RnoINT0039523 @ rn6
Intron Retention
Gene
ENSRNOG00000007657 | Col27a1
Description
collagen type XXVII alpha 1 chain [Source:RGD Symbol;Acc:735115]
Coordinates
chr5:79124993-79130033:+
Coord C1 exon
chr5:79124993-79125037
Coord A exon
chr5:79125038-79129979
Coord C2 exon
chr5:79129980-79130033
Length
4942 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGC
5' ss Score
9.88
3' ss Seq
TCCTGATGTGTCATTCCCAGGGG
3' ss Score
8.19
Exon sequences
Seq C1 exon
GGGGAACCAGGGGATCCTGGACGGCCAGGGCCTGTGGGTGAACAG
Seq A exon
GTAAGCTAGTGATGGTGCCAGTACAGTGGCTTCCCTGTGGGTCACTTACCTGTGCTAAGTCTAGTGCTGTGTGGTCACTCAGTCTGGGAACATTCCAGAACCAGGCCTCTTGCACATGCTCAAAGAAGGGCGGTCCCTAAATAATAAGGCTTGACACTTTAGTTTTTGATGCATTTGCTCAAATGGTTAATGTGATGTCACCTACTAAAACTGGGGTTAAACCGGAGTTCTCGGAAATGACTGTGTTCTTTTAGTTCAGTGATTTTTCAACCTATAGGTTGCGACCCCTTTGGGGGCAGGGAATCGAATGACCCTTTCACAGGGGTCACCCAAGACAATTTGTATATCAGATATTTAGATTACAATTCATAACAGTGGCAAAATTACAGTTATGAAGTAGCCACCAAAAATGTGTGGTTGAGATCATCATACCATGACGGGTCGCAGCATTAGGAAGGCTGAGAACTACTGCCTTATCTAGAGAAATAGATCCATTCTTCAGAGGCTCAGGGTCCAAGCCTCCCTTTGTTGTAAAGAAGAATCTCAAATCAGAGGCTCTGGGTATCTGGAAAGCAGGAACAAGGTCTGCAGAAGAAAGGTTGGCATTTGTCAGTCAAAAGTTTGAGAATCCTCACTCACCGTCCTTAACCAGTTAGAGAATCTCTTCTGGGTGCTGTGTGGGTGGCTACCTCAGGGCCTCCCTTCAGGCCTCAGTGCCTCTTGCCAGCTTGAGGGCCCAGACATGGAGTTGTATGATATTTTCCACACCTCTAAATGAGGACCCTCTAGGAGCCTTGGAAGAGGCCTCCTCAATCATGAAGGAGGAAGACTCAGAAGAATTCAGTTGTGCCCAGAAGGGCCATCCATGGCATGAGACTCCCATGTGACAGGCTTCCTCAAAAGGCCTGTAACATCTGTTGAGAAAGAGCGAGAGATAGGAATTAGAGCTGGGGGAGGCCAACATGTTTGAAATCTTTCAGTGTCATTTGAGCATGTTCTGTGGGAAGCCTGGAGCTTGGCGCAGCCTAGATGTATTTCCTGACTGGAAAAAAAACCAGCAAATTTAAGTTCATAGCTATGCTAATGGTTGGCCCTGGGGAAATAGATACTTAGAACCTTGGAACCTTCAAGACTTGGGGATTCCTAGAAGTCACTTTCTCCAGGGCCCTGACAGTTTTCCATGCCTTAGATTCCTTTGCCCAGCTAAGAAAGCCTGTGAATCCTTCCTTTGAGTAGATTTAAGTGGATAGTGTCATAAGTGGAGGATTGGAAGGCAGCCAGTAACAGTAACAGAAACTAAAACGTGTCTAGATGTGGCACACATGTATCTACTTCGTGCATGATTAACACCCTCAACAACGAAACCTACCAGTGACCGCCATGTTAAGGTGTATTGAAGCTCTGAGATCTGTGTAGGAATGATTGTAGTGATATGTAACCAGATGGAGAGTCTCAAATTTTATATGCTACTGGGGCTGGGTGCATCTGTGTTCATAGTTAGAGAAAGATGCAACATTTTAATAGGAATGTAATGCAAGTAAAAGCTGTGAGCTTCTCTGTTCAAATTCCCGGATTCCATCCACAGAAGCTTATAGGAGCCTCCAGCTTAAGAAATTCCGGATTCTGGCCCACATTTGCAGTTTGTGTCACAAACTTGGGAGGAAAAATGGAGTCAAATGTATGCTCATAGGGGCAGTGGCTGAACTGGAGCTAAGAGGTGTAGACACCCTGCCTGGGACAGCTCTGGCTCACCAGGACAGCAGAGCCCCTAGCTAGCTGTGTGTCCAGCAGTTATAAACTGTTACAGGAAGGAAGGCTGTCAGAGCTGAGACTCAACACTGGCCCCTGCATTTGCTCTAAGGCATGAGAGGACACCAGCCCCTCTCCAGGTGGCCATAGCAAAGGAGTGGGTGTTTCCTGCCCCTGACTGAACCACAGGCTCCCCAGGAGAGATCCCCAAGCTCACACCACAGGCCGTGCTTGCAATCACGATAATGGCTTCATTTGTTGCATGAGGTACCAGGCTCCATACCAAGCACTAGACACACTCCTCTGCGGTCCCTCCAACCGTTCTGTGATGGGAGCTGTGATGAACCATCCCCAACTTGCAAACGAGGAAACTGAGGCCCTGAGAAATTAAGTAGCTTGTTCAAAGTCTCATTGGCAGAAGCATAACTCACAACCAACTGACTCTTCAGACTCTGAGCTCCCAGGTTCTACCCTGACAAAAATGAAAAATCCTCTGATTTCCTAGAAACCTTACAGTCTTCTACCAATGAGCACAGACTGCTTGTCAGGCCCTGTCCTAGGTGCTGGGAACAAGGTGTGAGCCTTGCCTTCCCAGGACCTCTCCAGGGAAAATGAGCCTGTCAATACCTATCTGGAATGGTTGAACAGCTGTGGTCTCACAGCTGTCTGATTCTCAGAAGCATGAACCTCCTCCCTCCCATGCCCAACAGAATGCTGCGAGGAGAGGAGATGCACCATATCTTGCCAGCTAGAGAGGAGCAGGCTGTGCCTGTGACTTTCAGAGCTGCCTCTCTGGCCACCCTGTCAGGAGGAAGCCCTGTGTGCCTCTGAGAGACTGCTTCCTTTCCCTTTGACTCACTGCCAGTCCAAACCCCTCCCTACAGGAAGGCACCCCATGGAGCTCTGGAGGCCAGGGCAATAGCACTTGCTGGATGTCTCATTCAGATCCTGGCTGGCTTCTCTTTGGAGATTTATGTCTTCTAGGTCTCTAGAAATAATAAATTTAAAGTTGCCATGCAATTTATTTCTCCAGGCCCATAAGGCCATGTGTGTGTATTCCCTTCCCTGGCAGCGTTTGTCTGACTACTTCCTGTTGGGGAGGTCTGTCAGTGCTTTAGCCCTGGGCCCCTTTAAAAGCACCCGGGGTCGTGAACAGTCAGAGCCATCAGGAGGCGGGAGGGACCTTTGTTAGGTTGCTAGTTCTGTAGATATCATGTAGGTAGACCAGTTGGTTCAGGGTCCATACACCTGGAGTTTGAGTAAGAGTGGCATAGACAGAGTGCCAAGTGCAGGTTTAGGTATGTAACAAGCCCTCGGCACATGGACTCATAGGTGTTAATGTCACTGTCACCTTAGAAAGGCCCCAGTTTATTTGATTTGTTGTTGTTTGGTTTTGACTTTTGAGACAGGGACTCACTTTGTAGCCCTGCCTGTCCTGGTACTTGCTACATAGCTCAGGCTAGAACCAAACTCCAGATTATGCTCCAGCTTTTTGAGTACTAGGATTCCAGGTATGAGTTATCATGCCCGTGTTTTGTTTGCTTGTTGCAAAAGTGAGTACCTGGCTCTCCTCCATGAGCCCATAGCTCCTTATATCACCTCTGAAAGAGTGACCAGAGACTGGCCAGGAAGCCATCCTGCAGGTGGTGATGGCGCTGGCCCACTCACATGCACACCTTTGGGGCCTACAGTGGAGAACAGGTTCAAGAGGGCTGGGAGAGCATTGTCTGAGTCCCTGCCTCCACCCACTTGACTGCCACAATACTTGGTCCCTGGAAGCTTGGCACTTACAGCTGTCTTTGGGGAAGGAGAAATGGGCTTTCTGAACTAAGCAGCACCTCTTCCCCTCCCAGCTCCCTGGCAGGGAGGCTGGCTCTCCAGCTTAATTGAGCACTGGCCCTCAGAAGTGGGGCACAGGGAACAGATTTCACAGGACAAACCCACCCACTCCTGTATGTCCTAATTTTCTGGGAAATGCCTGGCTGTACATCTGTGGCACCCCAAAGCTTCTCTTGCCCTCCTGACCCACACAGGAACCCTCTGAGTGTGTGTCTCAACTGAAAGGAGGTGGGTTCCAGCAAGAATTTGCTTTACCTCCTTGGGGACTCTTGGCTGTTCACCTGCTCTAGGCATGCTCAGCTGCTCAGGGTGACAGCAGGACCACTAAGAAAAGCCTCTGGAACCTGGAGGCAAGTTGTCACACACACAAGAGTTAAAAAAGAGCCAAAGGAGGGGAGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTATGTGTGTGTATGTGTGTGTTTGTGCATGGGGTATGTATATGCATGTATGTGTCTATGTATGGTTCATGCATGTCTATATGTTATCTGTCTGTGTGTCTGTACATGCATGTTCATGTGTATATGTGTGTGTGTCTGCCTCTTTGCATGTGTGTCTTTGCCTGTGTGTGTGTACGAGTGTCCATGTGTATCTGTGTGTGTTTGTGTGTTTGTCTGTGCATGTGTTTATGTCTGTGTGTCTGAGTGCATGTGCTTTTAGCAAAGGAAAGCTCTTCAGTAGAAGCCTCCACTTCCTAGATTCCACCCTGTCTCTGCTGTAGGCTGTTAGGGTTTTTCTGTTCCAGTCAACAAGTTTGTTTCTCTCTGAAACAGCCCCAGAGCCCCCAAAGATGGAGACAGATGGCCTCTTCCCAGCTCACTCCCCCCACTCCAGATCTCCAAATGTGTAGGGATCCCAGCCTGCTTCTGGCACGGGAAGAATGCTCAGCTCCCAGCGTTGCTGGCAACAGCCCCACCACTTGGCTCTCAAATCTGAACCATCTGGCAGAGTGTGGGGAGAAGCAGCCCAGAGGCTATGCTTGTCCACAGCAGTCCCAGCCATAAGAGTCACTGGGCACGGGCTGAAGAGGGGTGGGGGGGTGGGGCTGGCACGGGAAGAATGCTCAGCTCCCAGCGTTGCTGGCAACAGCCCCACCACTTGGCTCTCAAATCTGAACCATCTGGCAGAGTGTGGGGAGAAGCAGCCCAGAGGCTATGCTTGTCCACAGCAGTCCCAGCCATAAGAGTCACTGGGCACGGGCTGAAGAGGGGTGGGGGGGTGGGGCTGAGGGGGTGGGGTAATGGGTGGGCTGGGCCCAGGGGATAGAAAACCTTGAACACTCAGCATGCCTCCAGATTCACTCCTTTTTCCTGATGTGTCATTCCCAG
Seq C2 exon
GGGCTTATGGGATTTGTTGGTCTGGTTGGAGAGCCTGGAATTGTTGGGGAGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000007657:ENSRNOT00000010333:24
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(17.3=100),PF0139113=Collagen=PU(16.3=93.3)
A:
NA
C2:
PF0139113=Collagen=PD(20.0=88.9),PF0139113=Collagen=FE(27.0=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]