RnoINT0039520 @ rn6
Intron Retention
Gene
ENSRNOG00000007657 | Col27a1
Description
collagen type XXVII alpha 1 chain [Source:RGD Symbol;Acc:735115]
Coordinates
chr5:79119739-79121174:+
Coord C1 exon
chr5:79119739-79119792
Coord A exon
chr5:79119793-79121129
Coord C2 exon
chr5:79121130-79121174
Length
1337 bp
Sequences
Splice sites
5' ss Seq
GAGGTGAGT
5' ss Score
10.03
3' ss Seq
TATGCCTCCCCCAACTCTAGGGA
3' ss Score
9.35
Exon sequences
Seq C1 exon
GGTAAGCCTGGAGCCCGAGGCCTACCTGGACCTCCTGGGCAGCTGGGGCCTGAG
Seq A exon
GTGAGTTGGCCCTGTCCCCTCTTGTCCCTCTTTGACTTCTCTAGCCTGTCCCAGCACCTACCTGGCTCTGTCCAGGGTACCAAAGCCATATCTGGGGCCAGGGCCCCTTGAGATTCATCACCAGAGCATGTGTTCCCTTACAGCCCTGCCTGTTTCTCTTCTCTAATCTAGTGGGACAAGTGACTTTCCATCCCCACCTGTCACAGTTCATCAGTCTCAAAATGAGAGGATAGGACATGTCAGACCCCTTTTATAAGTGGAGATCTTTCCTTGGAGATCCAGGGAAGGGAATGACTGCCGGGTCCTGTGTTGGTAGCAGGCAGGGCCTTGACTAGGACCTAGGTGTGCCAAAGTCCAGTCTGTGCTCAGATCCCCTGCTCTCCTCACAAACGCTCTTGGGAGACCCCAGAGCATCATGGCAATGCCATGACTTGCCAGTTCACCTGAACCTAGTCAGGAGGAGCTTGCCTCAGCCTATTGGGCCTTCCACAGTAGCCTGGCTTTTGCTTGTGCATGCTGCCCTGAGCCTTGCTTGGCACTGTGGTGCACAGCCGTGGGAGAATGAGCAACCGCAGGCAGGCCTTTGCTGATGCGAGCCTTTCTCCGAGCTGGGTGTGGGTCTGGCAGAGTCCCAGTGCTGGCTCTTCGAGTCACTGCATGGGGCTGCTTTCCGGGAAGCTGCAGTTGCTTGCTGCAGGGGCTGCTTTAAGGGGCTTGCGGTCAGGCTCTGGCTGCCAGAGGATCAGGCTGGAGACAGTTGTGACCTTTGGAGGGCTGGAGATCAAGGCCAGCAATAGGAATGAAAGGAAGAGAAGGAAGAGACAACTGCAGCCAAGGCCTCTCTGCCTGTGCTTCCATAGCTGCCCAGAAAAACCCTTACTGAGCCAGGCTCTGGGCCTGGGGACACTCGCTCCTTCCTACATTCACCAGGATCCCTGTGCCTTCCTGGGTGCTGTGTGCAGGGTGCTATGACATCCTTAAAACAAGATGTCATCCCTGGCCTCTAGGAGTCAGCATCAAGGATTCAGTCTGAGGAATCAGAGGCATACACCAGGGCTAATGTCTGCTATGGAGTAGAAAGCAGAGCTCAATACTGAATCTGTGTTTGAGCTGGAGCCTAAGGTCCCATTCTTGATGAACAGCTTAGACACTGGGGTTTGTGGTAAGATCCTTAGGTGGAGACTGGTGGACACCTCCCAAACCATGGGAACCAGGCTGTGAGCCAGGCACTCCGTCCACTTGCAAGGACTCCCTCCGTACAGCACGGGCTTTCCCAAAATTCCACTTTAACTTCCACCTTTGTCTTTCTTCTTTTTTTATGCCTCCCCCAACTCTAG
Seq C2 exon
GGAGATGAAGGACCCATGGGGCCACCAGGAGTCCCAGGCTTGGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000007657:ENSRNOT00000010333:21
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PD(9.2=33.3),PF0139113=Collagen=FE(25.8=100),PF0139113=Collagen=FE(18.7=100)
A:
NA
C2:
PF0139113=Collagen=PD(11.4=60.0),PF0139113=Collagen=FE(17.5=100)
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]