HsaINT0068658 @ hg19
Intron Retention
Gene
ENSG00000162676 | GFI1
Description
growth factor independent 1 transcription repressor [Source:HGNC Symbol;Acc:4237]
Coordinates
chr1:92944145-92946042:-
Coord C1 exon
chr1:92945905-92946042
Coord A exon
chr1:92944311-92945904
Coord C2 exon
chr1:92944145-92944310
Length
1594 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGC
5' ss Score
9.88
3' ss Seq
CTCTCTCTCTCTCTCTGCAGGAA
3' ss Score
15.36
Exon sequences
Seq C1 exon
GTGTTCTCCACGCCGCACGGGCTCGAGGTGCACGTGCGCAGGTCCCACAGCGGTACCAGACCCTTTGCCTGCGAGATGTGCGGCAAGACCTTCGGGCACGCGGTGAGCCTGGAGCAGCACAAAGCCGTGCACTCGCAG
Seq A exon
GTAAGCGCGGGGCGCACCGCCGCGCGCGGCCCTGCTCGGGGATCTTCTGCATCTCCTCGGTGCAGCACCAGCCACTCTCTGCCTGGAAGTTTTCTCCTCGACTTCCCCCAGTTTCCTCCCCCAAGCCCTCCGCTGCGTCCCCTTGCCCTGGTGCAGGTGTGTAGGGAAAGGAGGATTGTGGCCGGCTCAGGCCTTGAGGCAGCCCTGGATTTTGGTGTCACACCACTGTGAGCCTCGAGAGTGTGATCCTCATTGTTACTTTGGGCTTGAGGTAGGTTTGTATGCACTGATTCGTGCTGCTGATATATCAGACTTACTAGCTCTGTTTCTTTGTGCCTATTCTTTTCACCAAATGGTTGTCACTTAATTTGCATTGACCCCTCTCGACTGAAAAGGCAGGAATCTCAGCTCATTTAGAGCATCTAGTAGCATATTCACCCCGCTATTCATTCTTTCCTTCCTTCCTTTCTTTTCTTTTCTTTTTTCTTTTCTTTTCTTTCAGAGTCTGGCTCTGTTGCCCAGGCTGGAGGGCAGTTGCACAATCTCAGCTCACTGCAACCTCCCCCTGTCAGGTTAAAGTGATTCTCGTGCCTCAGCCTCCTAAGTAGCTGGGATTACAGGCGCATGCCACTACAGCACAGCTAATTTTTGTGTTCTTAGTAGAGACGGGATTTCGCCACGTTAGCCAGGCTGGTCACGAACTCCTGGCCTCAAGTGATCCACCAGCCTGGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCATGCCCCACCGCCGCTATTTATTCATTCATTCATTAATAAATATTTGTTGGCTAACTTCCAGGTGCCAAGTACTTAAGAATCTTATAACACATCAGGTCCTTGACAGCATGCCCACATGAAGATTATAGTTTAGCTGAGAGATGGAGAGTAGATGAGCAAGTAAATATGCCAATAGCTATCTCAGGAGAATGCCTACTTACGAAGGCTAAAAAGAGTATTAGCCCATCTCCCCCAGCACCCACACTGGCTGGGGGGAGGTGGCATCTCAAGTGACTGAGGTCTAAGCCTCCTGTTGAGGAGGGTGGAGAAGTGTGTGCTAATGGGTGTCAAAAAAAGCAGGGTGTGGATATGTATTTGCCATGGGGTGTGGAAGGTTGTGGGTGAAGAATGTTTTGGTAGAAAAAGTGTTGAAGGGCCAGGCACGGTGGCTCACGCCTGTAATCCCAATACTTTGAGAGGCCGAGGTGGGCGAATCACTTGAGGCCAGGTGTTTGAGACCAGCCTGACCAACATGGTGAAACCCCATCTCTACTAAAAATACAAAAATTAGTCAGGTGTGATGGCGTGTGCCTGTAGTCCCTGCTACTTGGGAGGCTGAGACACGAGAATTGCTTGAACCTGGGAGGTGGAGGGTGCAGTGAACTGAGATCGTTCCACTGCACTCAAGCCTGGGCGACAGAGGAGACTGTCTCAAAAAAAGAAAGAAAAAGTGTTCAAGGGATTTTAGGGTCAGCTGAGGGGTGAGGAGAGCAGCAGTCTAGTTGACTGCAGTAGGAGTTCTGCATCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTGCAG
Seq C2 exon
GAACGGAGCTTTGACTGTAAGATCTGTGGGAAGAGCTTCAAGAGGTCATCCACACTGTCCACACACCTGCTTATCCACTCAGACACTCGGCCCTACCCCTGTCAGTACTGTGGCAAGAGGTTCCACCAGAAGTCAGACATGAAGAAACACACTTTCATCCACACTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000162676-GFI1:NM_001127216:5
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
No protein impact description available
No structure available
Features
Disorder rate (Iupred):
C1=0.065 A=NA C2=0.107
Domain overlap (PFAM):
C1:
PF134651=zf-H2C2_2=WD(100=58.7)
A:
NA
C2:
PF0009621=zf-C2H2=WD(100=41.1),PF102764=zf-CHCC=WD(100=39.3),PF134651=zf-H2C2_2=PU(38.5=17.9),PF0013017=C1_1=PU(11.8=10.7)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTGTTCTCCACGCCGCAC
R:
CAGTGTGGATGAAAGTGTGTTTCT
Band lengths:
304-1898
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
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)