RnoALTD0007279-2/2 @ rn6
Alternative 5'ss
Gene
ENSRNOG00000031475 | Col16a1
Description
collagen type XVI alpha 1 chain [Source:RGD Symbol;Acc:1310982]
Coordinates
chr5:148271084-148271612:+
Coord C1 exon
chr5:148271084-148271194
Coord A exon
chr5:148271195-148271425
Coord C2 exon
chr5:148271544-148271612
Length
231 bp
Sequences
Splice sites
5' ss Seq
ACTGTGAGT
5' ss Score
7.94
3' ss Seq
TCATATACCCTGTCTTTCAGGAG
3' ss Score
8.86
Exon sequences
Seq C1 exon
GGTGACCCCTGTGAAGTGTGTCCAACGCTGCCCGAAGGGTTCCAGAACTTTGTGGGGCTCCCTGGAAAGCCAGGGCCTAAAGGAGAACCAGGTGATCCTGCTCCAGCCAGG
Seq A exon
GTGAGTGCCCAAGTGGCCACTGAGAAACATACACAAGACAGACCCCGAGGAAATGGGTGCTTCTCAGTACCACCAAGATTAGACCCAGAGTTGCCTAGATGGGATTTGAACCATAGAGCTTGGGGTGGGGCTAGAGTGTCATCCCAGGTTTCCATGGCAACCTCCCAGCACTTTCCCCCCCAAGAGACTCTACAGTATCTTTTGGACTAGATAGGGTAGAACCATCTCACT
Seq C2 exon
GAGGGCCTAGGAACTGTTGGACTGAAAGGTGACCGGGTGTGTAAAGAACTTTCTAATGTGGACATTTAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000031475-33-36,34-36-2/2
Average complexity
Alt5
Mappability confidence:
NA
Protein Impact
ORF disruption when splice site is used (sequence inclusion)
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PD(14.3=21.6),PF0139113=Collagen=PU(49.1=70.3)
A:
NA
C2:
PF0139113=Collagen=FE(17.5=100)
Main Inclusion Isoform:
NA
Main Skipping Isoform:
ENSRNOT00000067663fB3377
Other Inclusion Isoforms:
NA
Associated events
Conservation
Mouse
(mm9)
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:
GTGACCCCTGTGAAGTGTGTC
R:
TCCACATTAGAAAGTTCTTTACACAC
Band lengths:
172-403
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]