RnoINT0039405 @ rn6
Intron Retention
Gene
ENSRNOG00000024824 | Col22a1
Description
collagen type XXII alpha 1 chain [Source:RGD Symbol;Acc:1309081]
Coordinates
chr7:113015747-113018478:-
Coord C1 exon
chr7:113018401-113018478
Coord A exon
chr7:113015935-113018400
Coord C2 exon
chr7:113015747-113015934
Length
2466 bp
Sequences
Splice sites
5' ss Seq
CAGGTATGA
5' ss Score
9.46
3' ss Seq
TCTTTTGCTTCCTGGGCCAGGCC
3' ss Score
7.23
Exon sequences
Seq C1 exon
GTGAGAGAGGAGCCAAAGGTGATCCTGGCACACCTGGAGTTGGCCTTCGAGGAGAGATGGGTCCCCCTGGAATACCAG
Seq A exon
GTATGAAGGTTCAGCGTCTCAGGCTGGGTGGACATCAACCATGGAGGCAGGGGCACACAGTGGTACCTGTGCTTGTGGGAAGAGAGGCCCATCTGGGCCACTCTAAGGAGAAACATATAACTCATTGGTTAATGGAATATTTCTCAAACCCTTGAGGCATACATTCTAATTGGAAAGTTCCAGTGACTTATTTAGTGTTTCAAAATGAGCAGAATAAAGTATATTGATGTCTTCTACATAAATATATGATAAGTATTTGGGATGATGCAGAAGCAAATTGCTCCAATTTGTTCATTACATATTGTACCCATGTCCCCACCCCAAAGAATTCTCAGTGTAGGGCAGAATATTTGGCTCAGAGCTTAGAAGCACTATCTGCTTTTTGTAGAGGAACTGGGTTTGATTCCCAGCACTCACCTGGCAGCTCAGAATCATCTCTGTCTGGCTCTAGTTCCAGGGAATTTAATATCCTTTTCTGGTATCCACTAAAACTGCAAGTACTCGGCGCACAAGCATAAATGAAAAAATATACATGAAACATAAATAAGTACTCATTAAAACATCATGCCCCAGAAATATACAGAATTATTATGTTTCAATTAAAAATAATAATTGACTAAATATTGTGGGGAAATGGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGGCTCTAAATAAGTCTGTGCATGTTGGAGATGCAGCTCTCCTTAGGACTTTCCTTCTCTACTTTAACTCACCTTAAGTGGTTAGAACCCCACAGGCAAGGTGACAGCCATCTTCTTAAACCCAATATGAATCCAGTAATATTTCTCAGAATATGACCAGGGAACCTTAACCAAAGGTTTAGCCAAAGGCCATCCCTCTTGGAGCTGAGGGGTTGCAGAGTCTTGGGACTTTCACTTCTGAAACCTAGAAATAACTAAGGGAATGGCAGCCAGTTGACCACTGTGCCTGGCGGAGGTATTGGAAGAGCCCCTGCAAGACTCTCACCTCTGGTTTGTAAAATTCTACCTCACCATTGTGTGTGTTTGTGTTTGTGTGTGTATGTGTATGTGTATGTGTGTGTATGTGTGTGTGTGTGTGTGTGTGTGTGTGTGCGCACGCACGCGTTTAAGTATGTGTATGTTTGAGTGTATATATTTAGGGAGCAGTGCTAGAAACTGAACCTAGGGCTTCATGCATGTTGTACCACCAAACCCCATTCTCAGCCCTGTGGATTTTACGTTTTAAAGTTAACTCCTAGCTTTTATGACTATTCTGGATCATTTATGGACATCTGACTTACATATAATTTAACTTTAGTTTTATCCTGCCATGATTTTCCATAGTTTCTACAGTTGGATATGTATGTTATTTTTCTATTAGAGGTGATATTACATAAATATTGTTTATATCTTGCTGACTTTCAAATAGAATAGAATATAAATACCACACTGAAATTGGAGAAGTAGAACAGCAGAGTGGAGTCCATCTAGAGGAGAATGTGTAGACTATCTGGCAGTTACACCTGGCGAGGTTGAATCAAGGGCCATTGCCAGTACATCTCAGCGGAAGGAATGATTAGCATAGCTGAATCAAGGATTTCTTGTAAACAAGGATGTACACTAAGTAACTCTTGTCAGAAAAACAGCAGAGTTCCAAAGTTCTAAAGTCACTCACAATGGAAAGGTTCACTTGTCTACATTCTAAGAAATCTTTTGACAGCATGCTAAGAAGTGAGGGAGAATGTAACCTGAAGAATGTGGTGGCCAACTTGGCCACCACACCTAGCACCAAGCTTCCCAGTTGTTCAGGCAGAAGAGGAAGCTAGTGAATTACACATGATGCCATAGCACACTTGGTAAGCGTAGGCATAGCAGTTCATATGTAATATTCTCTCAGTCTAAACTTAGACTCTAGAATGGTCAGTTCTGTCTATTCCAGATGCTATATTTCTTACTGGGTATAATAGAATAATATACATAATATGTGGTTCGGGTTTAACAAGTAAAGTTGAGAAAAGATAACAGATCCCAGACTATCTGAAGGATCATCGGGTGTCCCTGTAAGACCAGATACACCAGGCCAAAGCTCACTAGGCTGCTTTATTGTCCCACTCTGAATTCAGATGTGTCTACTAGACTGTGTGAGAGAATAGTGTTCTGCTTTCTCTTTTGACTTGAGTGGAAAGCTTGCACCCCAAGGGCCTTGAGTTGCTCTTGTCTGTTTTTCTTCTCTGGTATCTGCATTTTTTTCCTCAGACAGTAAAGACGTCCCCAACTGTCGCTTGCAGAGGTGCTGTTTTACCTGATGCTCACATAGGCTACTCTGTCTCTTAGTGTGGAGCACTAACAGAGGCTATTCTGAGTACACATTGAACCCTAGTTTACAACACAAAGGTTATAAGGATGTTAAACTCCTGGATATAGAATGTAAACTGCCTTCTGTTTCTTTTGCTTCCTGGGCCAG
Seq C2 exon
GCCAACCTGGAGAACCTGGATATGCTAAAGATGGACTTCCAGGAAGCCCTGGCCCTCAAGGAGAGACAGGACCAGCTGGACATCCTGGCCCTCCTGGTCCCCCTGGCCCTCCTGGCCAGTGTGACCCCTCCCAGTGTGCGTACTTTGCCAGCCTTGCTGCCCGGCCAAGTAATGTGAAGGGCCCCTAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000024824:ENSRNOT00000034672:65
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PD(23.3=51.9),PF0139113=Collagen=PU(24.1=51.9)
A:
NA
C2:
PF0139113=Collagen=PD(74.1=68.3)
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]