BtaINT0061824 @ bosTau6
Intron Retention
Gene
ENSBTAG00000048155 | FCN2
Description
Bos taurus ficolin (collagen/fibrinogen domain containing) 1 (FCN1), mRNA. [Source:RefSeq mRNA;Acc:NM_001010996]
Coordinates
chr11:106822997-106824511:+
Coord C1 exon
chr11:106822997-106823128
Coord A exon
chr11:106823129-106824397
Coord C2 exon
chr11:106824398-106824511
Length
1269 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGA
5' ss Score
9.22
3' ss Seq
AACTCCGCGTTTCTCTGCAGAGG
3' ss Score
8.12
Exon sequences
Seq C1 exon
CGCAAGAGCTCGGGCACAGACCACAGGACATGGAGCTGGGAGGCGCGGCCGGGGCCCTGGGGCCCAGTGGCCCGCTCCTCGTGTGCCTGTGCTTCGGGACCCTCGCTGCCCAGGCTGCAGACACATGTCCAG
Seq A exon
GTGAGATGGACCTGTTTCCGGCCCCTGAATGCTGGAGCTCCCCACTCACTGACCATAGGTAGCATCCAGGGTGAAACCCTCTATCCGCACCTTCTGAAGACTCAGCAGCTCAGCTGCAGCTCAGCTTCATCCTCAGACTAGGAGACAACGAACGGCCCAAGGCCATGTGGGAGGAGCGGGAATTTAATCCGTGTCTGTCTCCCTCTCAAGCCTCGGATTTGCTCCACGGAGCATCCCGTCAGGTCTTGGCTCTGCAGCCAAGAAGGACAATGCCCCCTGCTTCCTGTGTTCTCCTGGACTTTTTAGAAAGGTTCTCTAATCCCAGGGCTCCCACGCTCCCTTGGGGTTTGTTACTGCAGATTTTTGGCTTTCATGCCAGAGTGTGAATTGGCAGGTTTGAGGTATAAGAGTGGGTGGCCTCCCTTCCGATCTGTGCAGGGGGCTGCGCCCACGCCTGGAAAGAGATATCCCTGAGGACAGACCAGTCTCACCGTGAGTTGAGGATGTATTTGTGGGGGAAGCATAAACTTGTTCCCCTGAGAGCATCTCTGGTGGAGACAGATTCCACAGTAGCAGCTCCCGTGTCTGCAGCGTCTCTGTGCCTGGCTGACTCCCACACACTCTAAGTTGTCTCTCGTGAGGATGTTTTAGTTTTGAAATCAACAAAACTAATTTTTCTTTTTTTCCCGAGAAGGAAATGACCCCCTGGTTCCTGTTCTACTGGAATTTGCTCTGTGTTCTTAGATCAAATGCATCTTCTCTCCGGGGGGACCTACAGGGACCCCTTCCAATTCAGGAGCTCTATGGTCACAAGTCCGAGGCCTGGGGTTGAAAATGTTATGCTCTCCCCAACCCCCAAGTCTTATAAATATTTATTGTTGTCATGTAGTGGAACTACATGCCATGAAGTATACCAAGAATCTAAAAATCTGCATTATCTGATCTAATTCTCCCCACAGCCTTATTTTTGTCCCCATTTGGATTCCCAGAACTCAGAGGGGTTGAGTGACTTGCCCAAAGACACACAGCATGGAGGTGGGGGGCTGGGAATCAGGCAGGGTGGATTCCATGCCCAGGCATGGCCTCCCCACTTGACCAGTGCCCACCAGAGGCAGGAAGCTCACTGCCAGGCTGACCCCTCATCTGAGACCAGTGACACCAGCCGGAGCCGAGGGACCAGGTCGCCTTGTGGCAGACACTCTTGGCTTGGGCGGCATGTCGCTGGCCCTGTGATGAGCGCCCTGACCCCAACTCCGCGTTTCTCTGCAG
Seq C2 exon
AGGTGAAGCTGGTGGGTCTGGAGGGCTCCGACAAGCTGTCCATCCTCCGAGGCTGCCCAGGGCTGCCCGGAGCCCCAGGGCTCAAGGGAGAGACGGGTGCCGCTGGACTGAAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000048155:ENSBTAT00000065623:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.050 A=NA C2=0.333
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0139113=Collagen=PU(39.7=59.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CAAGAGCTCGGGCACAGAC
R:
CTTCAGTCCAGCGGCACC
Band lengths:
243-1512
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development