RnoINT0060319 @ rn6
Intron Retention
Gene
ENSRNOG00000009342 | Fcnb
Description
ficolin B [Source:RGD Symbol;Acc:621222]
Coordinates
chr3:6624208-6626284:-
Coord C1 exon
chr3:6626086-6626284
Coord A exon
chr3:6624322-6626085
Coord C2 exon
chr3:6624208-6624321
Length
1764 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGA
5' ss Score
9.22
3' ss Seq
ATGCTTGTGCTGTTCTGCAGAGG
3' ss Score
7.81
Exon sequences
Seq C1 exon
CCAGGAAGTGACTGTCTCCTGGGGATTGGAGCCCAAGATGGGGATCTAGGGTTCCTGCCTTATAAGAGCAGGGTACCCCTGCAAAGCTATTGAGGGGCTGCGAGCTGAGCAGTTGCCATGGTCCTGGGATCTGCTGCACTATTCGTCTTGAGCCTGTGTGTCACTGAGCTGACCCTCCATGCTGCTGACACCTGCCCAG
Seq A exon
GTGAGACACACTCAGTCCCTGAGAGCAGGTAACTGCCCACTCAACACCCATCTAGTGTTCCTGTGCCCACCTCACCTGAGAAGCTCCTGTCAGCTCAGTGTCACCCTCTAAGGACAGACTCTGAGTGACCAGCACCAGGTCAGGTGGAGACTCTGTGGATCTGTGGCTGCCAACCCCGAGGCCTTCAGACTGACCTCAGAAACTTTACAGATGACGATGACGCCGGTGTATCCATCTTCTTAGGGATGTTGGAGAGCGATACTAGGGTCCTCTAATCTGTGGCTGCCACAAGCCCTTGGTAACTTTGGTACAGATGCACCCCGGAGTCTGCTGGTACACATAGAGAAAGATTTGGGGTTGGAGAATGTTCCTGGGCAGCTCTGTCCTCCCTGGGGATATTGCTCCTAAGCACAGGATGGCTGTCTCGAGTGGTGGCATGGTTAGAGAAGGGACTCAGACAGCAAGGCACAGCCCACCACAGGGAAGGAGCCCAGCAGGGAGACTGGACAGGGAAAAGCCTACGAGGCCTCAACCCTACACAAAGAACTCCAGGCAACTAAGGAATGCTGGGAGCAGGAGGGGTCGTACTTCCTACTAATTGATGTCGGCTCTGGGGACACACACACCAGTAACATTATATAGACTCAATGGGTTGTTTGGGAATTTATATGTATATAAATATATTATATGTACATATGTATATATACACATATATATCATATAAATATACATATATGTGTATGCATATACGATAATAATTTGTGAAAAATGAGGCCATGAATTTGATCATGGGAAGGGGATTTGGGAGGACTTGGAGAGAGGAAAGATGTTGTAATTATAATCTAAAGCAAACAAACAACAAGCAAACAAAACAAAACCCGGCAAGAAGCATCCAAAGTCAGTTCTCTGGTCTTTGAGATGAGCCCTGACCTGTTTTGATATCTCCAGAGTTCTGCCAAGGTATGCACTTTGCAAGTCAGCACATTAACAATACTTTACAAACTGTAGCAAGTTCTGTTTGGTTCCAGCTGCGCCTTGGGGCATGCATGTCCCCTCCCCTAGAAGACCTCTTTTAGTCATTGCATGACCAACCCTCAAGTGTTGGAAGGGGAAAAAGTTACATTAACTCAATTTCCTAGCAAGATTGACTACTGTTCTTCTGTGACCATTTCCAAAGCTCTCTCTAAATTCTAGAATGATGGCAAAACTTTAGTTTTCATTCTCAAACTGAGTCCTTGCTACAGCCCTGAAAACATAGTTTTGAGTGTGTGTGGCTGTTTTGCCTATATGTATGTCTGTGCACCGGGTGTATGCCTGGTGTCTGCAGAATCCAGAAGAACGCACCATTTCCTCTAGACCTGGAGTTACAGACAGGTGTGAGGTACCACGTGGGTGCTGAGAATCACACCTGGGTCCTTTGCAAACCTCTGAGCCATCTCTCTAGTACCTACAACCACTTGGGGCAGAGGAGACAGACACAGGGGGCTTGGGTGATCAGCTCTGGTAACCGAAGGGCTCATTCTCACGCAGTCCCCGGACACCAGACATAGATCTATGCTGCATCCCCCTCCCGTCTGCCCAGCTTCCCAGGACAATGGTGGACCTCATCTCCAGCAAAGGAAGACCTGACTTCTGCCCCACCTCTTCAGAGGAGGCTGGCGATTCTGTCCTCAGCCCTCTGTCAGACATGGCTGAGCTGGCAGTTGCCCTCAGGGCAGGCGTCATATAATGCTAATACCAACTGATGCTTGTGCTGTTCTGCAG
Seq C2 exon
AGGTGAAGGTCCTGGATCTGGAGGGCTCCAACAAACTCACCATCCTTCAAGGCTGCCCTGGCTTGCCTGGAGCCCTGGGGCCCAAGGGAGAGGCTGGTGCCAAAGGAGATAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000009342:ENSRNOT00000012494:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.333
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0139113=Collagen=PU(37.7=59.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGGAAGTGACTGTCTCCTGGG
R:
TCTATCTCCTTTGGCACCAGC
Band lengths:
310-2074
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]