GgaINT0096254 @ galGal4
Intron Retention
Gene
ENSGALG00000016037 | SPAG1
Description
sperm associated antigen 1 [Source:HGNC Symbol;Acc:HGNC:11212]
Coordinates
chr2:128208421-128210128:+
Coord C1 exon
chr2:128208421-128208792
Coord A exon
chr2:128208793-128208935
Coord C2 exon
chr2:128208936-128210128
Length
143 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAGA
5' ss Score
10.57
3' ss Seq
AACCTAATGTGTTTTCTCAGGTG
3' ss Score
8.58
Exon sequences
Seq C1 exon
GTAACTGATGAACAGGAAGAGGGGCAGCTTGAGACAGCAGAAGATGTTGTGACTGACAATCTTAGCTCTAAAGAAGCGGTTCAGAAGTGTGTGCCATCAAGGACCTGTGAAAAACTGACCATTTCTGAACCATCCAATGCCTATGATTTTGGTCAGATTGTAAATGCAGTGAATGCCAGTAAGGATCAATCTGCTTGTGCAGATCTTCTAACAATTACTGATCCAAAAAAACTGCCAGTGCTGCTAAGTAACAAACTTGAAGGAGAGATCTTTTTGATTTTCATCCAGTCATTGGCACATTACATCCTTGGAAAAGATCCTGGCCTCGTATATCAGCATCTTTTCTACTTGAGCAAAGCAGAAAGATTTAAG
Seq A exon
GTAAGAACTTAGGCTAAACGAGTACTTAAATCAAACAGAAATTTAGGAGTTTCATATTTCAATAGGAAATGATTGTTATATTTCTGTCAAATGTTATGATTTTCAGTTGCCTGTGCTGATTATAACCTAATGTGTTTTCTCAG
Seq C2 exon
GTGGTGTTGGCTCTTCTCAGCAAAAACGAAAAGGAACAGGTTCAGCGACTGTTTGATTTGCTCACGGAAAACCAGAACCATCAATACTCTTTGGAAGAACTGGACAGCCTTAAAAAGGTTTATGAACTTTAAGAACTTGAAATTTATTTGTTGCGTGGATAGAGTTGTCGGTTGTAAGATGGCTGTACAAACTCTGCAAGCACGCATGGGTTGAAGTGGGTCTCGACATGGACTGTCTGAATTCTATTTTATTTTGACAGCATACACATATTTAAAACTTGCTGCTCTTTTTTTCTTTTTAGTTGTATACAGTTTTAGTCTAGAATTTAATGCATGTCTTTGTGTTCAGTCCTGGAGTTCATGTTTGGCATCCTGATTTTATTTAGACATGGAAATACCTATTTTGCATTTATATATAGCATGAGATACCTTGATGCTACAATAGCAATACACTTTCAGTCACCGCTTATTGTATCACTTCATGGGTTGTACGTTCTTGTGGTGAAGAAGCACCTTAGTGACAAATGGGTCCATTAGCAATAGCTTTGCTATAAAGAACTTACAAGTATAAACATTCTTCAAATCAACTGCACAGCCCATCTGTTTCTTTGCCCCCCCCCAGCCTGTACAGAACAGATGTAAATATTTTTGGTGCTGGACAAAGATGAATGAATAATATATTAGCTTGTCATGGAACACTTTGGCTCAAAATAATTAATTATTAACTAAATGGGTATGTTTTTTACATGACAAACGAGTAAGTTTTAGTGCAGAGAGAATTTTGTTTTCTGTGTGCATGGAAGGATTGCTAGTTTGCACAGCTTTTAAAGGAACAAACGGCTGCATCTAACAATTAAAATGTTTAACTCCGAGTCTGTAATTAGATTACTTAAAGTACCAGCTATTGCTGTTTCCAGACATATTCATAAAGCTAAAACTAAGGCCGTTTGGTGGACCAGTAGGGTTTTTGTTTTCTTTCAGGCAGTACGTCTGTTTTATATTTCATTCTGACAAAGCTCCCTTTTTCAAGATGAAGTGTTAAAACTTAACATGCCCCAATGCCTTCTTTGCACATTTAATCTAAATTATATCATACTCACAAGTGCTGCAGAAGTATCATTAAGGATGTCGTTGCAGTGAAATCTTTTCTCAGGTTACTTAAAAAAAAAAAATAAAGGTCTTTTTCCTGAAAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000016037:ENSGALT00000025838:20
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.056 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF138771=RPAP3_C=PU(86.5=66.9)
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
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TCCTGGCCTCGTATATCAGCA
R:
GCTTGCAGAGTTTGTACAGCC
Band lengths:
256-399
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]