DreINT0049045 @ danRer10
Intron Retention
Gene
ENSDARG00000078322 | col12a1a
Description
collagen, type XII, alpha 1a [Source:ZFIN;Acc:ZDB-GENE-090728-1]
Coordinates
chr17:49807352-49809395:-
Coord C1 exon
chr17:49809250-49809395
Coord A exon
chr17:49807482-49809249
Coord C2 exon
chr17:49807352-49807481
Length
1768 bp
Sequences
Splice sites
5' ss Seq
CAGGTATCC
5' ss Score
7.91
3' ss Seq
GTTGCATTCCTCTGTTGTAGATG
3' ss Score
8.56
Exon sequences
Seq C1 exon
GAGGAGGACCAGAGCCACCCACTGATCTGACCACCTCAGAGGTCACACATTACTCTTTCCGTGCCACTTGGGTGGCTCCTGACGGGCCTGTGGAGAAGTACAGAGTGGAGTATGTGAGCACCGCTGGAGGAGAACCACAGCAACAG
Seq A exon
GTATCCGCAAATATTTTAAAGGAGCTTTTGACATTAAAATTGCCCAGTTTTGGTTAAAACTCAAACAATCCAAATGTATGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTATATATATATATATATATATATATATATATATATATATATATATATATATACACGTTTGAAACCAGTATAAAAAAATAAGTCATATTTAATGTGACAAAATTTTTTCTCTTTTAGGTTAGTTACGATTATTACATTTGTTTCTGTTATGCTTAATATCAGAATAATGAGAGAGAGATATTTTTGAGAAACTGTTATACCTTTTCTTAAAAGTCAAGTTTCCATACAGTAAGATTATTCTGCTTCTGAAAAAGCTCAGATGATGGTGTCGAGGTTTTGGAAGTTTCTGATTGGCTAATTGAAAACATTTAAGTTAATTGGAGGCACAACTGTAGAATAGTATTTAAGGAAAAGCTCAAACACACTGCTTCCTTGTGTGACAACATGGGAAAATCAACAAGCCAGAATCAACAACAAAGCCAGATTACAATTGGCTAAATTACACTGGGAAAAAGACTCATATTTGGAGACATGTTCAGTGCTCTGATGGATCTAAGATTGACCTGTTTGGCCATAATGGCCAGTGTTACATTTGGAGAACAAAGGGGAAAGCTTATAAGCCTAGGAGCACCATCCCAACTGTGAAGTATGGGGGCGGCAGCATCATGTTGTGGGGCTGATTTGCTGCTGGAGGGACTGGTCCACTTCACAGCATAGATGGCATCATTAAGAAAGAACATTATGTAGAAATACTGAAGCAACATCTCAAGACATCAGTCAGGAAATTAAAACTTGGCCACAAATAGGTCTTCCAAACAGACCATGACCCTAAGCACACTGCCAAATTAGTTAAAATGTGCTTTAAGGACAACAGAGTGAATATTTTGGAGTGGCCATCACAAAGCCCTGATCTCAATCCTATAGAAAAGTTGTGGGCAGAGTTGAAAAAGCTTGACAGCCTACAAATCTGACTCAGTTACACCAATTCTGTCAGGAGGAATGGGCCAAAATTCCTTCAAAGATTTGTGAGAAGCTTGTGGAAGGATATCCAAAACATCTGACCAAAGTTGTACAGTTTAAATGCAAAGCTAAAAAATACCAAGGAAATGTATGTAAACTTTTGACTGTCAAGAAATTAATAAAAACTCTCATTATTCTGGCATTTAGCAAATTTAAATGCTTTAGGTAATCCTAATGGACCTAAAATAGTAAACGCTTAGTATGATTTACCATCAGACATTTTTTTAAATGGTTATGTTCCATTTTTTGAGTGTATGTCAACTTCTGCTTTCAACTGTATACATATATACATATTTATTTATTTATTTATTTATTTTCTATATATATATAGAACAATTTCGTCATTTGTTCGAATTGCATCATTCACAGGAACCACACCGCAGGATGTCTATCACATCTTTGCATAGACATGTAAATCACTTTCGCTTAACAATTCATCTGCATCTGGTGTAATTCACCATCAGAATGAACTACCAATAGTGGCAAAGTGAGGGTTGATGCCTTTGTGTTGAGCTTAAGCTCGATTTCTTCAGGAAGCCTGGAAGTCCGGAAGTGATTTGGAGAGGCTAACTTGAATTTGACCTAGAAAAGCTGGATTTTTTTGCTCTGAAAACACAGTGGTGTCCTGCTCTTGCTGACTCCAGGTTATGTTGCATTCCTCTGTTGTAG
Seq C2 exon
ATGTTTGTGGACGGGACGGTGACCACTGTGGTTTTGGAAGGTCTCACTCCGCTGACCGAGTACATAGTAAAGGTTTACTCAGTGGTGGGAGAGGACAGCAGCGACCCACTCAGAGGCATAGAGACCACAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000078322:ENSDART00000154728:22
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.469 A=NA C2=0.227
Domain overlap (PFAM):
C1:
PF0004116=fn3=PU(54.3=89.8)
A:
NA
C2:
PF0004116=fn3=PD(43.2=79.5)
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:
GAGGAGGACCAGAGCCACC
R:
GTCTCTATGCCTCTGAGTGGGT
Band lengths:
271-2039
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]