RnoINT0039510 @ rn6
Intron Retention
Gene
ENSRNOG00000007657 | Col27a1
Description
collagen type XXVII alpha 1 chain [Source:RGD Symbol;Acc:735115]
Coordinates
chr5:79098500-79102418:+
Coord C1 exon
chr5:79098500-79098544
Coord A exon
chr5:79098545-79102364
Coord C2 exon
chr5:79102365-79102418
Length
3820 bp
Sequences
Splice sites
5' ss Seq
CCGGTAAAG
5' ss Score
6.84
3' ss Seq
CTTCTCTCTCATTCCCTCAGGGC
3' ss Score
11.89
Exon sequences
Seq C1 exon
GGTCTCCCCGGCATTCCTGGCAAGAGGGGCGAGATGGGTAGGCCG
Seq A exon
GTAAAGATTTTCCGTGTCTATTACTCAGACTCTATGGGTAGCCCCACCTCCCGCTGGCCGTTCTGCACTGCTGGTCCCTGAGACCTGGCACTGTCTGCCTCTCAGCTCCGGTTCTCTGCTCTGGGTGTAGGGTGGGGAAACCGGGTGCAAGCGCTGGCCTGAGATGCGGCCTGGAGTTCTTGCTGCTCCAGGTTCTCCTCTATCCCTATGTGCTTCAGCAACTTGCGGGTAAAGCTGTATGTCTGGGGTTTCTGTCCAGATGTTCATGTTAGTGCCCAGCAGGCACTAGGGAACCTAAGTCTTCACCTGGACAGCACACCATCTCCACAGTGTCAGGTCTCCCACTCTGTCTTCCTTTATGCACACGTAGGCTAGACGACTAGGAAGTGTGGTAGGCCACAAGAGTAGTCCCGGAAATGGTTCAGTATCGACCCTCCACTCAAATCCACTGGCTCTGTTTAGGCCTCTCCGTTGCCATAAGGGATTGGTTTTCCTTTTGCTTGGCCATCTATAAGGCATAAAGAGAAAGACAAGGCCCAGGGAGGTTAAGCAATATTGCAGTCTCTGAACAGTTGGAGCAGGAGACATCCAGGACTGACTCTTGGGAAAACCTACCATTAACTAGAGAATGCAAGTCACTTGACCAGGGTCACACAGCAAATTGGTAGCAAGTCCAGATCCGAACCTAAGACCCTTGATAGCACAGGGTGTGTGCCACAGCGTCTCTTTTCTCACCATCAACTCCTTTCTCCTCCAGCGGAACCTACAGCTCTCATCCCTGCCTCAACTCTCGTGCTAGAAAGGGAGTGTGTAATTTTGGCAGAAGGTCCAAATATAAAATGCTGGCAATTGGCTAGAACAGGCAGGACTTATGGCTCGGCTGGTTCAGGGTTATGCACAGCAGATGGCAGAGCCAGGTCCTAGCCAGAATCTCTCATTGATTCTAGAAAGGAGCTATAGTGAGTCTTCTTGTCTAGCATTTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCCTCTCTCTCTCTCCCTCCCTCCCTCTCTCTCTCCTCTTTCTCTCTCTCTCTCTCTTTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTTCCTCCCCCCCATCAGTGCCCTTGGGATTCCTACCCCCACCATACTGCTTATGACCTGGGCCTGCCTGCTGTGACTGGGCCTGCACAGAGTGAGGAAGGCAGTCCTGACACTAGATCAGTTGACCCAGGCTTGGCTCTGTCTCTCACTGTGTGACTCAGAGACACTGAGAGCTTGCCTGAGGACACACAGCTATCTGGTTCAGGACACAGATTCCTGCCCTGGACTTTCCCTAGTCATCAGATTGGGAAGGAGAGAGTATATATTCCCACATGGGGAAACTGAGGCCCGAAGAGATGAGGGGGAGGGTCTGGTTTTTCATTTAGATGTGAGCCTCAGGTGTTGGTGGCTTTTGAGTCTCCATGAGACTTCTGCCTGCCTGTCTCCATCTCTTTCTCCCTTGGTAGCATAACACGAGTGATTTTCTAGTTTCCTTCACAGGACAGAGTAGGACATGATCTGCTAGACCTGTAGAGAGAATTCCAGAAATTAAATACTTAGCTATTATACCTCTGTAAGTGCATGGCTCCCATTGGAGCCTATTGAATAGCCCCATGGAGGGTACCACCCCTGACTAGTGGTTTAACATTGCACTTTAGCTTACCAGGGACTTGTCAATGATGCTTAGCTTAGTCTTGCCCGGGATGCAAAGGGGTGACTGGTTTGCAGGCTAGAAGACAGCCTGGAAGCTCAGTGGGTCATCCGTTGAATGCCTAGGCTTCCCTGGCCCTGAATCCATCCTCTGTAGCAGAAGAGCAGATTCTGGAGGCAGGGGCTTGGCTGAAATGCCTTTAGATGTCTGGGCCTTGGTACACTGCTGTCCGCACCTCTGGCCCTGTGAACTGTTGCCATCCAGAGAGAGGGCGGAGCCTGGCCCTACTCTATTTTCTTCTGCCGGGCCTGGTTCTGCTCACAGTTTAAGGCGAGGCGTCCAGTCCCAGAGGGGCCCGACCTGGGGAAGCAGGGAAGCCACGTAGCGGGCGGCAGCAAGCCAAGTTCATTCCTTGGGCCATGGGCCAGGCTGCTGCAGTCAGGGGTTGGGACAACAGAAGAAGGAAGTGCCTGCTGCCATAGGCTAATGTGCAGTCATCACGCATACATCAGGCGCAGCCAGTCAGCACCGGATGGTTAGCTGGGCAAAGAGTAGAGGCCCTGGGTAGCTGCTGGATGTGGCTGTCTCCTAGAGAGTGAAGCAGCGGCAGGAGCTTTGAGTCTCAGCTTGCTATTGGTGCAGAAAACTGTCGTTCACCTAAGCTATGGGCTTCCTCCGTCTCAGACCACTTTTAATTGTTCCAGCATCTTTAAAGCTTTCGCACTTCCTAACAGTCTTTTTACAATAAAAGGCCTAGACTCCTAGGTCACCCATCAGCAGGAGCAAAGCTAGAGGTGGAGAAGGAGAGTTGGTCTCCAAGGCCATCGCCCTGTGTCCAGGCAGAACCGGATTTAATGTGCATTAGTCTGGAGCTGTGATGGCCCTTTGGGATGCTGAACTTCTGGTTCTTCCGTTTATGCTTGATGTCATGTCACCGCAGAAATACCAGGAGAACAGCTCCGGGGCCAGACTGCCTGGATTCAAATCCCACCATGCTATCCCATAGCTGCGTGACTTTGGGCAGGTTTCTTAACATCTCTGGATCTCTTGATATCTAAAATACAGTAGGCACAAAGTCCCTTTCGTGAGTCTGCTGCAGCTGGATGTTACTGTCATGGCTGTGTCTACTGTCACTCATGCTGACCCAAGCTACTGCTGACCTTTCAACGTGTTTTGAAATCAACCTTCAGGGGGCAATGTCTTGAGACTCTCCCTGGTCTTAATAGTCTCTGAAATAAAACAGACATAACTCAGGTTCTTGGAGCCTTCTGAGTGGTAGAGCCAGGATGACTTGGGGCTTTTGGCCTGGCTACTGGGTCTGTGGGGAATGGTGGGCCAGCTTGGAGTTGCCCTGTATGCTGTCCTTCATCTTGGGAAAGCCACAGTTGGGGTTGGAAGAGGGGAAGGAGTTTAGAGGCTCTAGCTAAATCCCTCCTTTTCCTTTGAAGTGCGAATGGATTCCCCACCCCCACCCCCATCCCCCAGGCCTCCCTACAGCTGATGTTTTTCCAGCTGCCTGGCTCCCTGAGGACTGTGGAGCTTCTTAGTCAGGTCACAGAAGGGCTGAAGGGCCAGACCTGCCCAGGCTGGTGGCCCCTCTGTGACCACAGTGCTGACTCTCCCTAGCAGTGCAACTTTGCATGACCTTGCCACTTTCCCTGTCACAGCCTTAGTCTATAACATAGCGAGGATAATTCCACAGTATGGCTTCTGAGGTGCACAGCACAGCCACAGAGCCTTCCTTTGACCAATGGGGAAACTGAGGCCAACAGGTTCTGAGGAAGGTGCGCTACAAACTTCAGCGATCTGCAGTGGTCTAGGTCAGGGTCTCCCTTCCTGCCTCAGACCGTTATCTCCACTGCACTGGGAGTCCCAGTGTAGTCTCAGACCCGGGGGTTGTGCCTGTCCCATCTCTCAGATTAGCTGTATCCTGTCCCTTGGTTCCATGTGTGCCAGTGTCTGTGGGTAACAGGGAGGACTTCAGAACCCCAGATCGAGGAGTGAGCCTGCTCAGATATTGTCCTTGCATCCTGCTGGGGGTGTGGCTCAGAGCCAAACTGCAGCCTTGAACACTAACTTCCCGTATTTCTTCTCTCTCATTCCCTCAG
Seq C2 exon
GGCTTCCCTGGAGACTTTGGGGAAAGAGGTCCCCCTGGACTTGATGGGAACCCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000007657:ENSRNOT00000010333:12
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(8.1=40.0),PF0139113=Collagen=FE(12.0=100)
A:
NA
C2:
PF0139113=Collagen=PD(10.9=55.6),PF0139113=Collagen=FE(19.5=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal4)
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]