GgaINT0080063 @ galGal3
Intron Retention
Gene
ENSGALG00000016565 | F1N9F1_CHICK
Description
NA
Coordinates
chr3:107876746-107878273:-
Coord C1 exon
chr3:107878164-107878273
Coord A exon
chr3:107877833-107878163
Coord C2 exon
chr3:107876746-107877832
Length
331 bp
Sequences
Splice sites
5' ss Seq
CAAGTGAGA
5' ss Score
5.26
3' ss Seq
CACCCTCTCTGTCCCTGCAGTGC
3' ss Score
11.82
Exon sequences
Seq C1 exon
GAATGGAGTGACTACAAGCTGCGCTGGAACCCAGAGGACTTTGACAACGTCACCTCCATCAGGGTGCCCTCTGAGATGATCTGGATCCCCGACATCGTGCTCTACAACAA
Seq A exon
GTGAGATGATGCACCCCTGGGACCAGTCCTCCCATTCTACCTCATCTCCATCACATTCATCCCATCCCACCGTATCTCATCCCATTCCATAGTATCCCATCCCATCCCATCCCATAATATCACATCCCATCACACCACATTCCATCCCAACTCATCCTATCCCTTCCCATTCCATCGTATTCCACCCCACCCCAACCCATCCCACCCCACCCCATCCCATCCCACCCCACCCCATCCCATCCCATCCCAACAAAACTCATCCCATTCCACATGGATGGAGCTTCTGCTCCTGTTTCCTGGGGAGAACCCTTCACCCTCTCTGTCCCTGCAG
Seq C2 exon
TGCCGACGGGGAGTTTGCTGTGACACACATGACAAAGGCCCACCTCTTCTCCAATGGGAAAGTGAAGTGGGTGCCACCCGCCATCTACAAGAGCTCGTGCAGCATTGACGTCACCTACTTCCCCTTCGACCAGCAGAACTGCAAGATGAAGTTTGGCTCCTGGACTTATGACAAGGCCAAGATCGACCTGGAGAACATGGAACACCACGTTGACCTGAAGGACTACTGGGAGAGTGGCGAGTGGGCCATCATAAACGCCATTGGCAGGTACAACTCCAAGAAGTACGACTGCTGCACTGAGATCTACCCTGACATCACCTTCTACTTCGTCATCCGCCGCCTCCCGCTCTTCTACACCATCAACCTCATCATCCCCTGCCTGCTCATCTCCTGCCTCACCGTGCTGGTCTTCTACCTGCCCTCCGACTGCGGTGAGAAGATCACACTCTGCATCTCCGTCCTTCTGTCCCTCACCGTCTTCCTGCTGCTCATCACCGAAATCATCCCCTCCACCTCTCTGGTCATCCCACTCATCGGTGAGTATCTCCTCTTCACCATGATCTTTGTCACGCTCTCCATCATCATCACCGTCTTTGTCCTCAACGTGCACCACCGCTCCCCCAGCACCCACACCATGCCCCACTGGGTGCGGAGCTTCTTCCTGGGCTTCATCCCACGTTGGCTCTTCATGAAGCGGCCCCCGCTGCTGCTCCCCACCGAGGGGACGACGGGCCAATATGACCCCCCGGGGACCAGGCTCAGCACCTCCCGCTGCTGGCTGGAGACCGACGTGGATGACAAGTGGGAGGAGGAGGAGGAGGAAGAAGAGGAAGAGGAGGAAGAGGAAGAGGAGGAGAAGGCGTATCCCAGCCGTGTGCCCTCAGGAGGATCCCAGGGCACCCAGTGCCACTACAGCTGTGGACGCCAAGCAGGCAAAGCATCAGGGGGCCCAGCCCCCCAGGTGCCCCTCAAGGGGGAGGAGGTGGGCTCGGATCAGGGGCTGACACTGTCACCCAGCATCCTGAGGGCCCTGGAGGGTGTGCAGTACATCGCGGACCACCTGCGAGCCGAGGATGCTGACTTCTCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000016565:ENSGALT00000026738:3
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=0.051
Domain overlap (PFAM):
C1:
PF0293118=Neur_chan_LBD=FE(17.4=100)
A:
NA
C2:
PF0293118=Neur_chan_LBD=PD(55.6=41.5),PF0293211=Neur_chan_memb=WD(100=54.9)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGGTGCCCTCTGAGATGATCT
R:
TCTCAGTGCAGCAGTCGTACT
Band lengths:
351-682
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]