RnoINT0065012 @ rn6
Intron Retention
Gene
ENSRNOG00000042373 | Ggta1l1
Description
glycoprotein, alpha-galactosyltransferase 1-like 1 [Source:RGD Symbol;Acc:1565200]
Coordinates
chr3:14563939-14570053:-
Coord C1 exon
chr3:14570018-14570053
Coord A exon
chr3:14563987-14570017
Coord C2 exon
chr3:14563939-14563986
Length
6031 bp
Sequences
Splice sites
5' ss Seq
CTGGTAAGG
5' ss Score
9.68
3' ss Seq
AGTCTTCTCTCTGTACCTAGGAG
3' ss Score
9.04
Exon sequences
Seq C1 exon
AACAAAGGATCACCTACAGAAGATGTACACCTGCTG
Seq A exon
GTAAGGGTCTGTCCTGTGTATGTTCTAAGAACTGTGAAGGGGGTGGTGCTTGGAGCAAAATGGGTTCCTAATAGAGATGCTGTACAGAGAAGTGTGCTTTGGCCATTGACGTCAATGTAAGCATCCTTGTTTGGGACAGTGATTGCTTTGGGTATCTTTAGACCGATATCTCCCTGTGAGCAGCCTGGTTTCTACCTGCAAGACGATGAACCTTATAGTTTCTTTGCATGTGAATCGTGGCTTCCAGCTTTCTGTTTTCAGGGGACTCCTGTGTGTGCAAACATGTCTCTGTGTTTATATGTTTCTTGTGACTTTTCTTTAGTTCCTTTTCTTCTGTTTGCATGTTTCGTCCTATTCTGATTTGGGTTTTTGTTTGCTTTATTATTCCTTAGATGCCCATCTGTTTTCTTTTTTCTTTTTCTTTTCTTTTTCTTGGATATTTTATGTATTTACATTTCAAATGCTTTCCCCTTCCCCCCCTCTCCCATATGCTCTTCCTGTTCCCCCTGCTTCTATGAGGATGCTCCCACTCCTACCTACCTCAACGCCCCACCTCAACGCCCTGGTATACCCTACATGGGGGAAACGAGCCTTCACAGGACCAAGGACTTTTCCTTCTATTGATGCTGGACAAGGCCGTCCTCTGCTACATATGTGGCTGGAGTCATGGGTCCCTCCATGTGTACTCATTGGTTGGTGGTTTAGCGCCTGGGAGCTCTAGTGGAGTCTGGTTGATTGATACTGTTGTTCTTCCTATGGTTTTGCAAACCCCTTTAGCTCCTTCAGTCTTTCCTCTAACTCCTCTATTGGGGTCTTCTTATTCAGTCCAATGGTTAGCTGTGAGCATCCTCAACCAGAGACGGAAAGGGTGTGAGTCCAGATGGGAAGGGAGGAGGGAGGAACTCAGGAGTTATGGGAGGGGAAACTCTAGTCAGAATATGTTGTTGGAAAAAAAAATCTATTTGGGGGCGGGGTAATCAGGGTGTTTGTTTGTTTGGTTTGGTTTTTTTCTAGACAGGCTTTCTCTATGTAGCCTTAGTTGTCCTGGAACTCACTCTGTAGAATTCAGAGGTCCACCTGTGTCTGCTTCGTAAGTGCTGGGATTAAAGACCTGCACCACCACAACCAGACTAAAGATCTATTTTCAATAAAAGAAGAATAAAATCTCAAGATGATGGACGTTGCTCAAAAATATATACAGCTAACTTGGTGTAAAACACAACCCCTCCCCCCCATAAACCAAGAGCGAACTTCTCTGTCACTACACAGTTTAATGAATTTCAGCACAGATACTTTGGATGTAGAAAGAGAACTGGGGGAATCCTACCGTGAAGGATCTTCAGCTAAAGACACTTCCGAAAATTGAGAGACGCATTCTCCATAACCTCCCACCTTATTTCAAAATAATTACCACTCACAGGAAGTTGCCCTGAAATCACGTGCACCTTTCACCTGATGTTCCCCCAGTGCTCCCCAAGGTTACAGCTCACATGACTGTACTCAAAGTCAGGAAACCGACACCAAGACAAGGTGCAGATATAATTTTGCCCTTTTTTTTTTTTTATCACATGTCGATATTCATACAAACAACACCAATCGAGATTCACTACTTTCCCATTACAGTCCGAACTATCCTGTTTGGGAACGTGTGATGCTGCTCCCTGTTCCAGATCCTACTTCATCCGGGATACCACTTCTAATCATTTTGCTATCACAACTTGCCGTCTTGAGACTTTTATAAACAGGGCCATAAAATACATAATCCGCTGGTAAGAGGCGTTGTCACTCAGCAAGATGCCCTTGACAGCCAAGGACGTTGTTTTTACTAACATTCCAGACCGCTTGACTGATAGGTAGTATTTCATACATGAACACAGCAAAATTTGTCAGACAAATTTTAGTGTAGACTTACATTTTTCAGAACCTAGCTTACGAAGGGTACTTAAATGCTTTGAACCTCCCTTCTAGCCCACCACCCACCTACCAGAGGTAGTGGAAAGGCAAAAGGATGTGGACCTGTTTAGAAATAGTTCTTTGGGGGAGACTCCAATATTCGTTGTCAGGATATAGGCAGGTCGGCTTACACACAGTAGCTAGATCCACTGGCAAACGCCATTCATAAATCAGCAATGGTAGTCCTAGCCAGAAGAAAATTCGAGGCTCCGTCAATCAGCTTGATTCCTTGGAAGCATCAAAAAGCCGCCACAAAACCACCAGAAGTTCTTTGGTGCTTTTCTCTTTAAGAAACCACAACGAACGTGGTCTTGCAAAGACTGGCAAGCTGAACCAATACCACGCCCACTGGCAAGCTGAACCAATACCACGCCCACTGGCAAGCTGAACCAATACCACGCAGCGTCGTCCACCGTCCGTTGGGTTATGCTTACACCCTTTCCAAACATCACATGGTCTCTCATGAATCCACTCTAGCAGAACGTCACATGCCCTTTCCCCGGGCAACTTCCAGAAAAACACGTTTGTTTTCAGCAAAACACCCTCCCACATGTCTGCTTCAGCAAAATCATCCTCTCGGAAGACAGTTTCCGTAAAAACACCACACAGCACAACTGAGTCTCCAAAGAATTTTCCACTTCATTTTAGTTAACAGCCTTTTTTTTTTTTTAATTTTTAGGTGATCTGGAAAATATTATGACACTTCGTTTTGGCCTCCATGGTTCCTCGTAAGAAACTTACTTGTTGAATGTCTGTCTTCGACAGGTGAAGGATCATCTCTCTGGCTTCTTTTGAGATGTTTTCCTTGAGTTTTCATGAATTGATGCCTGTTTGCAGCTCAATTAGATTCTTAAATCTCTCTCTCTCTCTTGCTATATTTGGGAAGTTCGCCGCTGCTGTTTTTAAAATTTATTTTATGAGTTTATGAGTGCTCCGTCTGCATGAACACCTGTACACCAGAAGAGGGCATCAGATCCCATCACAGATGGTTATGAGCCACCGTGTGGCTGCTGGGAGTTGAACTCAGGACCTCTGGAAGAGCAGTCAGTGCTCTTAACCGCTGCGCCACCTCTCCAGCCCCTAAGTACTGTGTTCTAGGGTTACTAGTACTACGATGAAACACCAAAAGCGACTTGGAAAGGGTTTATTTGGCTCGTACTTCCACAGCAGTGTTCAACACTGAAGGATGTCAGGATAGGAACTTAAACAAGGCAGGAACCTGGAGGCAGGAACGGATGAAGAGACCATGGAGGGGTGCTGACTGCTGGCTTGCTTACTGTAGCTTGCTCAGACTGCTTTTCTTGTAGAACTCAGGACCACCAGCCCAGAGGTGGCCCAGTCCATTGCCGCTAAGGAAATGCTCCACAGGCTTGCCTGTAGCCCAATCTTATGGAGGCCTTGTTGAAATTCAGGGTCCCTCCACTCAGACGGCTTTAGGTTGTGTGTAGAAGAATGCAAATAGACCCATGTCTATCACGATGCACACAACTCAACTTCAGGTGGATCAAAGCCCTCAACATAAAACCAGACAGTCCAAACGGGAAGTGGGGGATAGCTTTGAATGCACAGGAACCAACTTCCTGAACAGAACACCAACAACTCAGGCTCTAAGATCAACAATTAATAAATGGGACCTTATGAACTGGAAAAACTTCGAGAAGGTCTAGGACACCACTAGGTGTCACCAAAAGGTCAAAACGGCAGCCTATAGAATGGGAAAAGATCTGCACCAATCCCACATCTGACAGAGGGGTAATATGCAAAATATATAAAGAACTCAGGAAACCAGATATCAACAAACAATCCATCTTAAAAATGGGCTTCAGATCTAAAAAGAGAACTCTCAACAGAGGAGTCTCTAATGGCTGAGAAGTACTTAAAGAAACGTTAACCATCCTTAGCCGTTAGGGAAGCACAAATCAAAACGAGGCTGATCTCAAGTCACAGACAGACCATGCTGGTGGGGATGTGGAGCAAGGGGAACTCCTCGACTGCTGGTGAGAGTGCAAATTTGTACAGTCACTTTGGAAATCAAAATGTCGGCTTCTCAGAAAATTGGGAATTGATCAACCTCAAGACCCAGCTATACCACTCCTGGGCATATACCCAAAGGATGCCCCACATCCCACATGGACATTTGCTCAACTGTGTTCATAGCAGTTTCATTCATAATAGCCAGAAACTAGAAACAACATAGATGTCCCTCAACATGGACAAAGAAAACACGGTACATTTACACAATCAAGTCTTACTCAGCTGTTAAGAACAACATCACGAAGTTTGCAGGCAAATGGGTGGAACTAGAAAAGATCATCCTAAGTGAAGGCAACCCAGGCCCAGAAAGACAAACATGGTGTGCACTCACTTATAAATGGTTATTAGCTGTGGGGGGAGGACAAAGGGAACGAGTACTGGGAAAGACAACTGGAATGGTGAGGGTGGCATCTCTGGGATGAGCTAGAAACCTAGGGCAATGGAACCTCCCAGGAATCTAAGAGAGTGACCCTACTAAGACTCCTCCTAGCACTGGGGGGTATGGAGCCTACCCCGCCATCTCCTGTAACCAGGCAAGACTTCAATGGAGGGACTGGAACACCAACCCAGCCACTAAACCTTCAACCTACGATTTGTCCTAACAAGGCATGCTGGAATAAAGATGGGGCAGAAATTGTGGGAATGGATAACCAATGGCTGGTCCAGCCTGAGAGCCCCGTGCCATGAGAGGGAGCTCAGCCTAGTGCTGTTAAGGACAGTATTCTGCTATACTTGCAGACAGGAGCCTGGCATAGCTGTCATCTGAGAGGCTTCACCCAGCAGCTGACGGAAACTGATGCAGAGACCCACAATTGGGGAATCCTGAGAAAGAAGGGGAGGAAGGACTGTAGGAGCCAGAGAGATCAAGGATGCCACAAGGAAACCTACAGGACTAACCTGTGCCCATAGGGGCTCACAGAGACTGAACTGCCAGTTAGGGAGCCTGCACGGGACTGACTTAGGCCCTCTGGACATATGTAATAGTTGTGCAGCTTGGTCTTCATATGGGACTCCTAAGAACAGGAGCAAGGGGCTGTGTCTGACTCTGTCGCCTGCCTTTGGGACCCTTTCCGCCTTCTGGGCTGCCTCTTCTAGCCTCAATAGGAAAGGATGCGCCTAGTCTCACTGCAACTCTTTACTGCAAGGCCAGTTGACACGCATGGGAGGCCTCCCCTTTTCTGAAGAGAAAGAGAGGGAGAATGGATGTGGAGGAGGGGAAGTGGGTGGTGGGGAGGACAGAGAGGAGAAGAGAGAGGGGAAACTTCAGTTAAGATGTAAGATGAACTAATCTTTTAAGAAGACATAATGCCAAGATGGTGATGATAACTATATTTTCCAGCACATACTGCTTTAACCACTCTTCTCCTTCTCTCCTCTCCTTCCTCTCCTCTCCTTCTCTCTCCTCTCCTCTCCTCTCCTCCCTCCCCTCCCCTCTCCCTTTTCTCCTCTCCCCTCCCCCCTCCCTTCCTCTCCTCTCTCTCTCTCCTCTCCTCTTCTCCTCTCCCCCTCCCCTCCCTCCCTCCCATCTCTTCCTCCTCTCCTCTCTTCTCCTCTCCCCTCTCCCGTCCTCCCTCCGTTCTCTACCTCTCCTCTCCTCGTTCTTCCTCTCCTCCTCCATTTCCCTTGAGACTCCAGTCAACAAGAATGTCCCGCTGTTGTTATGGCCCATCCCATCCTTCAAACTTCTCTTTTGTTGCTTTTAGCTTTGTCTCAGTTGTCCAAAATCGAGCGGTTTTCTTACTCTATATTCACTTGGAGAGTCCTTTCTTGGTCCTCAACACCAACACTGTGATTGACGACCCACCCCCTGAGTTATTTCTACCTCACCCCACTCCCACTGTTGAGCCCCACCCAATGAGCTATTTCTACCCCCACTTGTTAAGCTCAAATGCTGAGTTATTCTATCCCCTCCTACCCACCCCACCCCCGCCCCGCCCCCACTGAGCCGTCTCTATCTCCATTTGATGCTGTTGGTAAGATTTTCTACTTCCGTTTCTTTGCACCAAACTACGCCCACTAAGGTGAGTCTTCTCTCTGTACCTAG
Seq C2 exon
GAGAGATCATCTGGAAGAACCTCAGCTCGAGTCTTGGTTTAATCCAAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000042373:ENSRNOT00000060013:2
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:
PF034148=Glyco_transf_6=FE(3.9=100)
A:
NA
C2:
PF034148=Glyco_transf_6=FE(5.2=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Mouse
(mm9)
No conservation detected
Cow
(bosTau6)
No conservation detected
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]