RnoINT0039534 @ rn6
Intron Retention
Gene
ENSRNOG00000007657 | Col27a1
Description
collagen type XXVII alpha 1 chain [Source:RGD Symbol;Acc:735115]
Coordinates
chr5:79141508-79143200:+
Coord C1 exon
chr5:79141508-79141561
Coord A exon
chr5:79141562-79143146
Coord C2 exon
chr5:79143147-79143200
Length
1585 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGA
5' ss Score
8.68
3' ss Seq
TTGTGTTTGGCTTCTCCTAGGGT
3' ss Score
7.95
Exon sequences
Seq C1 exon
GGGCCGCCTGGTGCAGTGGGAGAACCTGGCCTTCCTGGGGACTCCGGTATGAAG
Seq A exon
GTGAGACAAGATGAAAGATGGGAAAATGACTTGTTGACATCAGTTCCCAGCTGGCAGCCTGGTCCTCTCCCTGAAGGAGAAACAGACCTTTCTTGTGCTTGGGATAATGGGGTCTCTGTCCTGGCTAGGGAGCAGGCCTGACATGCCCACTGTCCAGTTCCCAGGCAGCTCAGAGCCCCTGCACTATCCCCTGCCCAGCTGTGTTTTGTCTGGCACCTGTTTTGGTCCCCCCATTGGGGCATGTGCCCCTCCTGGTCTGCATGATACCATCAGCATTTCAGCACAGGTGACCCCATTAGCTGTGGGGACACAGGCACCTATTGATACCCAGCCCTGGGGAGCCCTATCCGTCTTCTGCTGTTGGAGGAGGACCCTGCTTACCCTGCAGACCTGAGAGCCTAGGAGCCACGCTGGCCCGGAGGACTGGAAATAGGCAAGGGACTGTAGGACGGCAAGAAAATCCTTCCTGTCCCGTGGTTCAGTGTCCTGTCATTCTAAGGGAGCTAAACCAGGCCTGGGGCTCCTGGCCTTGGCTCGGCTCTGCCTCACTTTGCCCAAGCAATTAGAAAAAGCCATCAACCTATGAAGTGCCATTCACATATAAAGTGCATAGGACTGGCTTCTTCCACTCAGGACTGGGCTGGGGCACCATGAGCCACTTCCTAGTGTCCAGACACCAACAGAGAACGTGGTGTACATGTTTCCAAAAGAGAGGGGCCTTTCAGGGGAGGGTACAGGTGTTCTGAGTTCTCCCTTGCTTGGTTTCTTACCAAATCTCAAGGAAGAGGAAGGATGGCTGGTGTTCATCCCCACTGCTCTCCAGCCATGGCTACCCTAGTCATTCCACCCACTTTGACCCTGAGTCTGTCATTTGGGCTAGCTTCTGAAGGATGACACTGTTCCCTCAGGATTTTGCAAAGGTCCAGCTCATTCGAATGAAAATGTATTTAGAACAGCATGACCAACTCTGATGGCAGTGATGACGGTGTTGGCAGTGACAATGGTGATGCAGTGGTGGTGATGCAATGATGGTGGTGGTGATGCAGTGATGGTGATGGCGATGCAGTGATGGTGGTGGTGGTGATGGTGATGCAGTGATGGTGATGGTGGTAGAGATGCAGTGATGGTGATGGTGGTGATGGTGATGCAGTGATGGTGGTGGTGATCTAGTGATGGTGGTGATGGAGATGGTGGTGATGCAATGATGGTGATGGCAGTGATGGTGATTGTAGTGATGCAGTGATGGTGGTGATGGTGGTGCTTCTGATAATGATAGATTGATGGTGGTGGGGATGGTGATGATTGTGATGGTGGTGATGATGGTTTTGGTGATCTGGGTCCTGGTAGTAATTAATGGTAGTGATGAAGGTGATGGTGAAGGAGGTCTGACCACCTAGTGGAGGAGCATCCCATGGCCAGGACTTACCTGGAGCAGGGTTTGGACTTGAGTTAGAATTTCTCTATTGTTCTCGAGAAGGAACTTCCCCCAGCTTCTCCAGTCCTAATCAGAGCTGGAACTAAGAGGGGCTGGTGGAGGCTAAGGTTGGCTATACCCACCCAACGGATTGTGTTTGGCTTCTCCTAG
Seq C2 exon
GGTGACCTTGGACCTCTGGGCCCTCCTGGGGAACAAGGGCTCATTGGGCAACGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000007657:ENSRNOT00000010333:34
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=FE(19.8=100),PF0139113=Collagen=FE(26.2=100)
A:
NA
C2:
PF0139113=Collagen=FE(19.5=100),PF0139113=Collagen=PU(21.5=94.4)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal4)
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]