HsaINT0075830 @ hg19
Intron Retention
Gene
ENSG00000010704 | HFE
Description
hemochromatosis [Source:HGNC Symbol;Acc:4886]
Coordinates
chr6:26091069-26093188:+
Coord C1 exon
chr6:26091069-26091332
Coord A exon
chr6:26091333-26092912
Coord C2 exon
chr6:26092913-26093188
Length
1580 bp
Sequences
Splice sites
5' ss Seq
AGGGTATGT
5' ss Score
8.34
3' ss Seq
CCTTCCTCTTTCCTGTCAAGTGC
3' ss Score
7.09
Exon sequences
Seq C1 exon
GTTCACACTCTCTGCACTACCTCTTCATGGGTGCCTCAGAGCAGGACCTTGGTCTTTCCTTGTTTGAAGCTTTGGGCTACGTGGATGACCAGCTGTTCGTGTTCTATGATCATGAGAGTCGCCGTGTGGAGCCCCGAACTCCATGGGTTTCCAGTAGAATTTCAAGCCAGATGTGGCTGCAGCTGAGTCAGAGTCTGAAAGGGTGGGATCACATGTTCACTGTTGACTTCTGGACTATTATGGAAAATCACAACCACAGCAAGG
Seq A exon
GTATGTGGAGAGGGGGCCTCACCTTCCTGAGGTTGTCAGAGCTTTTCATCTTTTCATGCATCTTGAAGGAAACAGCTGGAAGTCTGAGGTCTTGTGGGAGCAGGGAAGAGGGAAGGAATTTGCTTCCTGAGATCATTTGGTCCTTGGGGATGGTGGAAATAGGGACCTATTCCTTTGGTTGCAGTTAACAAGGCTGGGGATTTTTCCAGAGTCCCACACCCTGCAGGTCATCCTGGGCTGTGAAATGCAAGAAGACAACAGTACCGAGGGCTACTGGAAGTACGGGTATGATGGGCAGGACCACCTTGAATTCTGCCCTGACACACTGGATTGGAGAGCAGCAGAACCCAGGGCCTGGCCCACCAAGCTGGAGTGGGAAAGGCACAAGATTCGGGCCAGGCAGAACAGGGCCTACCTGGAGAGGGACTGCCCTGCACAGCTGCAGCAGTTGCTGGAGCTGGGGAGAGGTGTTTTGGACCAACAAGGTATGGTGGAAACACACTTCTGCCCCTATACTCTAGTGGCAGAGTGGAGGAGGTTGCAGGGCACGGAATCCCTGGTTGGAGTTTCAGAGGTGGCTGAGGCTGTGTGCCTCTCCAAATTCTGGGAAGGGACTTTCTCAATCCTAGAGTCTCTACCTTATAATTGAGATGTATGAGACAGCCACAAGTCATGGGTTTAATTTCTTTTCTCCATGCATATGGCTCAAAGGGAAGTGTCTATGGCCCTTGCTTTTTATTTAACCAATAATCTTTTGTATATTTATACCTGTTAAAAATTCAGAAATGTCAAGGCCGGGCACGGTGGCTCACCCCTGTAATCCCAGCACTTTGGGAGGCCGAGGCGGGTGGTCACAAGGTCAGGAGTTTGAGACCAGCCTGACCAACATGGTGAAACCCGTCTCTAAAAAAATACAAAAATTAGCTGGTCACAGTCATGCGCACCTGTAGTCCCAGCTAATTGGAAGGCTGAGGCAGGAGCATCGCTTGAACCTGGGAAGCGGAAGTTGCACTGAGCCAAGATCGCGCCACTGCACTCCAGCCTAGGCAGCAGAGTGAGACTCCATCTTAAAAAAAAAAAAAAAAAAAAAAAGAGAATTCAGAGATCTCAGCTATCATATGAATACCAGGACAAAATATCAAGTGAGGCCACTTATCAGAGTAGAAGAATCCTTTAGGTTAAAAGTTTCTTTCATAGAACATAGCAATAATCACTGAAGCTACCTATCTTACAAGTCCGCTTCTTATAACAATGCCTCCTAGGTTGACCCAGGTGAAACTGACCATCTGTATTCAATCATTTTCAATGCACATAAAGGGCAATTTTATCTATCAGAACAAAGAACATGGGTAACAGATATGTATATTTACATGTGAGGAGAACAAGCTGATCTGACTGCTCTCCAAGTGACACTGTGTTAGAGTCCAATCTTAGGACACAAAATGGTGTCTCTCCTGTAGCTTGTTTTTTTCTGAAAAGGGTATTTCCTTCCTCCAACCTATAGAAGGAAGTGAAAGTTCCAGTCTTCCTGGCAAGGGTAAACAGATCCCCTCTCCTCATCCTTCCTCTTTCCTGTCAAG
Seq C2 exon
TGCCTCCTTTGGTGAAGGTGACACATCATGTGACCTCTTCAGTGACCACTCTACGGTGTCGGGCCTTGAACTACTACCCCCAGAACATCACCATGAAGTGGCTGAAGGATAAGCAGCCAATGGATGCCAAGGAGTTCGAACCTAAAGACGTATTGCCCAATGGGGATGGGACCTACCAGGGCTGGATAACCTTGGCTGTACCCCCTGGGGAAGAGCAGAGATATACGTGCCAGGTGGAGCACCCAGGCCTGGATCAGCCCCTCATTGTGATCTGGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000010704-HFE:NM_139004:2
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.079
Domain overlap (PFAM):
C1:
PF0012913=MHC_I=PU(89.8=98.9),PF0765410=C1-set=PU(9.6=9.0)
A:
NA
C2:
PF0012913=MHC_I=PD(4.3=4.3),PF0765410=C1-set=WD(100=90.3),PF060247=DUF912=PU(0.1=0.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
Associated events
Other assemblies
Conservation
Chicken
(galGal4)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCACTACCTCTTCATGGGTGC
R:
TCATGGTGATGTTCTGGGGGT
Band lengths:
347-1927
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Genotype-Tissue Expression Project (GTEx)
- 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)