATGCTGCTTGGTGCTGCCTCTGGTCCTGAGGGGTTAGGGACATCCCCAAAGGGTATACCCTGGCTCTGCCACCCATGAACCAGCCCAGCATCCAGCCAGTGAGTGGGCACCCAATGCCTCTCAGGATGAGACCAGTAAATGCCGGAGGTGGAGCTGGGCAGCTGTGGAGCCCCAGGCCACAGGCCAGTCTCGCTTGGCTCTCATGACTGTGGTGGTGGAGATAGCGTGGGGAGCCTCGCCCATGGTCTCACGTGGCAAGAAGTGCCTTTAGCTCTGGATCCCAACCGTTTGGCACAGCTTTGGCCACAGCCAGGCCCCTCTGGAATTGTCCTTATTAAACCAGTTTCCCGAGAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000148308-GTF3C5:NM_012087:10
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.337 A=NA C2=0.973
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ATGACGGGGCAGAGAATTCCT
R:
TCCCTCATTAGGCCAGACACC
Band lengths:
346-1251
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)