DreINT0049049 @ danRer10
Intron Retention
Gene
ENSDARG00000078322 | col12a1a
Description
collagen, type XII, alpha 1a [Source:ZFIN;Acc:ZDB-GENE-090728-1]
Coordinates
chr17:49783692-49786056:-
Coord C1 exon
chr17:49785917-49786056
Coord A exon
chr17:49783825-49785916
Coord C2 exon
chr17:49783692-49783824
Length
2092 bp
Sequences
Splice sites
5' ss Seq
AATGTAAGA
5' ss Score
5.55
3' ss Seq
ATTCATTTTCTCTTCTTCAGGAT
3' ss Score
10.72
Exon sequences
Seq C1 exon
ATGTGGTTCCTGCCCCGCAGAACTTGAGGTTCTCGATGGTGACCCAGACCAGTTTTAGGGTTCACTGGGAGCACGGCGCTCCTGATGTCTCCCTCTACCGTATTGGCTGGAAAAAGAAAGGAACGACCGAGTTTCAAAAT
Seq A exon
GTAAGAGACTGAACCTCAGGTCTGATTTAGAGATCTGCGCGGGACTAAATTTTGAATCCCATTCCTGCCCGCACCCGCCAGGTTTTAGCCCAAACACGATCGCTCCCGCTTACATTCAGCATTTGTTGTCCCGCTGCCCAACCCGCCCCGTTTTCTACCCGCCGCACCCGATCCCGCTAAAGAGTGGGGGGGGAGAACAAAACTGAAAACCACCCAGCTATACAGAGTCCAGACAGCCTATAACAAGCTGTCTGTATAAACACACACACACATAAGCACCAAGCACACACACATAGACAAAGCTCTCTCTCTCATTCGCTCACTAACACGCACAAACACACACACATAAGCACCAAGCACACACACAGGCAAATCTCTCTCTCTCATTCGCGCAAGCACACACGCACCTCTCATTCGCGCGTGCGCACACACACACATACACACACAGCAACAAACAAGCTAAACACAGCATCGCGCTATTTCATTTACACACATACATACGCATGCTCGCTTGGGATATTGCTAGACGGACCGCTCCCGTCCCAAATTAAACCCATTACCGACCGCTCTCGCGCTTTATTCGGAAATTTATTCCCGCGCCGTAGAAATCCGGTCGGGTCCTGCGGGACAGCCACGGGGATGCAGACCTCTAGTCTGATTCACTAAGACATGCTAAGAACTTGACTTTTAATATAATTCCTAATAAATTAATTTATTTAGGATTTCAATATATTTCCAGGAATATCCTGATTGTTAGATTTATAGATGGTATAAACAATATGTTCATGGCTTAGTTCACTTAAAAATGCAAAAATTCCTCTTCAATTATTCACACTCGAGTGAATCTAAACGAACAGAAAACTATATGTTCTACAGAATGTTGTCATCCATAGTAGGAATAAAAGATAGTAAGGAAGACAATGGCGCTTTTCTTCCCAAGCATTCTTCAGCATTCTTTAACATTCCCAGCAATCCAGCATGTCTTCCAGTTCCAATTCCGTTCATGTTTATTTCTATGTATAGTTTGTGTCTAAGCAGCTGAATATAGAAGTTCTAGAAGTTCTTCCTTTGTGTTCAACAGAAGACACAAATTTAAACCGGTTTGGAACAAGTAGAAGATGAGTAAATGACAGGATTTTATCTTTGAGTGAACTGATAAGCAGTGCGTTTTTCGAAAACCATTGTTTGCCAGGTGGCAAATACCGTCATTACAAACATAGTTCGTTGATTTGGCATTTCCCAAATCCGTCATTCCAATGAAAATTCACAAACTGCATCGCAAACTTCTACGCTGGCAACTACAGCTAGAGCTGTAGTTAGAAGCATAGTGTGTTGGTTGTGTTCTATTCCCAGTTATCCCACTGAGCCCTGTTCATTTCGAACATTCCAGCATTTAAACTTGGAATGACTTAATATTTAATCATCTCTCTTAGGTGTAATTTGCTTTAAAAGGATTTTAAGCTGCTCCGCCCTGTTTAGAGCGCCATTATGGGCGTTTTACATTATAACCAGGGCCAGACGGAATCTGCGGATGTTTTTTGCTATTTCTGCGGAGAACTTTGGTAAAAATCTGCGGATTTCTGCGGAATTATTTTGGGAGTATCCAGCGGAGTATCATAACTAAAACCTTAATATATTAAATAAAAAGTAATAAATTACTGAATAAAAACTGAATAAATTCAGATTTACACATTTACTCAAGTAAATAAACAGAATTAATAATGGGCTAAAAACGTGCAGAAATCTGCGGAATTATGTTGAAAATCTGCGGAATTCTGTGCGCGCAGATTCCGTGTGGGCCTAATTATAACTAATGTGGTTCAAACAATGGATCTGCAACAATAAGTTACTAGAGTTTTGGGAAACACTTCTCACTAAATCGTTCTTTTCCCAAGCGATGCATCATACTATGATAGTTCAGCCGCAAGTTACGTCATTGTTCAGGAAACGCATCTCAGTCTGTGTTTGTTAATATCTAGCAATTGTACTTGCATGTGTGTATCTCAGTACTGGTAAATGGTAACATTCGGCTGTGAGGTGGATGTTTGGTTGATGTATACATTGTGTATTTAATTCATTTTCTCTTCTTCAG
Seq C2 exon
GATATCCTGAGTAGTGAAGACACTACATATGATCTGGTGGACCTGGAGCCAGACACACCTTATGATGTTTCGGTCACTGCCATTTACCCTGATGAGTCTGAGAGCGAGGATCTGCTGGGCACTGAACGCACTT
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000078322:ENSDART00000154728:26
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.021 A=NA C2=0.667
Domain overlap (PFAM):
C1:
PF0004116=fn3=PU(53.8=91.5)
A:
NA
C2:
PF0004116=fn3=PD(43.8=77.8)
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]