GgaINT0111791 @ galGal3
Intron Retention
Gene
ENSGALG00000009743 | RPAP3
Description
NA
Coordinates
chr1:33230397-33231963:-
Coord C1 exon
chr1:33231836-33231963
Coord A exon
chr1:33230519-33231835
Coord C2 exon
chr1:33230397-33230518
Length
1317 bp
Sequences
Splice sites
5' ss Seq
GAAGTAAGT
5' ss Score
9.82
3' ss Seq
TGTACTGTTCTTTTGCTGAGATA
3' ss Score
-2.99
Exon sequences
Seq C1 exon
GGTAATGGTTATTTCAAAGAAGGAAAGTATGAGGCTGCTATAGAATGTTATACACGTGGTATAGCAGCAGATGGCACCAATGCACTTCTGCCAGCTAACAGAGCCATGGCCTATCTCAAGATACAGAA
Seq A exon
GTAAGTTGGATTGTATGTACTATATTGTTTTTTTTTACTGTGAACCAGAAGAAATAATGATCCAGTGGGTTTTCACCTAAGTTTCATTACAGTCACTCCAGTTCTTCCTATTGTTCAGTCTAAATCATGCTGAAAGCAGTAAAGGAATTAAAAAACAAACAACAACAAAAAAACCTGAATATCTGTGATCTTCAAATGTATCTCAAAGGAAAGAAGTTCTGAGAAAATAAAACATCATCAGTTTGAAATTATAGCAAAACCCAAACAGCTTCGCGATTTTTCATTCTTGTGAAATACTACATATTTATCTTTTTCAAAGAGCCTACCCCAAGCTTTTTTAATTATATATATAAAAAAAAACCAGCAATCAGCTACTAAATATTGCACTGAATAAGTAAGTGGATTGTAACTTCTAACTTGAAAGGGAGTGCATTGGAGCTTCTTCAGAGAATAGTCATCTTTTAAAATATTTCTCTAATGCTAGTAATGAAGACATGTTCATACAATGTACTTAATTTTAATTACCCTTTACTGAAATAATCCAGTAACAGTAGGAAATGCATGCTTTATGGAACTTCTCTCATTTGACATATCACCATTTTTGAAATTGCCAAGTACTACTTTTTTTTTTGTTTTGACTCACTCTCATCACAATTGAGATGAGAGTTTAGTCCTTTTAAATTGATAGCATGAAAAGTAGAGATCTGAATATCTTGTTGGTGATCTCTTCTGATGTGATATGGCTGACTGTGTAGAGACAATGTGCTGATATTTTATAAACATAGAATTTGATAAGTTACACAGGTACTATTTCTGTGACATAAGATTTGTAATTTAGGATTGAAGCCGTGGAAGACATTATAATGCAGATAGTGTCAGTGAATTGGAGGAATTAATACTTTAACTTAATGACCACGCAGAAAAAATGACCTTTTAAGATATTGATGTCGTGAGTCTTCACACTTTGAAATGAGGACCCAAACAGGAAGTGCAACAAAAGCTCGTTGATACTCTCAAAAATGTCTACAATTGATGAGAAATACAGAAAATGCTATTTCCTGAAATTTAACGATAAATTCAAAGAGGAGAGAGGGAGGAATAAATGAAAATACTTTAATATGCACATCATGAAGTCATAGTCAAACATAACTGTAATGAGGAAATTTTATCTTACAACAAAAGCAAGTGACTGTAATACAAGGTATAGGTAATTAAGGTCTTCATGTTTTTACTGTTTTGACTAACTCTGTCTCTTCAGCTGAAACTGATAGCTGCTTTTGGAGCTGATTATTAATTTTGTACTGTTCTTTTGCTGAG
Seq C2 exon
ATATGAAGAGGCAGAAAATGACTGTACTCAAGCTCTTCTGTTAGATGCATCTTATTCTAAAGCTTTTGCTAGAAGAGGGGCTGCAAGAGTTGCTCTTGGAAAGCTAAAAGAAGCTATGCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000009743:ENSGALT00000015853:9
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF134141=TPR_11=FE(61.8=100)
A:
NA
C2:
PF134141=TPR_11=PD(23.5=38.1),PF0051523=TPR_1=PU(64.7=52.4)
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:
TTCAAAGAAGGAAAGTATGAGGCTG
R:
GCTTCTTTTAGCTTTCCAAGAGCA
Band lengths:
230-1547
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]