MmuINT0063793 @ mm9
Intron Retention
Gene
ENSMUSG00000026835 | Fcnb
Description
ficolin B [Source:MGI Symbol;Acc:MGI:1341158]
Coordinates
chr2:27938426-27940398:-
Coord C1 exon
chr2:27940311-27940398
Coord A exon
chr2:27938540-27940310
Coord C2 exon
chr2:27938426-27938539
Length
1771 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGA
5' ss Score
9.22
3' ss Seq
ATGCTTGTGTTGTTCTGCAGAAC
3' ss Score
9.66
Exon sequences
Seq C1 exon
GTTGGGAGCCGACCAGTTGCCATGGCCCTGGGATCTGCTGCACTATTCGTCTTGACCCTGACTGTCCATGCGGCTGGCACATGCCCAG
Seq A exon
GTGAGAAGGACTCTAAGTCCCTGAGAGCAGGTTAACTACCCACTCAGTGCCTTCTAGTGTCCCTGTGCCCACCTCTTCTGAGAAGCTCCTGTCAGCTCAGTGTCACCCTCTGAGGACAGACTCTGAGCAGCTAGCACTGGCTCAGGTGGAGACTCTGTGGGCCTGTGATGCTGACCCTGAGGCCTTCAGCCTGACCCTAGGAACTTCACAGACGAAGATGACACCTATGTTTTCCACCTTCTTAGGGACTTTGGAGAGAGATGCTAGGATCCTCTACTTTGTGGCTGCCACATCCCCTTGGTAACTTTGGTAAAGATGCATCCCAGAGTCTCCTGGTACATATGGGCAAGGATTTGGGGTTGGAGAATATTCCTGATCAGCTCTGCTCTGATATCCCCTGGGGATATTACTCCTAAGCACAGGGCAACTGTCTCAAGTGGTGACATGGTTAGAGAAGGGACTAAAACAGCAAGACACAGCCCACCCACTGCAGGGGAAAGAGCCCAGCAGGGAAACTGGACAGGGAAACACCTACGAGGTCTCAACCCTACACAAAGAGCTCCAGGCAGCTAAGGAATGCTGGGAGCCAGAGAGGTGGTCCTTTCCATCAATTGATTGTCTAGTGCTGTACTGTGAGCCCTGTAAACATACTCACAAGTAACATTATATGGGCTCAACAGGTTATATTTGGGAATTTATATGTATATAAATATACATATATTATATGTGTATGAATAAACAATAACAATTTATGAAAAACAAGGCCATGAATTTGAGCATGGAGTTTGGGAGGATTTGGAGGATTTGGAGAAAGGGAAGGGAGAGTTGTCATAATTATAATCCCCCCAAACCAAACCAAATAAAAAACAAAAACAAAAACCTGGTAAGAAGCATACCAAAGATAGTTCTCTGGTCTCCAAAGTGAACCCTGCCCTAGTCTGATATTTCAAGTGTTCTTCTGCAGAGATATGAATTTCACAAATTAACAATATTTTACAAAATGTAGCAACTTCTGTTGGGTTCCAGCTGTGCCTTGGAGCATGCATGTCCCCTCCCCTAGAAGACCTCTTGTAGTCCATGGTCAACCCTCATGAGTTGGAGGAAAAAAAAAATGTTACATTAACTCAGTTTCCTAGCAAGATTGACTCTTGTTTTTCCATAACCATTTCCAAAGCCCTCTCTAAATTCTAGAATGACGGCAAGACTTTAATTTTCATTCTCAAGTTGAGTCCTTGCTACAGCCCTATTCTCTAAGAAAACATATTTTTAAGTGTGTGTGGCTGTTTTGCCTGTATGTATGTGTGTGCACCATTTGCATGCCTGGTATCTGCAGAAGCCAGAAGAGGGCATCAGATCCTCTGGAACTGGAGTTACAGACAGTTGTAAGGTACCATGTGGGTGCTGGGGATCAAACCTGCAACCTCTGCAGAAGTAAGTGCTCTTAACCCCTGAGCTTTAGTTCCTACAACTGAGTGGGGCTGAGGAGGCAGACACGGGGGCGGGGTTTGGGTGATCTGTCAAATGACAGCACTGGTAACTGGAGAGCTCATTCCCAAGCAGTCCCACTCCCACCGGATACAGATCTGTCCTGCATGCCCCTCCCATCTGCCCAGCTCCCCAAGGCAATGATGGGCCCATCTCCATCACAGGAAGACCTGACTTCTGCCGATTCTGTCCACAGCCCTCTGCCTGACATGGCTGAGCTGGCAGTTGCTCTCAAGGCAGGTGGCATATGATGCTAGTACCAACTGATGCTTGTGTTGTTCTGCAG
Seq C2 exon
AACTGAAGGTCCTAGATCTGGAAGGCTACAAGCAGCTCACCATCCTTCAAGGTTGCCCTGGCTTGCCTGGAGCTGCAGGGCCCAAGGGAGAGGCAGGTGCCAAAGGAGATAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026835-Fcnb:NM_010190:1
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=0.000 A=NA C2=0.393
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0139113=Collagen=PU(36.1=56.4)
Main Inclusion Isoform:
NA
Other Inclusion 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:
GTTGGGAGCCGACCAGTTG
R:
TCTATCTCCTTTGGCACCTGC
Band lengths:
201-1972
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types
Other AS DBs: