HsaINT0063317 @ hg19
Intron Retention
Gene
ENSG00000160339 | FCN2
Description
ficolin (collagen/fibrinogen domain containing lectin) 2 (hucolin) [Source:HGNC Symbol;Acc:3624]
Coordinates
chr9:137772658-137774485:+
Coord C1 exon
chr9:137772658-137772767
Coord A exon
chr9:137772768-137774371
Coord C2 exon
chr9:137774372-137774485
Length
1604 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGG
5' ss Score
11.08
3' ss Seq
CCACCTGTGTTTTTCTGCAGAGG
3' ss Score
10.48
Exon sequences
Seq C1 exon
ACCAGAAGAGATGGAGCTGGACAGAGCTGTGGGGGTCCTGGGCGCTGCCACCCTGCTGCTCTCTTTCCTGGGCATGGCCTGGGCTCTCCAGGCGGCAGACACCTGTCCAG
Seq A exon
GTAAGGGCACTCCAGGGCCTCCTCCTGGAAACTTCTCGTCCCTGAAAGCTGGCAGCTTCGTGATTGGTGGCTTCCTGGCTTCCAGGCCTTGCACCAGGCCGTGTGGAGCATCGTCTAACGAGACAGCAGCTCTGCATGCCTCATCTTATGTGAACAAACGCAGAGGCCCCGAATGGATGTGGCATCTCAGAGACGGAGCTTCCTCTGCTTGCCCTCCCATAATGGAAACCGAGGCAGGTTTCCAGTCTCCCTGGGCCACATGTCCCCCTCTAAGCGTAAAAAGCGTAGTCATGGTGTTGTGTGGGGAGGTGAGGCTTGTGGTGCCAGCTGGGTAGACACCAGTCAGATATTCTGCCATGGTCGCCATCACAGAGAGACAGGGTGTGAGGTGGGGATAAGCACCCGGAAAGACAGGGTGTCAGGCGGGGATGAGCACTGCAGGACCTTTCCATCCAGGACCTGCTGGGCTCTGGAGATGGCAGTTCCCATGGTGTCCCTGATGCGGCACAATAAGGGTGGCATTGTCCCCGTGAGTTCTGGACCTCCTTCGGGGCTCCCGAGGGGACACTCGGGTGCCAAACCATGGGCTCCGGCGCATGCGAGGGCAGGTTGAAAATGCAGGTTCTGGAGTCAGGTCCTGACTCCGTCTACCCGGGGCTGGGATGCAGGGTCAGGAATTTGTGATGCTCCTGATGCTTGCAGAGATTCGTGTCAGGATTTCTGGAATGCATGTGAGACACAGAGCTCTGCGGTGTGCTGTGACTAGCATCGCATTCAAGGAGCAATCCGTGGCGTGAAGTGTGACACAGGCCAGGAACAGCGGGGATTCGCTTGGAAACTCCTAGTGGCTCGTTGTGGAGTGGTGGGGTTAGGGTGGCATTATTTTCTTCCTTAAATACTTCTAGAGTTTCTAAATGATCAAATAATAGCACGTGTTATTTTTGTAACACACTCACTTGAATTTGAGTTATCTAATTAAAAACAACAAGCTGCATTCCAGCTCTAGTTTCGCACCAACTTGTTCAGTGTCCTTGAAGGACGCCTCCCTCTGTGGAGGAACAAGGTGGACCCACAGGAGCCCATCCACTCTCAGATCTGCTCCAAGATCAGGCGTGGGAGTTGCAATGGTAGCCTCTCTCCCTGTGTCCTTCTCACCCGATATTGATTACAATGATATGATAGATGAGAACAGACGAGATTAGGATGCTGTCTTAAATGGTAGGAGCTGAAATGAACCTGCACCCCTCGGTAGGTAAGGGAACAGAGGCTCAGAGGGGTTAAGGGACTTGTTTCAGGACACACAGTACTGAGGAAGTAAGGTTTGCCTTCAGGCAGGGTAGCCTCCAAGGCCAGGGTTCTGCCCCAAATCACCTTTCTGCCTGACCAGTGCCCAAGAGGTGAGGACAGACCAAGTGCCCACCAGGGCAGGAAAACCTCCCTTCCAGGTGACCCTCCAGCTGAGGGAGGTGGCTGTGGCTATAGCCATCTGCCCAGTCCTGATGTCACCAAGATGGCAGATGCCTTTCAGTTGAGTGGTATATCTATGGCTCAGTGGAGTCTTCAGGCCCAGGTGACACTGAGTGGCCACCTGTGTTTTTCTGCAG
Seq C2 exon
AGGTGAAGATGGTGGGCCTGGAGGGCTCTGACAAGCTCACCATTCTCCGAGGCTGTCCGGGGCTGCCTGGGGCCCCTGGGCCCAAGGGAGAGGCAGGCACCAATGGAAAGAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000160339-FCN2:NM_004108:1
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.024 A=NA C2=0.590
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0139113=Collagen=PU(55.0=84.6)
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:
CAGAAGAGATGGAGCTGGACA
R:
CTCTCTTTCCATTGGTGCCTGC
Band lengths:
222-1826
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)