RnoINT0141953 @ rn6
Intron Retention
Gene
ENSRNOG00000010078 | Spag1
Description
sperm associated antigen 1 [Source:RGD Symbol;Acc:1310702]
Coordinates
chr7:75053042-75054293:+
Coord C1 exon
chr7:75053042-75053386
Coord A exon
chr7:75053387-75053482
Coord C2 exon
chr7:75053483-75054293
Length
96 bp
Sequences
Splice sites
5' ss Seq
GAGGTAAGC
5' ss Score
9.85
3' ss Seq
GGACCCTTCCCCTCTTCCAGATG
3' ss Score
10.06
Exon sequences
Seq C1 exon
GTGGATGACAGCAGTGATGAGGAGCCTGAGCGGCCCGCAGAGGCCTCTGCCGTGGAAGAGGGGTGGTCTGCAGAACGAGCCGGGAAGATCGAGGTGTGCAAGCCTAGGAACGCCTATGAGTTCGGGCAGGTCCTGAGCACTATCAGCGCCAGGAAAGACGAAGAGGCCTGTGCACAGCTTTTAGTCTTCACTGCTCCCCAAGACCTGCCTGTGTTGCTAAGTAACAAACTGGAAGGGGACATGCTCCTCCTCATCATGCAGTCACTGAAAAGTCACCTTGTGGCCAAGGACCCCTCACTGGTGTGCAAGCATCTCCTGTATCTGAGCAAAGCAGAGAGGTTTGAG
Seq A exon
GTAAGCGGCAGTGTGCCTGGGAGGGAGCCTGCGGTTTCTGGGTTCTCTAACTTTGAAAGTGTTGCCTATGCTCACAGGACCCTTCCCCTCTTCCAG
Seq C2 exon
ATGATGCTGGCACTGACTAGCAAAGACCAAAAGGAGCAGATGGCGCAGCTGTTTGATGACCTGTCAGACGCACAGGCTGACTGTCTCACGGCAGAGGATATACAGGCCCTAAGAAGGCAGTATGTGCTTTAACTCGGGTGCTGAGTTCAAAGCAGTCTCTGATGGAGTTGCATGGGTAAAGCCACACCCAGAAGGAGCCACACCCAGAAGGACCCATTTGGACATCAGACGTTATACTTATTTTTGTATCCAGAACATGTATATTCTATAATCTGATTCTTATTTATTGTAAATATTCTCTTCTGTACTAGAGCCAATACCTTTATATTTAATAACTATATTTGGAACTTGGCAAACACTAATTTATAAAACATTTTCTTTTAATGACCTACCCATAAAAATTTAAACACATTCTTCATTGTGGCAATTCTTTCAGGTTTGACAGAACCCAGGTCTTCCGTTCTTTAAAAGCAAATGTTAGCACTGATAACTCCATCAGATGCACAAAATCTACTTTAGAGATTGAAACAACACTTGCATCTTTGAGGTCATTATTAGCTTATTAACTTAGAGCCCTAAGGGAGTTATTTTTCTCTAATATTTTTACTGTGACTTTCTTCTTGTTTGTAAACCTTTCACCCTACCTTTGTATTTGAATTGCCACCCTAGCCAATAGTTGCTATTCACACGCCCTTCCCAATCTGTTTTCTGCTTGGTTTCTTTACTGTAACAAGTGAGAAGTCACTGGATGTTCCCTTTTCTGGGTTAAAGGTATTCCCTATGCAATAAACAAACATCCAAGCCTTAATTT
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000010078:ENSRNOT00000013801:18
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.177 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF138771=RPAP3_C=PU(86.5=72.2)
A:
NA
C2:
PF138771=RPAP3_C=PD(11.5=25.0)
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:
TGCTCCTCCTCATCATGCAGT
R:
CTGTGCGTCTGACAGGTCATC
Band lengths:
179-275
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]