RnoINT0141952 @ rn6
Intron Retention
Gene
ENSRNOG00000010078 | Spag1
Description
sperm associated antigen 1 [Source:RGD Symbol;Acc:1310702]
Coordinates
chr7:75051898-75053386:+
Coord C1 exon
chr7:75051898-75052041
Coord A exon
chr7:75052042-75053041
Coord C2 exon
chr7:75053042-75053386
Length
1000 bp
Sequences
Splice sites
5' ss Seq
GAGGTATTT
5' ss Score
7.63
3' ss Seq
CTGTAATTTCTGTTGGGAAGGTG
3' ss Score
3.34
Exon sequences
Seq C1 exon
AATTGCCGGGAAAGAGTGGCGGATCCCAGTCAGGTTGTCCTCCTAAGCCCAGATTCCAGTGAAGCAGCCAGGCACCTGGACACTAAGAATGACACAGCACCTCCCAGCAGAGAGAGGGAGAGGAGGAGAATTGAAATCCAAGAG
Seq A exon
GTATTTGTATTTCATACTCTTGAAGGCACCCTGCTGAGACTATACACAGAATCTAAGGTTATCTCCTGTGAATTCAGGACCTCTTTTTTTTTTTTTTAATCCTGATTGCCAATGAAAACAATTGTGAAGTGACCCAGTTGTGAAGACAGAATTTGCCCTTTGATGCATCATTGGCCACCATGTTTCTCAGCAGGGGCCATGGATAGGGGTGTCCCAGGGTGGGGGATGTTGTTCTCACTGCCCTGGAGCCATAGGCCATTGGCGTCCCTCGAAGTAGACATGCAGAGATGAACAGGACTTATCTTCAGCCCTGCCAACCCTGGCGGAAGCTCTGCTCTTCCGCTGCTGACTTTCCTTTTTTATTGTTGTTGTTTTGGTCACTCAAAGAGATCTGCCTGTCTCTGCCTCCCAAGTGCTGGGATTGAAGGCACACACCATCCCTCCGGGGGTCCTCATCTCTCTCTCTTTTTTTTTTTTTTTTAACTCTTCAATAATCTGGGCTTCTCCAAGACAGCCTGGCCATCACATTTACCTCTGTGATTCCTAGAAAGCCACATGGTTTAATGTCAAGACATAAATTCCTATACACCCGTGAATGCTAACTTTCTATTTACAGTCTGACATTTTGACTAAGAGGCAACAGGTCGGAAGCCATGATTTTTTTTCCCCTTTAAGTAAGAAAAGAGTGTTTTAAGAGACACAAAAAATACAGGATCATTTGTTAAATATAAGGAAATGGAAATTAATGTAAAATTAATCCTGAAAACAAAAACTAATATAGGCCTTCAGATTTTTTTAATGTAGAATATCTTCTAAAAGTGTCTTATGTTCTAACTTCTCTTTCTTAAAGAAATAATGTATTTTAAAATGTATTAAAACTTGTATTTTCACTTAGAACTTTCCTGAAATACGGTGCCTATCTGTCAGTTCACAGTGCTAAGTGAACTTGGGCATGTGCCTGTAGTCAGTGTCCTGACATGCTGTAATTTCTGTTGGGAAG
Seq C2 exon
GTGGATGACAGCAGTGATGAGGAGCCTGAGCGGCCCGCAGAGGCCTCTGCCGTGGAAGAGGGGTGGTCTGCAGAACGAGCCGGGAAGATCGAGGTGTGCAAGCCTAGGAACGCCTATGAGTTCGGGCAGGTCCTGAGCACTATCAGCGCCAGGAAAGACGAAGAGGCCTGTGCACAGCTTTTAGTCTTCACTGCTCCCCAAGACCTGCCTGTGTTGCTAAGTAACAAACTGGAAGGGGACATGCTCCTCCTCATCATGCAGTCACTGAAAAGTCACCTTGTGGCCAAGGACCCCTCACTGGTGTGCAAGCATCTCCTGTATCTGAGCAAAGCAGAGAGGTTTGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000010078:ENSRNOT00000013801:17
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.722 A=NA C2=0.177
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF138771=RPAP3_C=PU(86.5=72.2)
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:
GGTTGTCCTCCTAAGCCCAGA
R:
GCATGTCCCCTTCCAGTTTGT
Band lengths:
356-1356
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]