HsaINT0063309 @ hg19
Intron Retention
Gene
ENSG00000085265 | FCN1
Description
ficolin (collagen/fibrinogen domain containing) 1 [Source:HGNC Symbol;Acc:3623]
Coordinates
chr9:137808194-137809806:-
Coord C1 exon
chr9:137809615-137809806
Coord A exon
chr9:137808308-137809614
Coord C2 exon
chr9:137808194-137808307
Length
1307 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGA
5' ss Score
9.22
3' ss Seq
GCACCTGTGTTTCTCTGCAGAGG
3' ss Score
10.11
Exon sequences
Seq C1 exon
GGAGTTGAGAAACTGTGGCACAAGGCGAGAGCTGGTTTCCTCTGCCCTGTTAGAGCTGGGGGACTCTTCAGAGTCAAAGGCCAGAGAGCATGGAGCTGAGTGGAGCCACCATGGCCCGGGGGCTCGCTGTCCTGCTAGTCTTGTTCCTGCATATCAAGAACCTGCCTGCCCAGGCTGCGGACACATGTCCAG
Seq A exon
GTGAGACAGACCTGGGTTTTCTGGTCCCTAAAAGCTGGTAACAACCCCACTCACTGACACTCGGGTGTCCCAGGCAAAACCTTTTATGCACATCTTCCTGTGAAGATGCCCAACAGATCTGTTTTATCCTCAGGCAAGGACATGGAGGCTCAGGGCAGCTGAGGCATTGCCCAGGGTCATGGAGGGATAGGGGAGGGATGTCACCAGGTCTGTCTGCCTCGAAAGCCCAGGATTTGCCCATTGGAGCTTCATAGGTGGGTCTGGAATCTGTCACTGAGAAGGAAGAAAATACTGTTGACTTTATCTTCTTACGGGCTTACCAGGGAGGCACTCTAAGACCCTCTAATACGGTGGCTGCCACACGGACTTGGGGGGTTTGTTAAAAAGGCAGATTTCTGGCTCTCCTCCAAGAGAGTCGGAATCAGTTGATAGGGACAAGGGTTTGAACGGTGGTAAGGTGTTTCCCTCACTGATTCAGGAGCAGGTGGTTCTGTGACGCTCAGCAAGAGACTGCTCCTAAGGACGGCCTGGTGCCCCTGGCTGATAACATATTTATGAAGGAAACATAAATAGTAAATTACAGCCTGCTCTAGTGGAAGGAGGACTGGAAACACAGAAAGGAAATACCCCAAAAATGGCAGTGCCATGTCTCCGGTGAGAGCACTGCTCCGTTCCATGGTCTCTAAGAGCGCCCTTAGCAGGGCGTGTAGATTTTGTAATGAACAAAATGAAAAATATTTTTTCAAAGAAGTAAACAACTTTGGTTTGGCTGCAGCTGTGCCACACCTGGCTCTGTGTCCTTGGACCCCACACTGCCCCTCTCCAGAGGACCTAGAAAGCCCCTTCCAGCCCAGTAATTCTACAACCACATTCCCAAGGTCTGGGAGGGAAAATGCTTTGTCAGCCCCAATTCCCCAAGTTTCTTAGAAATATTGATTGTCATTAGTTATTGAAAGTGCCCGCTGTTTATTAAGCTCTTTCTAAATGCCATAAATTACAATAAGAGATTTAAAATGCACATTCTTTAACCAAATCCTGGCCGCAACCTTGTTATTATCCCCGCTTGGCAGCCCAGGGCACAAAGCTCAGAGGAGTTAAGTTACTTGCTGCAGGACACACAGCACTGAGGAGATGGGGCTCCCCTAGGTCGGGGTGGCCTCCAAAGCCAGAGCTCTGCCCCCCATCACATCTCCGCCTCACCAGTGCCTGAGGGGTGAGGACAGACCAAGGCCCCAGCAGAGCAGAAAACCTCACTTCCCAGCCACTGTTGGGCCAGGCACTGAGTGGGCACCTGTGTTTCTCTGCAG
Seq C2 exon
AGGTGAAGGTGGTGGGCCTGGAGGGCTCTGACAAGCTCACCATTCTCCGAGGCTGCCCGGGGCTGCCCGGGGCCCCAGGGCCAAAGGGAGAGGCAGGTGTCATTGGAGAGAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000085265-FCN1:NM_002003:1
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.029 A=NA C2=0.419
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0139113=Collagen=PU(37.7=59.0)
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:
GGAGTTGAGAAACTGTGGCACA
R:
TCTCTCCAATGACACCTGCCT
Band lengths:
303-1610
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)