GgaINT0123415 @ galGal3
Intron Retention
Description
NA
Coordinates
chr16:57280-58307:-
Coord C1 exon
chr16:58106-58307
Coord A exon
chr16:57556-58105
Coord C2 exon
chr16:57280-57555
Length
550 bp
Sequences
Splice sites
5' ss Seq
GGAGTGAGC
5' ss Score
2.46
3' ss Seq
CCATCCCCCCTTTGCTGCAGCAC
3' ss Score
7.5
Exon sequences
Seq C1 exon
TTCAACAAGAACCCTCTGCTGTGCTACGACCCCGACGTCCACCGCTTCTACCCCTGCGATTGGGGGCTGCTGCACACCATTGCCACTTTGCTCGCCGCCATCCTAAATGATGATACCACATGGGTGCAGCGTGCAGAGGCACGCAGGCAGGCGTGCACTGAGCTGGCTGCACAGTTCTGGACACACACAGCACTGCGCAGGA
Seq A exon
GTGAGCACCGCTGCATGCAAGTGGAGCATTGCAAACACGGGACGTTGCATGGGGGTGTTGCATGGGGGTGTTGCAATGGGGTGATGCACAGCCGGTCATTGCATGAGACGCTGCACGGGGATGTTGCAAAGGGAACTGCATGGGGACATCGCACAGCAGGTTGAATGGGATGTTGCATGGGGACTTTGCAAGGGAACTTTGCACAGAGCATTGCAGGGGATCCACGCAAGGAATTTGCATAGGGAATGCACAGAGATGTTGCCTGGGAATGCTGCATGGGGTCATTGCATGAGGAACTGAGAGAGACATTGCACAAGGAAATGCAAAGGGGCATCACTAGGGGACATGGCACGGGGCATTCTAGGGAGCATTGCATGGGGACATTGCAAAGGGAATGCAAAGGGACATTGCATGGGGACATTGCAAACAAATTGAGTGGGAGATTGCACCGGGATGTTGCATGGGGACATTGCATGGAATGTCCCACCAACCACCCTGCAGGGTGACACTGGGACCATCCCCAGCTCTGACCATCCCCCCTTTGCTGCAG
Seq C2 exon
CACCACCCCAGGTCCGCATCGTCCCCATCCCCATCTCCAACGACCCCGACACCGTCCACCTCATCTGCCATGTTTGGGGCTTCTACCCACCCGCAGTGACCATCCAGTGGCTGCACAACGGCCTCGTGGTGGCCTCAGGTGACACCAAACTGCTGCCCAACGGGGACTGGACCTACAGGACACAGGTGGCCCTGAGGGCCAGCACTGCAGCAGGGAGCACCTACACATGCTCAGTGTGGCACTCCAGCCTGGAGCAGCCGCTGCAGGAGGACTGGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000000162:ENSGALT00000041213:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0096914=MHC_II_beta=WD(100=82.1)
A:
NA
C2:
PF0765410=C1-set=WD(100=84.9)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
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:
CGCCGCCATCCTAAATGATGA
R:
GTGCCACACTGAGCATGTGTA
Band lengths:
352-902
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]