HsaINT0063315 @ hg19
Intron Retention
Gene
ENSG00000085265 | FCN1
Description
ficolin (collagen/fibrinogen domain containing) 1 [Source:HGNC Symbol;Acc:3623]
Coordinates
chr9:137802979-137804461:-
Coord C1 exon
chr9:137804332-137804461
Coord A exon
chr9:137803114-137804331
Coord C2 exon
chr9:137802979-137803113
Length
1218 bp
Sequences
Splice sites
5' ss Seq
AGGGTAGGG
5' ss Score
5.76
3' ss Seq
TTAAAATCTTTTTCCAACAGGAA
3' ss Score
10.4
Exon sequences
Seq C1 exon
GTTTTCCAGCGGAGGATGGATGGCTCTGTGGACTTCTATCGGGACTGGGCCGCATACAAGCAGGGCTTCGGCAGTCAGCTGGGGGAGTTCTGGCTGGGGAATGACAACATCCACGCCCTGACTGCCCAGG
Seq A exon
GTAGGGCCACTGCCGTGGCTCAGGGGTTGGGGGGCCCTGAGGTGCTCCTGCCCCTTAGGCCTGGGCCATCTGCAACATAAGCACCTCTTGGCCCACAGGGGATTGGGCCCTGAGCACACTCAGGTGGCACTGGGACCTCTAAGGGCTGCGTCCCCTGCCGCAGGCTCTGGCAACATCGGGAAGGGAAACGGTTAGAGCCCTGGGCTGAAGGCCTCTTCAGGTCTTGGTCCTACTGGCATCTTAGATCCTGAGAGTGGGAAGCAGGAGAGAGACCACTGGGGCTTGGGGTAGCCTTCCCCCATCTCCAGCTGTTGATCTGCCTCTGAAGCTGGCATCTTAGTCCCATGGAGAGCCCACGCTCGCCTCCTCCAGCCCACGCCTCAGCAGGCCCCCCACAGCCGCACTCACCTGAGTGAGAGGGCCTCCCCCCAACCCTCTGGGGCAGGGGATGAGTTTCACAGCTGGTCCTGAGGCAGTCTGTATAATTGCTGGTCCATTATCCCTGCCCACTGCCCTGTGGCATGATTGAAGGAATCCACTCAGGTGCCTCAAATTCCTGCAAAAGAAACTACAATTAGAGCTTCGCCCACTGCTGTGTTAGTGGCTCACCAACCCTTAGAAGGAGAAGGTACACTTTCAAAATGAAAGAATGCTCCCTTCCACCCAGTGAACTCCAGTGGGGCATGTTCAGTTCTCTGAAATAACGGGAAAGGTGTTTAGAAACAGAAAGCCATCCCTGAGGGCCTGATAGCAACAAGGGATTTTCTGACATTTCCGGTTGATTTTTTTCCTGGATGCCACGTTCAGACATCCCTTAAGAATATATCCATCCCCAGCCGGGCACCGTGGCTCACACCTGTAATCCCAGCATTTTGGGAGGCTGAGGCTGGTGGATCATGAGGTGAAGAGATCGAGACCATCCTGACCAACATGGTGAAACCCCATCTCTACTAAAAATACAAAAAAAAAAAAAAGTAGCTGTGTGTGGTGGCACACACCTGTAATCCCAGCTACTGGGGAGGCTGAGGCAGGAGAATTGCTTGAACCCAGGAGGCGGAGGTTGCAGTGAGCTGAGATGGTGCCATTGCACTCCAGCCTGGGCAACAAGAGCGGAACTCTGTCTCAAAAAAAAAAAAAAAAAAATTACCCATCCCCAGCCCTCATGCCTGGTGACAGAAAGATCTTAAAGGCTGGGGCCTTAAAATCTTTTTCCAACAG
Seq C2 exon
GAAGCAGCGAGCTCCGTGTAGACCTGGTGGACTTTGAGGGCAACCACCAGTTTGCTAAGTACAAATCATTCAAGGTGGCTGACGAGGCAGAGAAGTACAAGCTGGTACTGGGAGCCTTTGTCGGGGGCAGTGCGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000085265-FCN1:NM_002003:7
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.010 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0014713=Fibrinogen_C=FE(20.2=100)
A:
NA
C2:
PF0014713=Fibrinogen_C=FE(21.1=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CGGAGGATGGATGGCTCTGT
R:
GCACTGCCCCCGACAAAG
Band lengths:
254-1472
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)