Special

RnoINT0040541 @ rn6

Intron Retention

Gene
ENSRNOG00000023317 | Colgalt1
Description
collagen beta(1-O)galactosyltransferase 1 [Source:RGD Symbol;Acc:1309002]
Coordinates
chr16:20039969-20041154:+
Coord C1 exon
chr16:20039969-20040215
Coord A exon
chr16:20040216-20041043
Coord C2 exon
chr16:20041044-20041154
Length
828 bp
Sequences
Splice sites
5' ss Seq
GTGGTGAGC
5' ss Score
6.64
3' ss Seq
CTTGTCCTGTCTGCTCACAGGGT
3' ss Score
11.42
Exon sequences
Seq C1 exon
CGATGGCGGCGTTGCCCTGCTGGTCGCGCGGGCTGCTGTTGCTGCCGCTGCTCCTCCTGTTGCTGCTTCTGGGCGGTCCGCGCGGCGCTGATGGCTACTTCCCAGAGGAGCGCTGGAGCCCTGAGTCCCCGCTACAGGCGCCTCGCGTGCTCATAGCGCTGCTGGCGCGGAACGCCGCACCCGCGTTGCCGGCCACGCTGGGCGCCCTGGAACGGCTGCGCCACCCACGGGAGCGCACGGCGCTGTG
Seq A exon
GTGAGCTGCGGGCCTTGGCGCTGGCCACGGGAACTAGGCTAAACTCAAGCTCGTACCCGAGGGACACGGTTATGCACTTGGTGGGCTCGGCTGTTCACTGCAGAGACTCAGTTATGCTTCCGGGGAACTCGGTCTTCTACCTGGGGACCTGAGCTGTGTCCCGAGGATCTGATTACGCACTTGAGGGGACTGGGCTCTGTACCCATAGTACTCGGCCTCGTCCCCACTGCGGCTTGGGACCCCGAGCTACTACTGCCTCCTCCCCCCAAGTATATAGGAATCTGTTCTGGGTTGCTGCCAGCCCACACAGCGAGCTGCCACCCTAGGACTCCTGACCCCTCAGAATGGGCCAGGCTGGTGCTTCCAGACCCTTATAGAGAACTCCGCAGCTTCCAGATGAGACTCTGGAGGCTCGGGCCGCATTCCACATTAACAAAGTCAATGAAGTTATCTTTGTGACTTGGGTCTCACACAAGTGTGCTTTCCAAACAAGCAGGTTCTGTTCAGCCTGTGTACTAGTGAGTTGGGTGTCCTCTACTGCCCTGTCTGTCACCGACAGATGGGCAATGAATAGGCTTGGAGTGTAGCGAGTTTTTTTTTTTTGTTGTTTGTTGTTGTTTTTTTGTTTTTTTTGGTTCTTTTTCTTTGGAGCTGGGGACCGAACCCAGAGCTTTGCGCTTCCTAGGCAAGCGCTCTACCACTGAGAACCACTGAGCTAAATCCCCAACCCCGGAGTGTAGCGAGTTTTATCCAAGGCCTTATAGCTGTTGGGTCTGAGCTAGGATGGGAAACCCCCCAGTGCCATCATCTTGTCCTGTCTGCTCACAG
Seq C2 exon
GGTGGCCACAGATCATAATACTGACAACACTTCAGCCATACTTCGAGAGTGGCTGGTGGCAGTGAAGGGTTTATACCACTCTGTGGAGTGGCGGCCGGCAGAGGAACCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000023317:ENSRNOT00000024866:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact

ORF disruption upon sequence inclusion (1st CDS intron)

No structure available
Features
Disorder rate (Iupred):
  C1=0.024 A=NA C2=0.132
Domain overlap (PFAM):

C1:
PF137041=Glyco_tranf_2_4=PU(21.5=31.7)
A:
NA
C2:
PF137041=Glyco_tranf_2_4=FE(30.6=100)


Main Inclusion Isoform:
NA


Main Skipping Isoform:


Other Inclusion Isoforms:
NA


Other Skipping Isoforms:
NA
Associated events
Conservation
Primers PCR
Suggestions for RT-PCR validation
F:
CTGCTGTTGCTGCCGCTG
R:
CTGGGTTCCTCTGCCGGC
Band lengths:
326-1154
Functional annotations
There are 0 annotated functions for this event


GENOMIC CONTEXT[edit]

INCLUSION PATTERN[edit]