GgaINT0001720 @ galGal3
Intron Retention
Gene
ENSGALG00000013419 | PBX4
Description
NA
Coordinates
chrUn_random:30303416-30304941:-
Coord C1 exon
chrUn_random:30304855-30304941
Coord A exon
chrUn_random:30303883-30304854
Coord C2 exon
chrUn_random:30303416-30303882
Length
972 bp
Sequences
Splice sites
5' ss Seq
GACGTAAGA
5' ss Score
7.3
3' ss Seq
TTCATCTGCTTCCCCCACAGGCG
3' ss Score
11.57
Exon sequences
Seq C1 exon
ATGGATTCCTTGCACCATGTCATACACCAGGCAGGAAGATATGACACCATTGTGGGGAATCCTTTGTACACGACGCAGCGCATCGAC
Seq A exon
GTAAGATGCCCCAAGGCTTTAATTTATCCCTTCTCTGATACGAGTTTTGTTCTTAGCAGGGAGCTGTCAGTAAGTCCTAACGTAGTTCCTACCCACTGGGATCTCTGCTGTGGGGATAGGAAAAAGGTGGAAGAGAGATACTTAAGGCTTAAACCTTGGGCTTTGGTTCCCGTAAAACTTGTATCTGAGGACATAGTCCAGAATAGTTGTTCAAAGGGTCCTTACAGGTCTATTATGGGTTGCTCAGATGCAGTGGGTCCTTAGAGGTCACCTGTGGAGCGATTGGGTTCAAAGGGTCCTTACAGGTCAATTATGGATTGGTCAGATTCGGTGGGTCCTTACAGGTCAACTGTGGAGCGATTGGGTTCAAAGGGTCCTTACAGGTCAAGTGTGGAGCACTAGGGTTCAAAAGGTCCTTACAGGTCATCAAGGGAGCAGTTGGGTTCAAAGGGTCCTTACAGGTCAACTGTGGAGCACTTGGGTTCAGAAGGTCCTTACAGGTCAATTATGGATTGGTCAGATGCAGTGGGTCCGTAGAGGTCAACTGTGGAGCACTAGGGTTCATAAGGTCCTTACAGGTCATCTAGGGAGCAGTTGGGTTCAAAAGGTCCTTACAGGTCAACTGTGGAGTGGTTGGGTTCAAAAGGTCCTTACAGGTCAACTGTGGAGTGGTTGGGTTCAAAAGGTCCTTGCAGGTCAACTGTGGACTGGTTGGGTTCAAAGGGTCCTTACAGTTCAACTGTGGAGTGGTTGGGTTCAAAAGGTCCTTGCAGGTCAACTGTGACTGGTCAGGTTCAAAGGGTCCTTGCAGGTCAACTGTGGAACAATTGAGGTGGAATGGTCCTTACAGGTCAGCTGTGGATCGGTCGGGTTCAACAGGTCCTTACAGGTCAAGTGTGAAGCGTTTGGGGCGGAAAGGTCCTTACAGGTCAACCGTGTTCTGTGACTCCATTTCATCTGCTTCCCCCACAG
Seq C2 exon
GCGAATGGCAGCTGGCAGGACGCGACCACCCCTTCATCCATCACCTCACCCGCCGGAGACCCTGGGAGCGTTAATTCCGACGCGTCCAATTAAGCCCTTAGGACCCGACCGATGAGAGGAAAGAGGTCATTAGTGTAATTTGTCAGTGTTGCTCTTTTCGCCGATACTTATTAACGTGACACACAGCTAATTACCTCAGCCAAACCCTGGAACCAATAGAAGATTGTGACGACGACGACGACACCTCTCTACCTCTCAGCTGAGTTCTTTTTACTTATTATGGGATGTGAAATCGTTCTCGAAGAACTTGCTTCATTCTTCCTAACCAAATTTTGGGTTGGTTTTATTTTTATTTTTTCTTTTTTTCGGGGGTTGTTTTTATTTTATTTTTTTCTTTTTAATATGGATTTTATGGTAAGAAACTCAGTGTCTCTTCTAGAAGAAAAAAAAAAAAAAAGAAAAAGGAC
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000013419:ENSGALT00000021886:8
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.483 A=NA C2=1.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
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:
TGGATTCCTTGCACCATGTCA
R:
AGAGGTAGAGAGGTGTCGTCG
Band lengths:
342-1314
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]