RnoINT0057521 @ rn6
Intron Retention
Gene
ENSRNOG00000016325 | F2
Description
coagulation factor II [Source:RGD Symbol;Acc:61996]
Coordinates
chr3:80535020-80536041:-
Coord C1 exon
chr3:80535915-80536041
Coord A exon
chr3:80535188-80535914
Coord C2 exon
chr3:80535020-80535187
Length
727 bp
Sequences
Splice sites
5' ss Seq
ATGGTGCGT
5' ss Score
8.27
3' ss Seq
TGCACTCTGCTTCCCCATAGGCA
3' ss Score
11
Exon sequences
Seq C1 exon
ACTGTGGCCTGCGGCCTTTGTTCGAGAAGAAGTCCTTGACAGACAAAACGGAAAAGGAGCTTCTTGATTCTTACATAGATGGGCGCATCGTGGAGGGCTGGGACGCTGAGAAGGGTATCGCCCCATG
Seq A exon
GTGCGTCCTGGACAGATCTACAGGCCCACAGAAGGCCTGCCCCACCCACAGCCGCTGTAGGACCTGGCTCTGCAGCTGACATTAGCAACCACCCTCTAATTTTCCTCAGAGCTACCTCAGCCAGCGTTGCCATGTCTCCCAAGTAGATGAGGCCCAGCAGGCTTAAGTGGCTCATTCTCAGCCACACTGCTTAGTCAGGACTGTATCCAAGTCTGACTCCAGAGCTGTGCTGATCTATGTGAAGTCTACACTGGGAGAGCTCTGGTCCTCTAGGGCAGCCAAGTCAATATGAGATTGAGCCCTGGAGGCAACCCTGTCCCATTATCTTTTTTTCTTTTCTTTTTGTTTTTTGGGGGAGGGGACTCTTATGTAGCAGAGGCTGACCTTGAGGCCCAGCAGGCTTAAGTGGCTCATTCTCAGCCACACTGCTTAGTCAGGACTGTATCCAAGTCTGACTCCAGAGCTGTGCTGATCTATGTGAAGTCTACACTGGGAGAGCTCTGGTCCTCTAGGGCAGCCAAGTCAATATGAGATTGAGCCCTGGAGGCAACCCTGTCCCATTATCTTTTTTTCTTTTCTTTTTGTTTTTTGGGGGAGGGGACTCTTATGTAGCAGAGGCTGACCTTGAACTTGATGCTCCTTGCTTCTACTTCCCAAGGAACACCAGGACTCTTAATCTCTGCTAGGGACTAGGCTCCAGTTCCTAATGCACTCTGCTTCCCCATAG
Seq C2 exon
GCAGGTGATGCTTTTTCGGAAGAGTCCCCAAGAGCTGCTGTGTGGAGCCAGCCTTATCAGTGATCGATGGGTCCTCACTGCTGCCCACTGCATTCTGTACCCACCCTGGGACAAGAACTTCACTGAGAATGACCTCCTGGTGCGCATTGGCAAGCACTCCAGAACCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000016325:ENSRNOT00000022233:9
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF093965=Thrombin_light=PD(57.1=65.1),PF0008921=Trypsin=PU(5.2=30.2)
A:
NA
C2:
PF0008921=Trypsin=FE(22.4=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal4)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTGCGGCCTTTGTTCGAGAAG
R:
CTGGTTCTGGAGTGCTTGCC
Band lengths:
287-1014
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]