RnoINT0065014 @ rn6
Intron Retention
Gene
ENSRNOG00000042373 | Ggta1l1
Description
glycoprotein, alpha-galactosyltransferase 1-like 1 [Source:RGD Symbol;Acc:1565200]
Coordinates
chr3:14556033-14557266:-
Coord C1 exon
chr3:14557129-14557266
Coord A exon
chr3:14556703-14557128
Coord C2 exon
chr3:14556033-14556702
Length
426 bp
Sequences
Splice sites
5' ss Seq
AAAGTAGGC
5' ss Score
5
3' ss Seq
TCTATCTTTCGTTTTCATAGCTT
3' ss Score
8.41
Exon sequences
Seq C1 exon
AAAACGTCCTGATGTTATAGCAACAACTGGTTGGCTCGCTCCAGTCTTATGGGAAGGAACTTATGACAGAGAAGTTCTAGAACAATATTATAAGAGACTGAACATCACCGTAGGCTTGGCTGTCTTTGCTACTGGAAA
Seq A exon
GTAGGCACTGCTGGTAGCTGTCCTTAATACTCTGGAGAAATAAGGTTGAGCAGCCGTGGACTGTCTCTAGCCCAAGTACTGGTTACTAAGGAGTCTGTCATAGCTTCTTTCTGCCCTGTGAGGCTATGGAATAGTGGCTGTTTATTTGCTTTTTCTGTTTTGTTTCGTTTTATCCAGAAATAGCTGAATGTTAGAACGTGTGCAGTACATTGCTATCTAGCTAACTCTCTTTCCTTCTCTTCATAACAAACTCCTTGTCTTTTCCCAAGCTTACCAGATTGTCTTTCGCTAACCAATACAGCTGAAGGTACAGACACAGCCCCTCTATCATTATCTTCTTAGACACCAACATCTTACGTGTTAATTAAATGGCACACCTCTCCTGGGAATTAGTGAAGTGTTTTTGTCTATCTTTCGTTTTCATAG
Seq C2 exon
CTTTTCAAGTGAGTCCCTGAGACGCTTCATAAAATCTGCCAATAAGTACTTCATGGTTGGCTACAATGTTATTTTCTACATCTTGGCTGATGGCACGAGCAATCTACCATACCTTGAGTTGGGTCCTCTTCGGACACTTAAAATGTGGAGGCTCTCTGGAGAAGAGATGACTTATGAAGACAGTAATCTCAGGAACATGAATAACATGCGATACAAAATCATGGAACATATTCAATATGAAGTCAACTTTCTCTTCGTGATGACTGCGAACCAGATCATCAAGAACCACTTTGGAGTAGAAACCTTGGGCAGATCTGTAGCTCAACTCCATGCATGGTGGTATTTCAAACAGCCCAGAGAGTTCCCTTATGAGAGAAGAAGGAAAGCCTCAGCTTTCATTGCCTTCGAAGAGGGAGATTTCTATTACCACAGTGCCATTGTTGGTGGCACGCCCCTAGATGTCTTAGATCTCATCGAACACTATATAAAGGGAATTATAGATGACAGGACAAATGAACTTTCTAGCACGTATGAAAGACACCTAAATAAATATTTTTTTATCAAAAAACCCGTTAGGGTGTTATCACCAGAGTACAACTGGGATCCAAGATTTAAAACTCCTCCAGAAATCTGGCATATTAAGGTAGCATGGCAACCACGAATCACTTAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000042373:ENSRNOT00000060013:4
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF034148=Glyco_transf_6=FE(14.9=100)
A:
NA
C2:
PF034148=Glyco_transf_6=PD(71.8=99.1)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Mouse
(mm9)
No conservation detected
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGCTTGGCTGTCTTTGCTACT
R:
AGCTACAGATCTGCCCAAGGT
Band lengths:
348-774
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]