DreINT0049090 @ danRer10
Intron Retention
Gene
ENSDARG00000078322 | col12a1a
Description
collagen, type XII, alpha 1a [Source:ZFIN;Acc:ZDB-GENE-090728-1]
Coordinates
chr17:49685590-49690151:-
Coord C1 exon
chr17:49689984-49690151
Coord A exon
chr17:49687038-49689983
Coord C2 exon
chr17:49685590-49687037
Length
2946 bp
Sequences
Splice sites
5' ss Seq
CAGGTACAT
5' ss Score
7.79
3' ss Seq
AGTTCTTTAACCCGTTTCAGGTT
3' ss Score
6.88
Exon sequences
Seq C1 exon
GGCCACCAGGGCAGTCTCAGACCGGTCCCCCTGGTCCCTCAGGCTCACCCGGGCCCCGAGGACCACCAGGACAACATGGTTCTTCTGGAGTCACAGGACCACCAGGACCTCCAGGATACTGTGACTCCTCTCAGTGCGGCATGCCTTACAACGGACAAGGCTACCCAG
Seq A exon
GTACATCCAGTGCACTTGATCAAACAGTACTCTTCAGCTCTGTTCCCAAACCTAGTGAGACAATATGGAAAGGAATCTGACATTAGCATGTTGCTAAGCTAACACCCTGACATGCTACTAAACACATGCAAATATTGAGTAAAATAGTAAATACAGAACTCATTTTTCTTTACTTGAATTTAAAGTATGATGGGAGAAGATCTTTTAAAGGGACAGTTCATCCAAAAATGAAAATTCTGTTATTATTTTCTTGTTTTTTTTCTAAATATTTTTTTGATTCTTTCTTCGGATGAATATATATTTTAAATATATATTAGCATATATGTTCCTACTATGGATGTCAATGTTATATTTTGTGTTTAACAGAAGATAGTAGTTACTGAAGAAAACTAATCAACTGGTACCTTGATGTCAAAACAACATCAAAATTTGGCCCGAAACGCCAACTGATTCGACATCCGTTTGACATCCACACACTGATGCCCTTTTTGACCAATAAAAAAAATGACCCAAAAAGTGTTTGAGAAAACTTTTATTCAGCCGAAAGTATTTTGTATCTCTACAATGCATGTAAACAACCTTGATGTAAAATCGACATCAAATAGACGCCTAACATTGGCGTCAAAACACATCAAAAATCAATGAGAGAAAATTCCAATGTTAGATGTTAAACGTCAATGTTAGGGTGCTTTCACACCTAGACGTTTGTTTCGAAATCTGTCTCGTTTGCCCTGTTAGCGCGGTTCGTCTGACATATGCGGAACCAGCAATCGCACTCGCATCCATGCCAAAGAAATCGGTCCGATATCGCCTGAATGTGGTGGTCTCAGCTCGATTGAAACGAACTCTGGAGCGGATCGATTGTAGTGAAAAAGCAAAACAAACTAACCAACCAGGCTATGTCGCAGTTTATTGTGTATATGTAATTGCCATATATACGGATATATAAAGAGAGATTGATGAAATATGAAAGTTAAAGCATGCGAAATATTAGTGCTGCTTAACCATTACAAAAATTGACTGAAATTACCATCTAATAGCGTTTCCATATTTTTATCTTATAATATTTTGTATTAGGCCAATTGTTTTGTTAATTTCTAGATGACACCTCGAAAGAAAGATCAACATTGTTCTGCTTCACTTATTTCTCGCTATAATTTAAGCCTATAATGCAGAATGTCAACCTTTTTTATAGATTGATTGATTCAATAGAGGATTTTTACAACTCTTGATAATTAAAATGAGGTTTTGCTTGAGAAAGCCTGAACTCTGATTTGTATTTGGTGAGGATGTCTGCGAGTGTCAAAATTAAAGTGCACCTTTTCACTTATAATGCCTTATTGCTTATCATCATAAATTAAAATAATGACGTGACAGCAGAGCAGAATCTGTGGGAATTTGAAAATAAACCCTGAAAGTTTGACCAATGTGAGGAGAGTTTATTCGCACGTGACTTGTTTTAACTATTTTGATCTGTTTAGAAACATTGCCGTGTGAAAGCAAACTACACCAAGAACAAAAATAAACATCGTAACAATTTAAATTCCTGTTTTAGAATCCATCTACACGTGTGAAAGCACCCTAAGATGTCTATTTGATATCGTTTTGACATCAAGGTAGTCAATTTACATCAAATCGTTAGCATTTTTGATGTTTTTGTTGTCGTTTTGATATCAAGGTAGTCATTCGATTTCAAATCTTTAAGCATTTTTGTTGCCATTTTGACATCAAGGTAGTCAATCGACTTCAAATCTTTTAGCATGCGTTTTTGTTGTCATTTCGACATTAAGGTAGTTAATCGTCTTCAAATCTTTTATTAGTTTTGTTGTAATTTTGACATCAAGGTAGTTAATAGACTTCAATTTTTTTAGCATATTTGATGTTTTTGTTGTCGTTTTGACATCAAGATAGTCAATCAACTTTAAATCTTTTAGCATTTTTGATGCATTTCTGTTGTCGTTTTGACATCAAGGTAGTCAATCGACTTCAAATCTTTTATCTTTTTTGTTGTCGTTTTGACATCAAGATAGTTAATCGACTTCAAATCTTTTATCTTTTTTGTTGTCGTTTTGACATCAAGATTGTTAATCGACTTCAAATCTTTTAGCATTTTTGATGCGTTTTTGTTGTCATTTTGACATCAAGGTAGTCAATCGACTTCAAATCTTTTAGCGATTTTTGTTGTCGTTTTGACATCAAGGTAGTCAATCAACTTCAAATCTCTTAGCATTTTTGATGCATTTTTGTTCTTGTTTTGGCATCAAGGTAGCTAATCGACTTCAAATCTTTTATCATTTTTGTTGTCGTTTTGACATCAAGGTAGTTAGTAGACTTCAAATTTTTTAGCATTTTTAATGTTTTTGTTGTCGTTTTGACATCAAGATAGTAAAATTGACATCAAATCTTTTAGCATTTTTGATGCATTTTTGTTTTCGTTTTGACATCAAGGTGGTCAATCGACGTTAAATCTTTTAGCGTTTTTGTTGTTTTGACATCAAGATAGTCAATCGATTTCAAATCTTTTAGCGTTTTTGTTGTCGTTTTGACATCAAGGTAGTCAATCGACTTCAAATCTCTTAGCATTTTTGATGCGTTTTTGTTCTTGTTTTGGCATCAATGTAGCTAATCGACTTCAAATCTTTCAGCATTTTGACATCAAGGTGGCCATGGGTACTAATGATTTTCATTTTTGGCCAAACTATCCATTCAACTCCCAATCTGTTTCGACAGACTAAATCTTATGAAAAGCCTCCAGCAGCTCACTAGTGACTGGAACAGAGCTCTCGCATTAACTGCTAATGAAATCATTGCTATCAGTTTGCTTAACAATATAGCTAATCGGAAATAATAATACAAAAAAACTGCATGATTATGTTTTTTTTTTCACTTAAAGTGAGCTGATTTGCCACCAAAATAAACTAACCCCAGTTCTTTAACCCGTTTCAG
Seq C2 exon
GTTTTGCGTAGTATGCTATCTAGACTGCCTGATCCTTTACACATCCCGAGATTAGCACTCACTCTTGAGCTAATAAGGATAACCACCATGGATATGATTGCTGCACATTTGCTGACCAACTCTTTAAAAATCGATCAATCAAACCAAAGGACTGGACTGCCACTAACACCAGCTGAGCGCTTCTATATCATACTGGAGCCAGTGATGGTTGCATCTAGATGAGCGAGAGAGCTGAGGACGCATGTCAAACTACTAACAGCGGTAGATGGTGACATGACTGTACACAAAACTAATCGTGCCTTGTAAATGTTCTGGATGACCCAGTGGGCTACAGTTAACGGCAGTCGTCACGCTTGTGCCTGATAACTTGCTTCTCGCTGACGTTTCACGTTTATTCGTGGTTTCGGTTTATATGTATAGGCAACGCTCAGGTTCAAAACGCAGTGTGTGCCATTAGTATAGTCAACCATGAATTCTTATATATTTTTTTGATTTATATATGTGTATAATACCTCACAAAGATCCAATTTGTTTGTTTATTTTAACGCGAGTGTGTTAGATTAGTAATAGTTTATTGACAAATCCAACGCAAAGTTGTTGACAACTTCCGTATGGGTTTTGTGTTTGGTTAATATAGATGTTCTGTATTACTTTTTCGATAATTAACGCTAAAAATGAAAATGATTTGTTAAAATGACGCACATGCTCAGCTGGCCAAATAATATTTCCAAGCAGGCCCCTACCAGCCCGGGTCTGAAACCTACGTAGTGCCCATACCAGCCGCGCCATCGGAAGATATCGAGACACAGTCGCCAGGATTGCGCTACCAGCGCGGAAAAAGGTCGCTATCAAGAAAGGAAGCCGAAAGAATCAAAACATAAACGTGGAAGTGTGTCCGTCAAAAACTGCAAGCCTCCTTCGTTTTGGTCGATTGAGGAGGCTGTCGTACCAAACCTGTGTGTTCGCTGATGTTTGCTTGTAACATAACTGCATTTTTTGTATTTGTAAGAATCTCATGTTCAGTACTAGGTCCTATAAACACTCATGAACTGATTCCTTGCACATATGAAAGTTTGCAAACGTGCTTCTCTCTTTCTCGAGGAAAGCGGCTAAATCGGTTCGACTTCCCTTTATTCTCCCTTTAGACCTGGCTTTTGTTATTCTAAACCCTATATTTACCTGTCGTATACCAGCTCACACCAAAAAAAAAAGAGGAATTGCATGCCTGTGTTGTATATTTAGTAAGGACGTTTACCATCAGAATATAGTTGTTCGTTTCAGTGATATCCCTTGAAATGCAGTTGGAATTCGTTGCAAGTCCTTCGACATAGAAGATCTTTTTTTGTTTCCATGTCTGAATTGCACAGTGTGAATTCCACAGCCTTATTTTCTTATTTATTTCTGAATCAGAAGAGGCATTTTTCAATAAAACTACTGAAAATGTTGAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000078322:ENSDART00000154728:63
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(73.7=73.7)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion 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]