RnoINT0101072 @ rn6
Intron Retention
Gene
ENSRNOG00000000341 | Nid2
Description
nidogen 2 [Source:RGD Symbol;Acc:1311685]
Coordinates
chr15:4898478-4899257:-
Coord C1 exon
chr15:4899128-4899257
Coord A exon
chr15:4898650-4899127
Coord C2 exon
chr15:4898478-4898649
Length
478 bp
Sequences
Splice sites
5' ss Seq
CAGGTTGGC
5' ss Score
5.52
3' ss Seq
TGTCTTACCTTTATTTCCAGGTC
3' ss Score
10.57
Exon sequences
Seq C1 exon
GGCTCCATAGTCGTGGGGATTGACTATGACTGCCGGGAGAGGATGGTCTACTGGACAGACGTTGCCGGGAGGACCATCAGCCGTGCCAGCTTGGAGGCAGGAGCCGAACCCGAGACCATCATTACCTCAG
Seq A exon
GTTGGCAGCTTCTTCCCATGGATACCCCGCGGTACCTTTTATTTTACTGCATTGCCTGTTTCCTCCCGGTTTCTCCTGCTCTCATCTAAAGAGAAGGTTAAATTCTGCGCAGATTATTTCTAAGCTCCACAAGCCTTGTCCATCTGCAAACATGCATTTATATGGGACAAACAGAAAGGTGGTTTTAGGTCGAGATGAACTTCCCACAAAGGAGTGGTTCGCAGTAGGACTTCAGGGCTGGCAGGTTACAGCCTGTCCCTAGCAACACAAATGCCAGGTGCCATCGGGGCAGCAAGGTCCGGCACAGGAGAGACTGGATATGGTTGAAAAGGTGATAGAAGATCCATTCCTCTTAGTCTTCCTTCGTTCTGGGGACGAAGGCCTCTGTGCTCCGATTCTGTAAGCCGTTCAGCAGATACGGAACTTGAGTTCACCTTTTACGCTGGCCAGTGCTCTCCTGTCTTACCTTTATTTCCAG
Seq C2 exon
GTCTGATAAGCCCAGAAGGACTTGCCATCGACCACTTCCGGAGAACGATGTACTGGACAGACAGCGGCCTGGATAAGATAGAGCGGGCTGGACTGGACGGTTCCGAGCGTAAGGTCCTCTTCCACACAGATCTGGTGAATCCACGAGCTATCACTGTGGATCCAATCCGAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000000341:ENSRNOT00000000383:16
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.023 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0005812=Ldl_recept_b=PU(71.4=68.2)
A:
NA
C2:
PF0005812=Ldl_recept_b=PD(26.2=19.0),PF0005812=Ldl_recept_b=WD(100=70.7),PF0005812=Ldl_recept_b=PU(0.1=0.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGCTCCATAGTCGTGGGGATT
R:
TGGATCCACAGTGATAGCTCGT
Band lengths:
294-772
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]