BtaINT0061828 @ bosTau6
Intron Retention
Gene
ENSBTAG00000048155 | FCN2
Description
Bos taurus ficolin (collagen/fibrinogen domain containing) 1 (FCN1), mRNA. [Source:RefSeq mRNA;Acc:NM_001010996]
Coordinates
chr11:106827861-106828302:+
Coord C1 exon
chr11:106827861-106828073
Coord A exon
chr11:106828074-106828269
Coord C2 exon
chr11:106828270-106828302
Length
196 bp
Sequences
Splice sites
5' ss Seq
CCGGTACGG
5' ss Score
9.77
3' ss Seq
TGTCCTCTCTCCCACAACAGGAG
3' ss Score
10.25
Exon sequences
Seq C1 exon
TCCTCAGGGTCACAAAGAGTCGGACACGAGTGAGCACTCACAAGACACCGTCACATGCTTTGACGACAAGTACAAAGTGCGCTGGTTGGGGCCAAGCATACCCCAAACGCCCCCAGGACTTTCCACGACCAGAGGCTCTGATGGTGGAAAGTGACGGGCCCGGAGGAGCTGACCCTCAGTGCCGGGAGCCTCAAAGCCCAGGAGAGGCGGCCG
Seq A exon
GTACGGTGGTCCAGCCAGTTCCCCCAGCGAGCCCCGCGGCTGAGTCTCGGAACCGCTGCCCAGGGCTGGGGGCTGTCCGTCCTGAAGAGCTGGGCGACGGTTTCCACTGTCAGTGCCGTGTTCATGGAGCAGAGGGGCTGATGGGCCCAGGGCTGTTTCCAGACGTGTGACACGCATGTCCTCTCTCCCACAACAG
Seq C2 exon
GAGAGTCGGGGCAGCTTCATTCATGTGCCACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000048155:ENSBTAT00000065623:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.972 A=NA C2=0.625
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PD(1.7=1.4)
A:
NA
C2:
PF0139113=Collagen=PD(8.2=41.7),PF0014713=Fibrinogen_C=PU(0.1=0.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTCAGGGTCACAAAGAGTCGG
R:
GTGGCACATGAATGAAGCTGC
Band lengths:
242-438
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development