RnoINT0040554 @ rn6
Intron Retention
Gene
ENSRNOG00000028207 | Colgalt2
Description
collagen beta(1-O)galactosyltransferase 2 [Source:RGD Symbol;Acc:1304702]
Coordinates
chr13:69895892-69899368:+
Coord C1 exon
chr13:69895892-69896019
Coord A exon
chr13:69896020-69899161
Coord C2 exon
chr13:69899162-69899368
Length
3142 bp
Sequences
Splice sites
5' ss Seq
GATGTGAGT
5' ss Score
7.77
3' ss Seq
CTCTTCCCATCTCCTTACAGTTA
3' ss Score
11.22
Exon sequences
Seq C1 exon
GTTATTGACCGAGAGCTGGAGAAGACTCTCGTCATTGAGGACGATGTGCGTTTTGAGCATCAGTTTAAGAGGAAGCTAATGAAGCTGATGGATGACATTGACAAGGCTCGGCTGGACTGGGAACTGAT
Seq A exon
GTGAGTCACAAGGATGGGTAGCTCTGAAAGACAGCCTTTCCCAAGGCACAGAAAGCCCACCTCCCCAGCTGGTAGGAAATGCTGTCAAGCTTCCTTCCATTTACCTGGCTTTTACACCACAGATGTTCCCAGAAATAAGTAGGAAAAGGTTGGGTGTCTAACAGGGGAAAACACTGACTGACTGCTGGGCTTGTGATGGGAAGCCAGCCTCACTCAGGGAATGCTGGCTCAGAGCTGGTATAGCTGGTGCTTGGTCTCTTGCCTCTGAGCTAGCATCCTTTCCTTTTCCTTCCTTCCTTCTATCCCTTCTCTCCACTTATCTCTTTTTCTTTATCTTTTCTTCGAAAAATAAGCAACACTTCCTGTTCTTTCCAACGAGACAGAAACGTCCCAAGTTTTCCAACTGTGAATCTAAGACAACCCTGCCCAATTCGAGCTCCTTTGAAACAGCCCAGCTTTCCCTGCTCTTCTGTCCTCAGCTGGGAAGATAAATTTGGACCCTGACAGAACTCCTCTTTTGAACTTAAAAAGAAATTCAGCAATGGTCCAACTGACTAGGAAATAGACCTCAAACATCATACTATGTAACAAAAAAAGGCCTCCCCTGTCAGGGTTGTCATGCGATCTGTATTCTGAGCAGTCTGTTAGGATCACAGTTCTAGGCTCCAATAGTCACCGTTCTTCAGCCCTTCTGCATCTGTGCCTATATAGCCTGTGGTAAAAGACCACGCCCACGCAGACTGGAGGCCGTGTGCTTACGTGACACACTCAAAGGCAGCTTTGACTGATGCTCCATCATCACAGAAACACCATCCGGGACACCTAAAGCAGAGAGTCAGCATGCAGGTCTGCTCCTGGGTAGCATGGTTGGTGCGTTCTCAGGACAGAGCGTCACCAGATCCAAGAAGGAAGGACAGCTGTCCTGGTGAGGATAGAAAGAGTCCAAGAGTATCCTAAAATGCCACAGATTCATCTTTGAAAGAACCATTCACTACTTCAGTGAAGAAGTGCAACTCAAACCAAACACAGAAGCTAATCTGTCCATGATTAATAGCTGTGTTGTTTACAGAGGAAAAAAATAACAATAAATCAGGACACTCAAAACAGTCACTGGACTTCTCTGGGGAGGTTTTTCTGTTTTTGTTTTTGTCTTGTTTTGTTTTGTTTATTCAGTGGAAAATACAGTGTGGTCCATATATGTTATTTCAAATTTTCTGACCACACTGAAAGGTTAAAAAATAAATGAGGCAAAATGAGTTCTATTTCTTATGTTTTATTTAACCAAATATATCTAAGTATCACTATTTTAGCATGCAAATAATATTTTTAACCATGAATGATATAAGTTTATGGGTTTTGTGCCATCTTCAAAGGCCTGTGTGTGCTTAAACTCAGAACACATTTAAACCCAGAAAATAAAATGTCAACTGTTAAACTCTAATCCTACCAAATAATAATTTTGCTTTGCAGGAAAAAAAGCATTTTGCATATATAAAATATTAAAATTTAATTTATTTTTAAAATTCATTTTAAGTGTTTGAAATTATAATATACTTTCATCATTTCCCTCCCTTTCCTCCCTCCAATCCTTCCCATGTAGTTCTCCTTGTTCTCTCTCAAATCCATGGCCTCTTTTTCTTTATTGCTGTTTCATAAACATATATATGTATGTACATATATATGTATATATATGTATGTATATATATGTATATGTATATGTATCCTAAATATATAAATATTACTTGTTTAGTCTATAGAATGTTACAGGTACATATATGATTTCAGGGCTGGCCACTTGGCATTGGATATCCAATTTGGGGGTGTTATGGTTTGTATATGCTCAACCCAGCGAGTGGCACTATTAGAACGTGTGGCCCTGTTGGGGTGGGTGTGCCACTGTGGGTGTGGGCTTTAAGATCATCCTAGCTGCTTGGAAGTGAGTATTCTGCTAGCAGCCTTCAAATGAAGATGTAGAACTTTCAACTCCTCCTGCACCAGGCTTGCCAGGATGCTGTAACACTCCCACCTTGACAATAATGGACTGAACCTCTGAACCCGTAAGCCAGTCCCAATTAAATGTTGTCCTTGTAAGAGTTGTCTTGGTCACGGTGTCTGCTCACAGCAGTAAAACCCTAACTAAGACAGGGGTTTCTTCCCAGGGTTGGGGAGACTTCTGCTCTCAGTATTCCTTAGTTTCCTGTAATTCTTTACCTACGGCTGAAACCCCATGAGATTTCCCCCTTCTGTGTCTATTGGTGCTGTGCTTGCTCAGGTCTCATTTAGACAGCCATGTTGTTGAGACTTTGTGGTGTAGCTTCCCTGACATTCTTAGGAGATGCAATCTTACAACAGACATCCCACTCCTCTGGCTTTTACAGTCCTTCCACCCTTCCTTCCTTGATGTCTCCTGAGCCTTACATGTAAGAGTTGTATTAGGGATGGGTTAGTCAGGGCTGGGCTCTACCGCACTTGAGAAAGTCAGACTCTAAGGACTGATGCTTGAGGTCCCTAGAAGAGCTGAAAGCAGAATATGTTCTTGTTCTTCAGGCCTCTGTGTCCTCTTCAGCTCATGAGCGGAGTGTAAAGGGGAAAGACTTTCATTGTCATTCAGACTCCCCAGAAGGAACCCTTTGGGGCCCCTCTTGGGTCTCTAGGTCCTCTGCTGCAGACTCTTCCTCACCCACAGCCTTTTCTATGCTGTTTAGCACCAGCATTTGGAAAGTGGTACAGAAAGAATCCAAGGCAGAAGCTCTGGGGACATGAAGACAACAAACTCAAGATTCTCACATCTGGTTCCTTTTGTTCCTTCCCAACCTCTAAACACAGCTGGAAATATCATCCCAGGGAAACCGTCCAAGCAACTTTTTCATCTCTTTGCATCTTCCCTTTCTGGCCTAAAGACAGACCACTAGGCCTGAATACTTGGGGTACTGATAAATGGAGTTGGGAAACTGACTTTAGGAGGACTGATAGCAATTACAGATACCAGTGGAGTGATCTCTGTGGTGATAAACATTAGGAAAAGACACGAGAGTTCAGGCTTTAAAACATCTCTTAAAACTAAATATGTGCTCTGTTCTTATAATATTCAGTATCCTAATATTCAACTTGGAACTTTCCTCCTCTTCCCATCTCCTTACAG
Seq C2 exon
TTACATCGGTCGAAAAAGAATGCAAGTCAAAGAGCCAGAGAAGGCGGTGCCCAATGTTGTAAATCTCGTTGAAGCTGATTATTCCTACTGGACGCTGGGCTACGTCATCTCCCTGGAAGGAGCACAGAAGCTCGTTGGAGCTGATCCCTTTGGGAAGATGTTGCCAGTGGATGAGTTCCTGCCAATCATGTACAACAAGCATCCCGT
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000028207:ENSRNOT00000030109:11
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:
PF0175512=Glyco_transf_25=FE(22.6=100)
A:
NA
C2:
PF0175512=Glyco_transf_25=PD(32.3=85.7)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
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]