RnoINT0039245 @ rn6
Intron Retention
Gene
ENSRNOG00000012759 | Col19a1
Description
collagen type XIX alpha 1 chain [Source:RGD Symbol;Acc:1308920]
Coordinates
chr9:30537644-30541265:-
Coord C1 exon
chr9:30541203-30541265
Coord A exon
chr9:30537680-30541202
Coord C2 exon
chr9:30537644-30537679
Length
3523 bp
Sequences
Splice sites
5' ss Seq
CCAGTAAGT
5' ss Score
9.09
3' ss Seq
TATTCTTTTTGTTATTTTAGGGC
3' ss Score
9.73
Exon sequences
Seq C1 exon
GGTGAGAGAGGACCTGTTGGAGATAGAGGTTTTCCTGGGCCAGAGGGACCTTCGGGGAAGCCA
Seq A exon
GTAAGTACTTTTTCTTACCATCTAGAAACTGTTTTCTAAGAAGTGTTAGTCTAAGAGTTGCCTCTTCACGTTTCTCCTTAGAAGCTAAAGATTTGAGTCAGGGGCTTCAGAAAGAAATACGAACCGGTTCTAAAAATTGAATTAGGGGATACTAGTAGGGGATCCCTTCTGGAATTTTCTAGAACTTTACCTGGTGTCTTTAGATCTTAAACGATGGCAAGGAGATGTGAAATTTTCTAAGCATTCGTAAGGTAGACTTATTATTTGTTAGTTCGAATAACTTCAGTAGAGTTAAAATGAAATGCCCTATCTGATCCTAAAACATGAAAACACCAACAGCTCTCTTCTCCTGCTCCTCCTTCATGTACAATCCTTATCCTGACACTGTCATTGCTAATCACTGCAGTGGGTGTGTCAGGCCCATGCCCTAAAAGAGCTTGTGGCCAAAGATACAGAGTATTGACTTGACATTGTGACAGTCATCCCCACCCAGCATTTATACATCTAGGTCCTCCAATGACTAAAGGATGTGCTGGACCAGGAGCCAGGGATTCGAAGTTCCGGGGTATTTTGTTTTGTTTTAAGGATCTCCTTTTTATCTTTTAAGATTTACTTATTTTATTTTATGTGTATGAGTAACTGCATGCGTATATGTGCACCGTATGGTTGCCTGGTGCGTGTGGAGGCCAGAAGAGGGCCTCGGATGCGCTGGAACTGAAATTATAAGGGATTGTGAGCCTCCCGGCGGGTGGTAAGAACCACACTTGGTCCTCAGAGGAGCAAAGCATGCTATTACCTTCTGAGCCATCTGTTCAGCCCGCCACGCCCCTTGAATAGAATGCCTTGGTCACTTGCTGTGGTGTGTAAGAAAGGCTGGGTTTAAAAATAAGTGGAACGTAGGAGTTTTGTTTAATAGCTCTCTGACAGCTCAGAGCAGATGCATGGTCTGGTCCTCATCTCCTCAGAGAAGACAACGCAAGAGACAAACCGCGTATTCTTGTTTAGAGTCAGACATTCTAGGTCTAATCCATCTCACTGTTTTATGAGTTAGTTGGGAAGTATGAGGTATGGAAAGGCCTGCAGTGCTGGCTACAGGAAGCTAAGTGAACAGCACCATATCCTTCCGTGCTTCCTGTCACCTCTTCTTAACAGACTCCTCCCACCCTTGTGAGCCGTCTTGTTAAAGGCTTGGGTTTCCGGGGTATCATATGATACATAACTCTTTTTCCATGAAACAACCATTTTTGACCAACTGTTCCGTGCTAGGCAGTGGTTGGTGCCAAGAGCTCTTGAAGAAGGGAGAGCCATTCACATTTGAGGGCAGGTTGCCACCCTAACCCTGTGAACATTCCCACAGTGCTACTTGGATTTAGTCAGTCATCCAAAGAAGAGACCATAGAGGCGGGAGGAGCTTGTGTTCTGGGAGAGTTGGTGGGGAAAATGGAGCATGGAAATGATCATGGTTCATTGAATATATGTACGAATTTTTTTTAAAAAGCATACATTTGAAAGCCTCAAAGCATGAATTCCAGCTTTACGTTTGATTTATCTTGTGTTCAGCTGACACGTTGTTTCTCATTCTCTCCTTTAATCGGTTTGATCTTCATGGCTAGTGTTCTCGGGGCTAATAAATTCCTTGAACTATACACTTCAGGTAACATATTCTTAGTCAAAGAACTCTCGTAATTCCCAGGGTACTTCAGAGAAGTCCCGAGCCTACGGTCGGGTTACCAACAGCCACAGATGTCATCGTGATTTACAGCAGTGAAGACAGGTGGCTGTCTGCAGCTGTGTCCTTGTGGACTCGGTGCCTGCACAATAAAAGTCTCTCAGGCTTTCAGAGAGCATGTCCAGGCAACGCCTGCTGCTGGCTAGGAAACCTCATCCCTCACCTTGATCTCTCTCTCCAAATCACATCTCAAAGCCACATCTGCAGCTGGGCTCTGGGTCTTTGGTTTGACCTCAAGCTCTTTTCATCTGCCGGTCTCTGATGGGCAATTCTGTCAGTTTTATAAATCTCCTGCAGGGCTGACTTTATGGCCACTTCCAGAATACCTTTTAAAGGTCCCAGAATTTCCAATTTTCTAATAAAAAAGAATGCCACTGCTTAGTAGTCTTGAAAACTACAGTTACAGACTCTCAGCTTTCATTTTCTATTTTTTTTTCAAAAATAATGGTTCTTCTCCAGCTGACAGTTTATTTCATAGTATGTTATGAAATCCCCCTAGAAACAACTGGCAGTGTTTATTGAGAAGGATCCCCACACTTAAAGCTTTTTAGAAGGTTGTTACATTGATACTATCCCCAGGAAGACTTGAATGAGTGTCCCCACACAGAGATAGGCAATCAGTGATAGGGTAAAGTAAGGATACCAACAAAAGCAAGTTGGTGAATCATCGGTGAGTTTAACTGATACTACTTATAGGAGTTTAGGTGAGGAGTTATTGGCAGGAGCTTGTATAAATGAAGCTGCATCACCAAAAGCCCACTCCAGCACAGAAGATGCCCACAAATTCTGGAACCCTGAAACTCACTGTACAATTTACAGGCAGCTTAACAGGATGGAGTGTCACTTCTAGAAATTCTGTTGCTTCTGGTCCTCTTCCAGGCAGCTCAGCTTGTCTGAGGATGTCTCTTACTCCCAATATAATCTTGGGGAAGGAGAAGTGTAGTGAATATACTCAGTTTCAGGAACTTCCTGAAGATTTTGAGTTTTTCATCCTGAGTTTAACTAGCTTCCCTACAGGATGAAGGCTTTCACCTTCCTCTAAAATATTCCATTTTTGTTTGTTTGGGTATTTTATGAATCTACATTTCAAATGTTATCCCCTTTCCCAGTTTCCCCTCTGGAACCTCCCTCCCCCATCCTCCATTTCCCTACTTCTATGAGGGTGTTCCTCCTCCCACCCACCCACTTCCCACCTCACCATCCTGGCATTCTCCTACACTGGGGAATCAAGCCTTCATAGAACCAAGGGTCTCTCCTCCTATTGATGCCAGACAATTCCATCCCCTGCTACCTATGCAGCTAGAGCCATGGGTCCCTCTATGTGTACTCAATATCTCAAGTTTTAAGAAATTGCTCTCTGAGATGGAAGTCTTTATCTCAGAGAGGTTGTTGCAGAACAAAGGTATAAAAAACTCCTATATCTCAGCCACCCAATGGCTTCATTTTTCCTAGGAGGTGGAGAGAGCCATCTTGGATGACTACTTGAATGGACTCTACACTTACTGTGTTGTTGGGCACTTACTCCTGAGTTGTAAACTCACTCTTACATTCTTTCCTGTGTGCTTGAAGATGAGGATGCTACTCAGATGAAATCAATCCCCAAACCTGGTCAATGGAACCAGGAAATAGCAGAGTTTGAACTCAGGGGCACATGACTAAACCAAATATGTAGTCTATTTTGCCATGCAGATTTACAACTGAGATCAGAAGAAATACATAATGTGATTTCATTTTGCCTGTTTAACTATGACTGTATTCAGAGAAGGAATAGAAATATTCTTTTTGTTATTTTAG
Seq C2 exon
GGCATAAATGGACAAGATGGATTGCCAGGTGCTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000012759:ENSRNOT00000017169:44
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(29.9=100)
A:
NA
C2:
PF0139113=Collagen=FE(16.4=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
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]