HsaINT0063316 @ hg19
Intron Retention
Gene
ENSG00000085265 | FCN1
Description
ficolin (collagen/fibrinogen domain containing) 1 [Source:HGNC Symbol;Acc:3623]
Coordinates
chr9:137801431-137803113:-
Coord C1 exon
chr9:137802979-137803113
Coord A exon
chr9:137801892-137802978
Coord C2 exon
chr9:137801431-137801891
Length
1087 bp
Sequences
Splice sites
5' ss Seq
CGGGTGAGT
5' ss Score
9.89
3' ss Seq
CCCACATTTTCTGTGAGCAGGTA
3' ss Score
6.93
Exon sequences
Seq C1 exon
GAAGCAGCGAGCTCCGTGTAGACCTGGTGGACTTTGAGGGCAACCACCAGTTTGCTAAGTACAAATCATTCAAGGTGGCTGACGAGGCAGAGAAGTACAAGCTGGTACTGGGAGCCTTTGTCGGGGGCAGTGCGG
Seq A exon
GTGAGTGTCTGCTTGGGGCTGGTGGCCTGAGTGGGGCTTGGAAAGCAGAGAGAACCTGGCTCTGTCTCCCCTGGTGACCTTGGGCCCTCCTCTCTCTGAATCCCATTTCTCCATCTATGAAGCAGACACTAGCATTTGTGTCTCTGTACAGCGTGGGGCTCACAGGACATAGCGGCTGGTATTCCTAAGGCTATGTCTGCCGCACAGTGAGCTGCCTGGGCAGGGCTGAGACGACCCACCAGCATCACTGCTGAAACCTGGAAGACGTCGTCCTTTTCTCATGGGTGCCTTGGAGCTGTTTCCCAAACTGTGCTCCATGGAACACCAGCCTTGTGGGACATTCTTTACCAAAAGGAGTCTCTGGCTACACGATCTGGGGAGGCATTTCCTACAGGGCGTCTGCTTAGGGAATTCCCAGTGCACATCGTTCGTGAAAGGCACTGAGAATTGCTGCAGCTGGAAGTCTGTGTAACTAACTGCTCCATGGAGCAAGGCAGTCCCAGGGGAGCCTTGGAAATGACAGCCTTGGAGTCTGTGCAGTCCTTTCACAGGCACGATCTCACGCATGACCTCCAAGGAAGGCAGCAGGGCAGGGAAGGTCACCCCCATTTTGCAGGTGGTAAAACCGAGGCTCAGGGGGTGACATTTCTCAGCTATAGGAGCCAGGGATGAGCTTCCGGCTCAGGGCTTGAGATAGAGGAGAAGCCCCCAGGTGAGGGCTGTCCTGAACCTACCAAGGGCCACCAGGGGACGTGGGGAGAGACCGGAAGGAGCGGCGCAGGCTGGAGGAGGGAGGTCATTCCAGGAGAGAGCAGGAGGCCTGACAGTTTGCGGGAGCCCTGGAGGAAACAGGTGGTTGCTGGAGCAGGGGCCTCAGGTTGTGGAGAGAGATTTCCAGACCAGGTTGCCAGAGGTTGCCTCCTGCTTCCCCTTCCTCCAAGGCCTGGGTGGGTCATTTGTGCACCTGTAGCTCGGCTCATGCGTCGCTAAAGTGAGGTTGGCTCTGCTCAGAGGCAGGATGTGGTGAGGGTCTCACAGTGGCAGGGCTTTTTCCAGCATCTGCAAACCCCACATTTTCTGTGAGCAG
Seq C2 exon
GTAATTCTCTAACGGGCCACAACAACAACTTCTTCTCCACCAAAGACCAAGACAATGATGTGAGTTCTTCGAATTGTGCTGAGAAGTTCCAAGGAGCCTGGTGGTACGCCGACTGTCATGCTTCAAACCTCAATGGTCTCTACCTCATGGGACCCCATGAGAGCTATGCCAATGGTATCAACTGGAGTGCGGCGAAGGGGTACAAATATAGCTACAAGGTGTCAGAGATGAAGGTGCGGCCCGCCTAGACGGGCCAGGACCCCTCCACATGCACCTGCTAGTGGGGAGGCCACACCCACAAGCGCTGCGTCGTGGAAGTCACCCCATTTCCCCAGCCAGACACACTCCCATGACGCCCACAGCTGCCCCTTTGCCCCCAGCTCAGTCAAGCCGCCACATGCCCACAACCTCACCAGAGGGAGAATTATGTTTCTAAATATGTTTACTTTGGGACAGAAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000085265-FCN1:NM_002003:8
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.012
Domain overlap (PFAM):
C1:
PF0014713=Fibrinogen_C=FE(21.1=100)
A:
NA
C2:
PF0014713=Fibrinogen_C=PD(38.0=97.6)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CATTCAAGGTGGCTGACGAGG
R:
CACTAGCAGGTGCATGTGGAG
Band lengths:
352-1439
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)