GgaINT0136951 @ galGal3
Intron Retention
Gene
ENSGALG00000003800 | PABPC4
Description
NA
Coordinates
chr23:5732127-5733008:-
Coord C1 exon
chr23:5732909-5733008
Coord A exon
chr23:5732418-5732908
Coord C2 exon
chr23:5732127-5732417
Length
491 bp
Sequences
Splice sites
5' ss Seq
CTGGTGAGT
5' ss Score
10.1
3' ss Seq
TCTGACTCCTTTTCCTGTAGGAT
3' ss Score
10.77
Exon sequences
Seq C1 exon
GTGGAGGAGGCTGTTGCAGTGTTGCAGGCTCACCAAGCCAAGAAAGAAGCTGCCCAGAAGGTGGGTGTGGTTGCTGCTACCTCTTAAGCCAGGAAGACTG
Seq A exon
GTGAGTGTCTCAGTCCTCAGCTTCAATTGAAAGCTCCCAGGGCTGGTAAATAAAGCAAGACAGTTACTGAGTGTTCTTGGTCTGGGAGGCCTGTGTAGGTCTGGGAGCAGTGCTTGTCTAATTGTAGCCAATTCTTCAAAAATCTTTTAATTAAGCGTCGGAAAGATGATGCATAAATTGCCAAAGTGTTCCTGTGAGCTGGCATGTCATGGAAGTACAGCAGAGTGAGATGAGTCTTGTGACAGTGCTGATCTAGGAGATAATGTTCTGTGGCTTCGAGGTGAAGTACTGTGCTGATGCCCATTCCTTGTCCTGGCAGTTGTCTGCCTATAGCATGCATTAAAGGGCTGCTGTCAGCAGGGCCGTTTCCTGGTACAGGTCTGTCCAACGAGTGCTCTCTCTGGTGTTGAAAAGGAGCCAGCTCTGAACTCCTAAAAAAGGGCTTTATTTCCCAGTGCCTGGCAGGTAATCTCTGACTCCTTTTCCTGTAG
Seq C2 exon
GATGCAAAGAAGCCAAATAGCCCCTCCCCAGACATCAGCTCGAGATGTTTGCAGATTCTGCGCCGTCCTGCAGGACTCGATGCCATGCCACACATCACGTAGTTGTATTGCATTTTATAAATTAACCCTTCAGATCCTACAAAGCCAACTCTGTGCAGCTCTAGATTGCCAAAACCAGAATGAGTTTGCAAGCTTTTCCTTTGTGATCAGAGCAGAGTTACCGTTTGTCTTTTCTAATTGAGACGTCGAGGATTTCTGGTTGGAATGGTGTGGGTTTGGTTTTAACTGAAC
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000003800:ENSGALT00000006028:14
Average complexity
IR
Mappability confidence:
NA
Protein Impact
3' UTR
No structure available
Features
Disorder rate (Iupred):
C1=0.321 A=NA C2=NA
Domain overlap (PFAM):
C1:
PF0065813=PABP=PD(9.7=24.1)
A:
NA
C2:
NA
Main Inclusion Isoform:
NA
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Human
(hg38)
No conservation detected
Mouse
(mm10)
No conservation detected
Rat
(rn6)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AAGCCAAGAAAGAAGCTGCCC
R:
AACCCACACCATTCCAACCAG
Band lengths:
342-833
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]