HsaINT0078770 @ hg19
Intron Retention
Gene
ENSG00000138413 | IDH1
Description
isocitrate dehydrogenase 1 (NADP+), soluble [Source:HGNC Symbol;Acc:5382]
Coordinates
chr2:209106718-209108328:-
Coord C1 exon
chr2:209108151-209108328
Coord A exon
chr2:209106870-209108150
Coord C2 exon
chr2:209106718-209106869
Length
1281 bp
Sequences
Splice sites
5' ss Seq
CAAGTAACT
5' ss Score
4.45
3' ss Seq
TTTTACCTTTTGTTTCCCAGGCA
3' ss Score
10.22
Exon sequences
Seq C1 exon
AAGGTGGTGGTGTTGCCATGGGGATGTATAATCAAGATAAGTCAATTGAAGATTTTGCACACAGTTCCTTCCAAATGGCTCTGTCTAAGGGTTGGCCTTTGTATCTGAGCACCAAAAACACTATTCTGAAGAAATATGATGGGCGTTTTAAAGACATCTTTCAGGAGATATATGACAA
Seq A exon
GTAACTATAGTTCTTTTTTAACTTTTTCTTTATTCTCAAGTAAGCTGACATTTGCATATAGAGTATGTATCTCCCTATCCCTATGATTCTGGGTAAATTGAGTGAAAATCATCACTGTCTCTTAAAGATAAGGGCAAAACTGAGGTTTAGCAGGAGTGAAACAAAACCACTCTGACTTGCTTTTATAAGATAAACATGTTCTTAAATAAGGTCCCCACATGAATTGTTTTCAGAGCCAGGTTCTTTAATGTTTAAATAAACGTACGCTGTTAGTGATAAGTTCTAATTTTTCATGTGTGAGTTTCTAAGTCAGACCCATTTCCATTCTTTCTGAAGCCCATTGTTAGAATTTAAAATTCTGTTGGCCAGGCACGGTGGCTCATGCCTGTAATCCCAGCACTTTGGGAGGCCGAGGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCTGGCTAACACGGTGAAACCCTGACTCTACTAAAAATACCAAAAATTAGCCGGGCGTGGTGGCGGGCGCCTCTAGTCCCAGTTACTGGGGAGGCTGAGGCAGGAGAATGGCGTGAACCCGGGAGGCGGAGGTTGCAGTGAGCCGAAATCACGCCACTGCACTGCAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAGAAAAGAAAAGAAAAAAAAGAATTTAAAATTCTGTTTTAGTGGAGTCATTTGAACTTAAGTCTAAGTTTATAACAACACTGGCTTCCACAGCACAGGAGGTGAGCATGTGTTAATATTTAAGATTGGCATAACTCCCTTTAGGTGCAAGTGTTCAGGCCAAAATGTTCCTGAGGCATTTTGATTCCTCCTCCTGCTGCCCATCTATACCAAGCCCAGAAACTGTCTGGAATATATTTTAGTTTCCTGAATGACACCAAGAAGTAGAACAGTCTTTTCAAAAATGTATTTTAAAAATAAGCTGAATCTCAAGAATCTGATCTATAGTATAATGAAAACTGAAAAGTGAAGTAGTCATTGGGATACTCTACTGTCTCACTTAATTCTCACGGCTTCCCTGCAAGGTGGGTAAAATTGTTCCTACAGATAGTCAAATTGAGTTTTACAGTTAGAAAATGATTGGGCTAGGATTTGAGCCAATGTCTGTCAGATTCCTGAGTTTCTGCTACTTCTACTAAAATATGCTGCTTCTTGTGTGTCCGGTCTTCTGTTTGGGACAAGCAGATGATATCCCTAACAAAATCAATTTTCTTTATTATTATTCTCTTTTACCTTTTGTTTCCCAG
Seq C2 exon
GCAGTACAAGTCCCAGTTTGAAGCTCAAAAGATCTGGTATGAGCATAGGCTCATCGACGACATGGTGGCCCAAGCTATGAAATCAGAGGGAGGCTTCATCTGGGCCTGTAAAAACTATGATGGTGACGTGCAGTCGGACTCTGTGGCCCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000138413-IDH1:NM_005896:6
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
No protein impact description available
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0018015=Iso_dh=FE(15.0=100)
A:
NA
C2:
PF0018015=Iso_dh=FE(13.0=100)
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:
AAGGTGGTGGTGTTGCCA
R:
CTTGGGCCACAGAGTCCGA
Band lengths:
330-1611
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)