RnoINT0101073 @ rn6
Intron Retention
Gene
ENSRNOG00000000341 | Nid2
Description
nidogen 2 [Source:RGD Symbol;Acc:1311685]
Coordinates
chr15:4896672-4898649:-
Coord C1 exon
chr15:4898478-4898649
Coord A exon
chr15:4896830-4898477
Coord C2 exon
chr15:4896672-4896829
Length
1648 bp
Sequences
Splice sites
5' ss Seq
AGGGTGAGC
5' ss Score
7.75
3' ss Seq
ATCTTAAAACTTGTCCACAGCAA
3' ss Score
6.13
Exon sequences
Seq C1 exon
GTCTGATAAGCCCAGAAGGACTTGCCATCGACCACTTCCGGAGAACGATGTACTGGACAGACAGCGGCCTGGATAAGATAGAGCGGGCTGGACTGGACGGTTCCGAGCGTAAGGTCCTCTTCCACACAGATCTGGTGAATCCACGAGCTATCACTGTGGATCCAATCCGAGG
Seq A exon
GTGAGCTGGCTTGCGCCCTTCTCTCCTTTCACCTGTGCATCTGTTTTGGAGCCCAAGGCTCTTCTATGTGGCATAGAAAGGTCTAGGTAGACCAGAATAGAAACTCAAATACAGTAGTTCAGATATGTTGAGACGCTGTTTGGTGTCAAGCATTCTTATAGGCAAAATCAGGGTTGTTTTTAAATTTTATTTTGTTTTTAGGAACTTACACTGTATGAGGCAGGACGTAAGATGACATTCAGTAGGAGTGTTAGTTAGCCTGGGATAGAATGTGTCACGCCAAGAATCCAGGCTCCATCATGGGAGGGTCCAGAGCTGCCTGGATCGTGACCATTAGGCAAGGCCTTGGAAAATGATGGGTATACAGGAGGGAGCAGTTTCCTTCAACAGTACCTCGAGCACAGAAACCACAGAGGGGTTTCTATTTGCTTGTTTTTGTTTGTTCTGGATAGAGTGTACAAAAATCCAGATAAAAATGTTCTCTCTGTGACAACTACCAAGGCTGTCACCTGGGGTGTCCCAACCTGGGTCAGGGGTCCCCAGGATTATCAAGACGCAGCTTCCACAAACACAGTTGCAGAGAAGCCCTTCAAGGCAGAAAGATGGTTTGGACTCCAGTTCTTCACATGAAGGTTCCTTATCTGCAGGACTAACTAACCCTTAGGGCTCCTCTTTGATAGTTCTTGGTACTTCGTCTGACAGGGCAGGGACTGAACAGTGGCGCCTTGTTTGGTCATTAGGCTCCAAGATCTAGAATCTAGAGGACAATGTCACTTGAGCCTTCACGGAGGGTTGGCCACTCATCTCCAAGGATACTGCTCACTGAGTGGATCTCAGCCTGCCACAAAGTGGAAACTGCTCTCTCTTCCTGCCACCCACGAGGAGTGATGCCCGCAGCAGAGGAAACTCCGCTTCTCTCCTTTCTGTGGGGTTCTCTGTGGCTCAACCAACAAATAGCTCTAGCTCTCATGGAACTCTCACTGTTCTTGCTCTGTAGTAACCCTGCATCCATGTGTATAACTTCCAGTTAATGAGATCCCGCTTTCTGAGGATGTGTGCATTAGGTCAGAGTGCTTCTGTCCAGGTCATTGTCAGGTATAGGATAGCTAAGTTTCCCTTTCAACACTGTGTTTTCCCAGGAAACTCTCCGTCTATCCCTCGGTCCCACCTAGTTCTTTATAATAGGTCTCATAGCTTCTACCGCAAGACTGTTTTTAACAAATACATTTCTTTGGATTCTAGGCCCAAGCTCTAATTAATTAAATTATTTCCACAAATTAAAGGTTTCTGGGCAACTGCATCAGGTGTGTGAGAAGCAAGGATGTAGACAGTTAGCAGATAATGACTTCCCACACAGTTATGATTGTCAGAAAGCCATGGCAGCCTAAGACAGCATTGTCACTGTGAGTGAGGTATCTAGATGAGGTAATGTCAAGAAACAGCAACCAAGGTAGCGAGCGGTGGCCAGGCAAGGCCAGCGTGATCCAGACTTTCTGAGAAAGAAGGTCGCTGGCCACTGGGCAAAAGGTAGCTTGCTGTATAAAATCCAGCTTCGTATAAAATCCATGCTAAACAAAAACCCCACTACTAATCTGTATCCTCCAACCCCTGCACAGTTGTTCATAACAATCTTAAAACTTGTCCACAG
Seq C2 exon
CAACTTGTACTGGACAGACTGGAATAGAGAAGCTCCTAAAATTGAAACATCATCTTTAGATGGTGAAAACAGAAGAATTCTGATCAACAAAGATATTGGATTACCCAATGGATTGACCTTTGACCCCTTCTCCAAACTTCTCTGCTGGGCAGATGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000000341:ENSRNOT00000000383:17
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=0.019
Domain overlap (PFAM):
C1:
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)
A:
NA
C2:
PF0005812=Ldl_recept_b=WD(100=79.6)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GATAAGCCCAGAAGGACTTGCC
R:
GCCCAGCAGAGAAGTTTGGAG
Band lengths:
318-1966
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]