RnoINT0039403 @ rn6
Intron Retention
Gene
ENSRNOG00000024824 | Col22a1
Description
collagen type XXII alpha 1 chain [Source:RGD Symbol;Acc:1309081]
Coordinates
chr7:113020617-113022705:-
Coord C1 exon
chr7:113022639-113022705
Coord A exon
chr7:113020800-113022638
Coord C2 exon
chr7:113020617-113020799
Length
1839 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAGT
5' ss Score
11
3' ss Seq
CTGTTCTTCCCATTCCATAGCCA
3' ss Score
8.31
Exon sequences
Seq C1 exon
GGTGAGTCTCCATCCATTGACACCTTAAGGCGCCTCATTCAGGAAGAGCTTGGGAAGCAGCTAGAAG
Seq A exon
GTAAGTAGCTGGATTTCATTGCAGCTTCCAGCATAAGATCCCCAGCGAACAGTTGTTGTTTTCATCGTTAAATACTGGGGCAGTTGAGTGTGGAACAGCAGGTTTGAGAGGTAACTTGAGGGCCCAGCCTTATACTCCAGATCCTGGTCACCTCTAGTGACAATGACTCTAGTGAATGATGACACCAGATACTACCATCTGCTGTGAGGTGATCACCTACACTTTCTGTGTATTCAGCCGTGTGTGTGATTGATCAGTGTTCTGGAAAGGTGTGCAGAGAGCCTCATTGAACTCCAGCGGAAGAGGTAAGTCAGGAGACAGACAAAATGACTGCAGTGTCCTCAGAAGACATCTGTAATTTCTTTTTGGCACAGAGGGCATTGACAGAGGACAGTTGGCTCTGTTTGAGATAGCTCTAAGGTAAGGTATGGAGTGGGAAACTGGAATGGTGACAGCATTTGGGGTTCCTATCTTGGGAGGGTTCTTAGAGCCTGAGTGTGCCCATTGATAGCCTAGTAATGACCATGGGAAACAGTGTGGTTATTGGGGGGATAATGAGGATCAGGCAGGCTGAGATACTGGAATATAAGTCTGAGATTTACAGCCTTATTTTCTGTGCACTATACCACCATGTCTGTTTAGTAGCCATTCTTCCCATTTCCCCTATGATAAAAGCTTAGAAGAAAATGCTCATAAGCCTGTGACACGAAAGAGGTGGATCCTAAAGTTGTTTCCATTCACATGTCCCGTGTCCCTGAATTGTATGCGTCACACATTCAGACTGTGCTGGATACCTGGTTGTAGAAGCAAAGTGCCCCTCTCCTCTACCCCTCTGGAATCTAGGTGAATATGTATGGACTGTAGATGAGGAAGGTGGGGGAAGACAGGGATAGGCTAGAAAGAATGTGAGCCCCACTGGACGAGGCACGTCTAAGAACTTGTGTGTGGGAGTTCCAAGTTCTGCCTCTTGAATGTTAGACTTGTCAGTGATGGAGTGGCCTCTGCCCTAGTGGAGTGCCAACCACTAGTTTTTAAGGGGGCTGGGACTATATACTGGATTGAGTCCCTTTCAAAGAGCCTTTGAGGAGGAAATGTTGACTTGCAGCAAAGATAAGAAAATCAAAGACCAAGACAAGTTCAGCAAACTGCCAAGGTCACTTAGGTCACCTCCACAGACCCCTGGGCCTTGTGAAGGTGCAATGGCAGAGTGAGTCAATGAGGCAGTCAGGAATTCTCCTCTTGTTTAGTCTTATCAGCCAAAATATTAATGTTTCTCCTAGTCACTCTACCCATTGGATAGGCCTCTGCATCCAGTGCTCTCTGACTATACAAACTTAGGTGGCTCTTGGTAACCAGTAGGTAAGCACTGGATCCAGTGTCCAGCAGGAAAGTGAGTCCACCCACAGTTAGAGCTCTAGTTTGTTTGTTTGTTTTTTATTAGATTCTATAATGCTTGTATCACAGATATATAAACATCTCCAATTAGCAGTTTATTTGCCCCTTCAGTTGTTGATGGACTTGATTCAAAAAATGAATGTCACTAAATAGCTTTGTATAAGCTACTTAAACAGCCCAGGCCTCAGTTTCTCCAACCAGCAGTTTTCCCACTGCTATTACTGCTGCTGCCATCACAAACACCAGTACTGCTGTTCCTGCACTGTTAATACTACTATTAATTATCTCCACGGCTGCTATAGACATCCATGCAGTCAGAAATGTGTGTGCAGGACCTGTTCTTTGTCTTCAGCCCCAGTTGGTTTTTGCTTGCAGTGAGCTGCCAGTATGCCCGTTGTCCTCTCTCCATTCCTCAGGAACTTCTCTGTTCTTCCCATTCCATAG
Seq C2 exon
CCAAACTTGCCTACCTCCTGGCCCAGATGCCTCCAGCACACATCAAGTCCTCTCAAGGCAGACCTGGGCCCCCAGGACCCCCTGGAAAAGATGGGCTGCCAGGCCGGACAGGCCCCATGGGTGAACCAGGCCGCCCTGGCCAAGGTGGTCTAGAAGGGCCCTCTGGACCAATGGGCCCCAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000024824:ENSRNOT00000034672:63
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(6.8=17.4)
A:
NA
C2:
PF0139113=Collagen=PU(75.0=72.6)
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:
GTGAGTCTCCATCCATTGACACC
R:
CTTTGGGGCCCATTGGTC
Band lengths:
249-2088
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]