RnoINT0122309 @ rn6
Intron Retention
Gene
ENSRNOG00000026419 | RGD1560958
Description
similar to RIKEN cDNA 1700063I17 [Source:RGD Symbol;Acc:1560958]
Coordinates
chr1:201904973-201906327:-
Coord C1 exon
chr1:201906165-201906327
Coord A exon
chr1:201905352-201906164
Coord C2 exon
chr1:201904973-201905351
Length
813 bp
Sequences
Splice sites
5' ss Seq
TGGGTAAGA
5' ss Score
8.91
3' ss Seq
TTTGCGTGTCTTTTCTTAAGAAC
3' ss Score
6.44
Exon sequences
Seq C1 exon
TCACTGCTTCTCTACTTCTCTGCCCAGGTATGTTTAGTTCTTTTGACCTCCGGACGATAATCATGATCGTCATTGGTAGTGGGATCCTGGCAGCCATGTTTCTACTGACAGGAGTTGTGCTCTGTCTTTACTCCAAAATAGCCAGGGCTCTGAATCCATCTGG
Seq A exon
GTAAGAATGAACAATAACCCCTCTCATGGGGCACTGGGGCCCTCTGCTGGAGCTGGGTCACTTCTTACTGCCTTTGTAGGGGAAAGTCAAGAGCCACTGTCAGGTTTGAGAGTGAGGGCAAGTGGACACAGAAGTTTGAGGGTTCTCCTAGCTTGGGGTTGTGAGCCCCTAAGTCAACTGCTCTCAGCCTGGACAGCATAGGTGCCAGCATCACTTTTCTGTCACTTAGACACGGGAGTGAACCTTCAGTTACTTATCAGAGTCCTGCCAGACATCCTTTCTGTCCTCAGTACTGTAGACTGGAGAAGCCAGAGGATGCCTTGGGAATGGGCTGTCTCCTACTCACACAGAGCTTGGCCAGAGTGAGCTCTTCTCTGCTCACTGGGAAGCTCACCTGTTCCCACGCTCATTGGGAAGAGTGAAGTGGGCCAAGAGAATAGAGTCCATGGAGGACAGCTGACAGGGATGTAGGTCAGACAAGAGATGGTGTCCCTTACTAGGGACTTAGATTGTAGGGGCCAGAGCTGAGCCCAGCCAACTGCTGTGCCTTCTCCATCATCTCCACACTTCCTGGGCCTGTAGCAGCCACTGGGGTACAATTCACTCTCCTTCACTTATAATGGTGTCCTGGTCTCACACGCATAGCAACTGTAGGAGAGGAAAAGATGGGAAAGGAGCAGAGAGCTTTAACCCAAGGCTGGTGTCACATGTATGATGGGCTCCCACCCTGGACTTTCTCACATAGCCCTCATCGTTGTAAGAAGCTCAGTGGGAAGGAAAACTCTAAACTTGTTTTGCGTGTCTTTTCTTAAG
Seq C2 exon
AACTGGAAAGGAGTTAGACGATCAACTCTGTTCTGATCCGTGCAAGACCACCCAGGATCAGATCATCCGGGTCAACAGCCTCAATGCTGACACTTGCCGTCCCTTCCACGGCAGCACAATTGGTCTTGAGAACTGCCAGCCCCTCCAGTGTTTCAGTGCATGTGGCACGTATGAAGGCGCTAACTCCCTGACACCTTGCCTTTGTAACACAAAGGAAGGACTCTGACACGACACTGGCGGATAAAAGGAAATCTTCACCATCAGTATTTCAATTTCTTAGTACAATATTTTCTTACTCAAGCCAATTTCTATTGTGTTATAAATGTCGTGTACTATCTAACATGGTATTTATGTACTTTTGTATAAATGTACAATAATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000026419:ENSRNOT00000036625:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF151931=FAM24=PU(13.8=26.7)
A:
NA
C2:
PF151931=FAM24=PD(85.1=97.4)
Main Inclusion 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:
CATTGGTAGTGGGATCCTGGC
R:
TCCTTTTATCCGCCAGTGTCG
Band lengths:
342-1155
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]