RnoINT0117105 @ rn6
Intron Retention
Gene
ENSRNOG00000021493 | Prdm9
Description
PR/SET domain 9 [Source:RGD Symbol;Acc:1305247]
Coordinates
chr1:57553962-57555048:-
Coord C1 exon
chr1:57554944-57555048
Coord A exon
chr1:57554073-57554943
Coord C2 exon
chr1:57553962-57554072
Length
871 bp
Sequences
Splice sites
5' ss Seq
CCCGTGAGA
5' ss Score
3.61
3' ss Seq
AGTTAGTTCTTCATCCATAGGAC
3' ss Score
6.55
Exon sequences
Seq C1 exon
CTCCTCAGAAGGACGAACGGCGGCGGTGGCTGCAGAGCCACAGGATTCTGGACCATGAGTACAGGCGAAACCTTCAAGACCAGCGAGACTTTCTAGGCTCAGCCC
Seq A exon
GTGAGACCCCATATCCCCTAAATTAGATTCGGACCCCCTCAGCGTGACACAAGTGCGCGCTCACACGCACACGCCCCGTCACCTCAGCTTCTCCAAGTGCCCTTTGGCTTAGGTCCCAAATGCACCTGTGCAGAACCAACCCACCCTCTGCCTGAGGAACCTGGTAGCTCGCCTCAGAGACTAAATTTCCAGACAGGAAACCTGGACTCTTAGCGTAGAGACCCTCCTAAGTTCCAGAGACTCTAAACGCCCTTAGACTCGAGGACCTGTCACTCCTTAAGATAGGCTTCCAAGGTCCTAAATGCTCTCATCCAGCAGGACCCTAACTATCTTCAACATGACAAACCCCAAATCTTCTTGACATAATCGTCAAATCTTGTCAGTTTGCAAGCCCCCAAACCTTATTTCACAGCCTGAAAGACTCCCCTAGCCTACAAACCCAATTCCCTTAATCTGATGAACCCCAATCCTCAGCCCGAGGTTTCCTAAATTAAAATCTCAGCCAGAGGGTCCCTAAATTTTCACCAGAGGGACTTCAATCCCGTATACTCAGGATTCCCGAATCCGTCTACCTGAAAACATCTCTCAGACCCAAGTGCTCTGCCCTGACTGACTCCTTGGGCCAGATGAAGAGAAGTGGAGGTGGTGGCGGGGGGGGGGTGTGTGGACCCCAATTGGCGGGAAGAATCTTTCTTCACTTGCTGTTGCAGGCCCTGACCCGGATGTAGGGTCGGTGCCTAGGTTTAGGGGTCAGTCCAGAATCGGAGTCTGAAGAAGCCGCTGTGATGGCTGCATGGATTCCCAGCCTCCAGCTCCTTCCCATGTGCTGGTGGGCATCCCTGCTCGCCCTTAGTTAGTTCTTCATCCATAG
Seq C2 exon
GACCATAGGACCCTGATCTTCTCCAGGGAAATGTCCCGCACCATGAACACCAACAAGCCGGAAGAGAATAGTACTGAAGGAGATGCAGGGAAACTCGAGTGGAAACCCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000021493:ENSRNOT00000066370:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
5' UTR
No structure available
Features
Disorder rate (Iupred):
C1=NA A=NA C2=0.889
Domain overlap (PFAM):
C1:
NA
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Mouse
(mm9)
No conservation detected
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCTCAGAAGGACGAACGGC
R:
CTTGGGTTTCCACTCGAGTTTC
Band lengths:
214-1085
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]