HsaINT0063317 @ hg38
Intron Retention
Gene
ENSG00000160339 | FCN2
Description
ficolin 2 [Source:HGNC Symbol;Acc:HGNC:3624]
Coordinates
chr9:134880812-134882639:+
Coord C1 exon
chr9:134880812-134880921
Coord A exon
chr9:134880922-134882525
Coord C2 exon
chr9:134882526-134882639
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:ENST00000291744:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.039 A=NA C2=0.590
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PU(18.4=20.6)
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