RnoINT0064785 @ rn6
Intron Retention
Gene
ENSRNOG00000002042 | Gfi1
Description
growth factor independent 1 transcriptional repressor [Source:RGD Symbol;Acc:2680]
Coordinates
chr14:3061025-3061674:+
Coord C1 exon
chr14:3061025-3061187
Coord A exon
chr14:3061188-3061488
Coord C2 exon
chr14:3061489-3061674
Length
301 bp
Sequences
Splice sites
5' ss Seq
CAGGTGCGA
5' ss Score
7.75
3' ss Seq
CTCCTGAATCTTCTCCGCAGACG
3' ss Score
9.96
Exon sequences
Seq C1 exon
AACTCAGAGTAACCGAGGGTCCAAACATCCGACCAGCGGCTGGCCACCATGCCGCGCTCATTCCTGGTCAAGAGCAAGAAGGCGCACAGCTACCACCAGCCGCGTTCTCCGGGGCCGGACTACTCCCTGCGCCTGGAGACCGTGCCTGTGCCGGGCAGAGCAG
Seq A exon
GTGCGAGGCGCGCAGAGGCCGGGAGGGGCAGCTGCCAGGGACGCCGACTCTGCTTCAAGCCACCTCGCTCCCTAGGAATCAGGGGAGGCCACCCTAACGCCCCTCGGGTGCTTTTTTTGTTTCCGGGAGCTCAGATTTGTTGAGCTTGCCAGAGATGCCCCGGTGCTCGCAGTCGGGGCTCTTGAATCGGGGAGGGCTCCGGGCCGGGTCTGAGTGGACAGAGGAGGACGTGGGTACCACGGTGGAACCACTTCAGTTCGGCCAGGTTTAGGTTTATTTCTCTCCTGAATCTTCTCCGCAG
Seq C2 exon
ACGGCGGCGCTGTGAGTGCAGGAGAGTCGAAGATGGAGCCCCGAGAGCGTTTGTCCCCCGAGTCTCAGCTTACCGAGGCTCCAGACAGAGCCTCCGCGTCCCCCAACAGCTGCGAAGGCAGCGTTTGTGACCCGAGCTCCGAGTTCGAGGACTACTGGAGGCCCCCTTCTCCCTCTGTATCTCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000002042:ENSRNOT00000002807:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.897 A=NA C2=0.857
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ACTCAGAGTAACCGAGGGTCC
R:
GATACAGAGGGAGAAGGGGGC
Band lengths:
343-644
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]