RnoINT0039253 @ rn6
Intron Retention
Gene
ENSRNOG00000012759 | Col19a1
Description
collagen type XIX alpha 1 chain [Source:RGD Symbol;Acc:1308920]
Coordinates
chr9:30786158-30790640:-
Coord C1 exon
chr9:30790560-30790640
Coord A exon
chr9:30786284-30790559
Coord C2 exon
chr9:30786158-30786283
Length
4276 bp
Sequences
Splice sites
5' ss Seq
AAGGTAGGT
5' ss Score
10.29
3' ss Seq
ATTCTCTTTGGGGATTCTAGTGT
3' ss Score
3.16
Exon sequences
Seq C1 exon
ATTGAGCTTCACCAGCTCAGAATCTACTGCAATGCAAGCTTCCTAGCTGGAGAATCGTGTTGCAACTTATCGCCTACTAAG
Seq A exon
GTAGGTTCGTTTTCTTACCATGTGAAGCACAAGCAAGTGTGTTATCTTTTAGTTACCGTTCGTCATCTGTAGAGCCTATATATAGGGCACCGTGAAGTTTCTCAGTTGAAGCTGGCTGTGTAATCTATTCTCAGTATGGTGCTTAGAACCTGCTCACACTTCAACCACAGGGTTGCACACTAAAATTTGATGGTGATTTGTGCTCACATTGGCCTCAACCTAGTGAGAAGCAGCCTTAATGTATACCTTCCCTTGCCCTGTACTGTTGCCTTGTCTCAGCTGAGGCCCCAGATGATGGGAGGTGCTGTCAACATTTGTCAGATCTTTCCCTTTTAATGGACTCCCACATCTTAAGATTAGTCAACCCTTGTCTAGTTTTGCTTTGTGACACATTTCCATTCCCTTTGTCCTCGCCCTGCCATTGCCAAGTACATTTTTACGTTATGCCCAGCCATCATGTCAACTGCCTTTCTAATACACATTCTTTCCCCTGATAATATCACCAGAATGAGTCTCAAAATCACTGAATTGCATATATATTTGTTGTCTTCTAGTAAATATTTTTTTTGAGCGTTGCTCTAGTAAACACTGCACTAAGGAAAAAGACTGGCAGATATGAACAGGGTCCCAGTCTGGTCATCTTTTTCTTAAAGTCCTAAGTGATTCCTTGTTGGCAATAAAACATCAATCCAGTGAATTAGTCTCCCATACTAAATATTCTTGACCTCATTCTACAGCTATCACTACTGTATCTATGAATTTCATTCCAAGAAAAAAAATCTGGTGTTCTCTCAGTTTCACTCTAATAGTCTCTCATGCTGTGTCCCAATTTATGAATATAATTATAGTTTCTTTAAATTGATTAAAATATAAATAAAACAGTAACTGAGGATTTACTTTCAAATTCTTTTATTATCTAGCGATTTGTCAATGCATAATTATTTTGTTTTCTACTACTGTGATAAAATACCATGACCAAAGCTAACTTATGGGACAAAGAGTGGTTTGGTTTTATTTATTTATTTTTTTGGCTTATGGTTCCAGAAGAGGAGTCCATAATGGCGGTGGGGGAGGGGAGGCCTAGCAGCAGGCAGCTGGAGCCAGAAGCTGAGAGATCACATCTGTCTCAAACACAGAGTAGAGAGAATGAAGAGAAAGTAGACAAGGCTATGAAGTCTTCAAAGTCCTCCACAGTGACATAAGTCCTCCAGCAAGGCACCACCACCTCCTCAAAGGGCACCACATACTGGGGACCAAGTATCGAAATATCTGAGCTCCTGGGGATCTTTTCTCCTTCAAACCACCACACAGCAGGAGAGTTTCATTTCTCAATTTGTCAACTACAAAATCAAAGGCTTTCAAAACGGAATAATTTAAAAGAAACCTCCCCAAAAGAACATATGAAAATCATAAGTCCAATATTCAATGTTTTGCTTCTTTGGATCTTAATTTCTCCAAATTTCTACACTTACTAGGAAATCCATATGAAATTTTTAATCGGTGATTTTTTTTAGTTCAAAAACTCTTGTAACTCCTCTCATGTGGTTTGCGCAGTAGAGTGAAATCTAGCCAAATAACTCAGAGTCTTTCAAATATTATGCCTTGCTTATATAACTTGGCTGTATAAAGCATATCTCAAACCCAATTTATGAATCTCATTCCAAGCAAAGTGAAAGTCTGCCAAATATCTTTCTATAAATACCTAAAAAGATAGCTTGAATGCCAGTCTACAGACTTGAAATGCCGAGGCTTCCTGAACCTACACCTTTAATCATGAAGGTTTTCTTATTCTAAAACTTTGTTGTAAGTAATTGTCATCATGCTGTATTGGGGTTCTTAACATAACTATTTTATTTCACTTAAAAGTAATTTAATGATGTTTTTATATTTGTAAATGTTATGTTCATCATTATTCATTGACTTATGTTAATAGATTTCTATGAAAAATGGGTTAGATAGAAATAGACGAAGAATTGGATGAAGTCGCTTAAGTCTAACATGACTTCACACATTAATAGTCTACTTCACAGTGCTAACCTTAAAATTTAATAAAAAAAATAAATAATGATGTTTACAAGGATTACTTGCCAATCAGTTTTACAGTTGAAAATAACTTAGGACTTTATTCCAAGTATGTAAAAATAAACAAACATCGTATTTTTCATGTTGATGATCATTTGTGGGGATAGCATCCCCGTTCACTCCGTAATTAAAAGTAAATAGAAGTCTGACACATTTTACAAGCAGGAATACATAAATAAGATAATCTAAAAGCCATTAAAAACAGTTGATGAATGTTTGAAACCAACTGTCTGCTTTCTGTTTTAGAAAAATGTCCTGGGGCGGGGAAGGGTAGAGGGATGCCCCAGTGGTTCAGAATGCTTGCTGTGTAACCATGGCAAGCTGAGATCTTGCTCTTCTTTTAGCCTAATACTCTAGTGGGTGGGCAAACAGAGCATCACTGAGGCTTGCTGACTGCTACCCTATCCCAGTACTGCAAGCTCCATGTGTCAGGGAGAGACCCTGCCTCAAAGAATAAGGTAGAACACGATAAGGGAGGGCAGCTAGCTCCCTTGACTTCTGTGGAAGCACATAGGTCCACACACCTACATACACATAAACTACACACATATTGACAGTCACAGTAAGTGTATTGATAAGCACATAAATGTCTAAAGTCAGAAAAGTGTCATTCTATCTGTGCATTTAAAATTTTTATATGTTAATATCAAACCATACTGATCTTTATGTTGATATTTTATTGAGTACTTCAAAGGTGAAATTTATTCCAGACTATCTATGGACACACTCCACCTCTAAGAAGTCAGATTTTTCAGTCTCTGAAACAATCAGATTGTACATGACTGAATATGAAAGTAAAAAGTACATAGAAAATAATAAATCGTCTGGGAGGAATGAATTGTCTGAGTAGCAATCCTGTTTCATCTGAATATAATTTTTAGGCCTTTAAATTGAAAATGTATTAAGATCCCCAATGATCATCAAGTCTAGAAGTAATAAGCATGGAATTCCTAGGGCTAAATATGAGAATCTGGTCACAGTGTGTCTGGGTGCGCAGTTTATTGTGTGTTTTCTAGATACAAGTATTAGAGTGACACCTATTATTCAAAAGTCACTTATAAATTCTACTTTAGAACATTAAGGAAGGGAACAAACATCAGATAAGAAGACGAAAATAAAATTTACCCTGGGCTCATACCACATTAGCTGGCCATTGACTCTTTTATTTGCAGAACATGAATGTGTTTTCTACTCATGTATAATTTGAAGTATACAAGGCAACCAGGAAGTTTTTCCACCTGTTGCTTATTTTCACTGACACTGCAAATACGAGTTAGCCATGGGGAGTAGTGTGATATGAGTTGATGAGTTGCCAAGTAGAGAGGATACATCGAAATTCTCTTTAGAATCAATATATGATACTTCCTCTATATTTAAAAGTATTTATTTTATCTGAGGTCCACATCAAAAAATATTTATTTTAATTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTTGATATGTGTTCGTGAGTGCAGGAGCAGAAGAGACCATCCGAGGCTAGAGTAACAGTTGTGGTAGGCGTCCAGATGTAGGGGCTGAGAACTGAACTTGGGTTTCCTGCGAACCAGCCCCAGCTTTTAACTGGTGTCTCTCCAGCCTCTTGAATGAAATTAGACAGGGAAAATTCTGCCTCTTTATAACCTTGTTCAGCATGACCTAAACTCACCAGATTCAGAATCTTCCACTTTTATATCTTTAAAGAACACTGGCCTAGAGTAGGCTATACTGTGATTAACTAATCATTTTTAGCATGTAAAATGAAATCATCTCCAGATTTACTTATAGTTCTAACCAGCTTCCTGCAGTGCCTATATGTTACCCACTCAATTTATATGTTTTCATACTTTGGTTTCCCAGATACTATTCACATTTTGCTTGTGTGAAGTATTTTATTGCAAGAATGTACTGCTACCAATGTACAATACGACTATACTTATCATAAGGCCACCTAATGTGGCTTTACATTTCTCACCAAAAGAGTTTTCGTATATTCTCNGTTTGTGTGTTGTCAGTGTGGTCCCTGGAGGCTTAGTGATAGAGTAAAAATGTAGTAAGCTTTTATACATGGATGACAATCATGGTTTCTCAGAAGGAAGGATGGCAGGCATCCAGACATCTTGATGGGAGTGAGCAGCAAGAACTGACGTGATTCTCTAAATTCTCTTTGGGGATTCTAG
Seq C2 exon
TGTCCAGAGCAAGATGACTTTGGAAGTACCACTTCATCCTGGGTGACCTCTCACACTGGTAAAACATCTTCATATCTGCCAGGAAAGCAGGAAATTAAAGATGCATGCCAGTGCATTCCAAACAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000012759:ENSRNOT00000017169:6
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.524
Domain overlap (PFAM):
C1:
PF133851=Laminin_G_3=PD(7.0=40.7)
A:
NA
C2:
PF0139113=Collagen=PU(0.9=2.4)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
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]