GgaINT0135990 @ galGal3
Intron Retention
Gene
ENSGALG00000003709 | E1C209_CHICK
Description
NA
Coordinates
chr22:2764715-2765903:-
Coord C1 exon
chr22:2765790-2765903
Coord A exon
chr22:2764890-2765789
Coord C2 exon
chr22:2764715-2764889
Length
900 bp
Sequences
Splice sites
5' ss Seq
TAGGTAAGT
5' ss Score
9.66
3' ss Seq
TTTTGTTCCCTTTTGCTCAGATA
3' ss Score
7.85
Exon sequences
Seq C1 exon
CCTGCACTAGAAATAAATGCTACAATGGGGGCCAGTGTTCACAGGCATATTACTCCCCACAGCTCTTCATCTGCCGCTGTCACCACGGTTTCTCTGGGAAGCAGTGTGAAATAG
Seq A exon
GTAAGTATGCTGCTCCAGTTATTGTGAACAATGCTGCTGGTTTTAGCTGTGCAGCACAGAAGGATTAGGTACTCAGAAACCACTGCTGTACAGGGGTCTCTCTGCTAAGTTGCTGCTTTTTGTGGTAAAGCTAATGCTACAAACAACTTTAGAAAAGGACACCTGGGTTTCTCTGTGTCTCGTGAGGCCTCAGGTAGAATACTGCATCCAGATCTGGGGCCCCCAGCACAATAAAGATGTAGAACTGTTGGAGTGAGTCCAGAGGAGGACCACAAAGATGATTAGAGGGCTAGAGCACCTCTCCTAAAAATACGAGATAAAAGCATTGAGCTTGTTCAGCCTGGAGAAGAGAAGGCTCCATGGGCACCTCATTGCAGCCTTCCAGTATTTTATAGAAACTTCCAGTACTATCAGGAGGAAGATAGACTTTTTATACTGACTAGTAACAATAGGGCAAGGAAGAATGGTTTTAAACTAAAAGAGAGGAGGTTCAGATTAGATGTTGGGGGGATATTTTTCACTCAGAAGGAGGTGAAGTGCTGGAATAGGTTGCCTTGAGAAGGTGTGGATGCCACACCCCTGGAGATATTTAAGCCAAGCTGTATGGGGCCTGTGCAGCCTGATCAAGTGCTTGATTTGGTGGCTGGCAACCCTGCCCACATCAGGAGGGCTGGAACTGGATGATCTTTAAGGTGCCTTCCAACTCAAGCTGCTCTGTGATTCTCTGGCCTCTTGATAAAATACTAAGCTTTGAAGACAAAAACCTTTGTGTATATGTAGAGTTTGCTTGGAAAGGTGTTTCACTGACTTATGAGACAAGGCATCTGGAGCCAACTGTAAACAGAGCAGAGTCAGAGGAAGCAGAACTTGTGATGCTGTTTTTTGTTCCCTTTTGCTCAG
Seq C2 exon
ATACTGAAGTTAAGTGCTACAAAAATGCTGGAGTAACATACAGGGGTACATGGAGCATAACAGAGAGTGGAGCTGAATGCCTGAATTGGAATATCAATGGCTTGATGGACCATAAATACAGTGGCCAAAGAAAGGATGCTGCTGAGCTGGGATTGGGCAATCACAACTATTGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000003709:ENSGALT00000005886:4
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:
PF0000822=EGF=WD(100=87.2)
A:
NA
C2:
PF0005113=Kringle=PU(64.6=89.8)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCTGCACTAGAAATAAATGCTACA
R:
CTGCAATAGTTGTGATTGCCCA
Band lengths:
289-1189
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]