DreINT0049075 @ danRer10
Intron Retention
Gene
ENSDARG00000078322 | col12a1a
Description
collagen, type XII, alpha 1a [Source:ZFIN;Acc:ZDB-GENE-090728-1]
Coordinates
chr17:49860254-49863621:-
Coord C1 exon
chr17:49863571-49863621
Coord A exon
chr17:49860518-49863570
Coord C2 exon
chr17:49860254-49860517
Length
3053 bp
Sequences
Splice sites
5' ss Seq
TCAGTAAGT
5' ss Score
9.14
3' ss Seq
TTCATTTATTCGCTATGCAGAGT
3' ss Score
6.09
Exon sequences
Seq C1 exon
TTCAATCCAGCAACACAAGTGGACCAAGGAGGCCACAGTCAGAGGCTGTCA
Seq A exon
GTAAGTATATTCAATCAAATATCTCCTCATCATCTTGTCGCATGTCACCTATTAAATTAAATTCTGTAAGCACTGCTATTAGATATTTTTTTTTCCATTTTGTCTTACCAGCGTAGACTTGAAAAAAAACTTGTTACTACTTGCAAAGAATGATTGCTTAAGGTTGTGGTTGGGAATGCTAAATTGCCTTTAATTAAAAGCATTAAAATAGAATCAGAGCTCATAAAACATTTAGCTTTGTTCTGTTAGAAGTGGCTGTTAAACTGCAGAGGAGGACTGAGGTCTCCTCTAGCCTCATTCATTGACTCTCACACACCCGACATCTCTTTTTAAATCACTGGAAAGGATTACGGTCCTGACCCAGTTACACTCCTTCGCTCTTTTTCTTGCGAGTCCAAATCGAGTATCGGAGCCAAAATAAATCCCATTGAAATTCCAGAAAACCGGTTCTCAAGACGTACATTTCACAGTAAAGTTAATCATATCCAAGGGCACAAAAAAGGTTTATTAAAAATTTCCATTGATTTGCAAGGCTGCTTTTTCTTGTTACTTTGGAAATGTTGGAGAAAACTTGGACGTTTTTTAAGAGTCATTAATAATTAAGTGTTCTTGAAGAATAAACTAAATAAAATGCTTTCCTTAAAGGAAGACTTCACTTTTTGAAAATAGGCTCATTTTACAACTTACTTAGAGGTAAACAGATTCATCATTTTTAAATCCATTCAGCCATTTTCAGAGTTTCACAGGAGCACTTTTAGCTTAGCTTAGCATATATCATTGAATCGGAACATTAGCATCTTGCTCAAAAAACAACCAAAGAGTTTTGATTTTCTTATTTACATCTTGACACTTTTGTTGTTACATCATGTACTAAGACAAAAATACAATAAATAAAAACGAAAAATAAAATAGTTAAAAATTAAAATAAATACTATTTTCTAGGCTAATATGGCTAAGAACTATATTCTCATTCTAGCGTAAAAATCAAGGAACTTTGTTGCTGTACCATGGCTGCAGCAGAGCAATGATGTTACACAGCTCAGTACACTTTTTGCAGGTGACCACATTGGCAGTGTTGGGCAAGCTACTTAAAAAATGTAGTGAGCTAAGCTATTTGCTACTTCACTTAAAATGTAGCTTAACTACACTTAAAGCTACCCTCTGGGAAATGTAGCAAGCTAAGCTAAAAGCTACACGGCAAAAGTAGCTTATCTACATCTAAGCTATTTTTACAATTTTCATTTTTAAATCGAAGCAACTTAAATCCAAGTCAGTCATATCTTAGTGATCAATAAAACTGTCAATGAAACATATGAGGCAGAATAGTTCAGTTATTTACTGTAAATAATATGCTGTACTAAACAGAAACACATTATAGTATAACAGCTTAAAAAAAATCCAATAAATAAATGTGTTATACATTTTTAAATATTATAGTAATTTATAGCAAGGGGAAATATTTTGGAATAATAATTATATTGTGTGTGTGTGTGTGTGTGTATGTATATATCTATATATCTATATATATATATATATATATCTATATATATATATATATATACACACACACACACACACACACACACACACACACACACACACACACACACACACATTTCTGAGGAATCAGAAATAACTCCACTCCCTTAGACATCTTTCCATCAAGCAAGTTTTACCAGAGGTGGCAGTAACGCTCAAAAATGTTGTCGAACTCCATAAAACAGGAAGAAGATATCGTCATTCTCGCCATCATATGGATTTACTTCATCAGCTAGACACCGGCCTCACATCTCCATGAATGTTGGTGCCGTCACTTATTGATCTGGATCGGTAAATGTAGCTTGTGTGGACGCTACTGCGCTACTTGACTAATAAAATAGCTTCGCTATTGAATAGCTATTTGATTTAGAAACTAGCAATGCTACCGCCACGCTACTGAGAAATGTATTTGAGCTAGTAGCGTCACTACTTGTAGCGACGCTACTGCCCAACACTGCACATTGTAAATGATCAAACTGGGGACTATTTTCAGGTGTTGCATGATTGATCTTGCTGTAGCCATGGTACAGCAACAAAGTTTGCTGATTATCACGCCAGAATGAGAGTATATAGTTCCTAGCCATATTTAACTGAAAAATAGCAGCTTTTCATTTTCCATCAGTCTTAGTACATGATGTAACTACAGAACAGTCAAGCTTTAAAGAGGAAAATTGTTGAAACTCTGGTCATTTTTGAGCGAGATGCTAATGGTCTAATCTGATTTAATGATTTATGCTAAGCTAAGCTAAAGGTGCTTCCACTAGACCCGGAGATTGGCTGAATGGATTTAAAAATGGTAAAGCTCAACTGTAAAATAAAACTATTTCCAAAAAATCTGGAGCACTCTTTCACAGAAAGCATTTTTGGCTAATTAGCAAGCTAGGGACTATTTTCAGGTGTTACATATTATCATTGTTTCTGCTGCAGTCATGGTACGGAAACAAAGTCTTGATTATTATGCCAGAATAAGAGTATATTGTTTCCGCCTATAAATAGCAACTTTTCATTTTCCATCAGTCTTAGTAAATAATTTAACTACAGAAGAGTCAAGCTTTAAATAGGAAAATTATCTAAACTGTTTGGTCATTTTGAGCGAGATGCTAATGGTCTAATCCGATTCAATCCGATTCATAATTGAATTGAATGATTCAATTCAATTCAATTATGCTAAGCTAAGCTAAAAGTGCTTCCACTAGACTCGAAGATTGGATGAAAGGATATAAAAAATTATAAAACTCAACTGTAAAATAAAACTATTTCCAAAAAATCAGTAGTGCTCCTTTACAGAAAGCATTTTATTAATGATTTTGTTTATTTTTCAACTACACAAACTTAGTTATTAATGACTCTGAAACAAACAGCCAAAGTTTCCTTCAACATTTCCTTCAACAGTGTGCCTTTAAACAACATTCATTTCTCATTATCGTGTCAAAACAATAAGACTGCAGGAGATATTATGCTCTCATGTTATTATTAGTCTTTCTCTTATGCCTCTTCATTTATTCGCTATGCAG
Seq C2 exon
AGTGTTCAGTGAGTGCCGTTGCGGATCTGGTTTTCCTGGTGGACGGCTCTTGGAGTGTGGGAAGAGAAAACTTTAGATTTATCCGGAGTTTCATTGGGGCCATGGCCGGGGCCTTCGACATTGAAGAGGATAAGACCAGAGTGGCTGTGGTTCAGTACAGCTCGGACACCAGGACAGAGTTCAGTCTAAACACACATTTCAGACGACCCGATGTCCTGCGAGCCATTAAAAATCTGCCGTACAAGGGTGGAAATACCATGACGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000078322:ENSDART00000154728:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.778 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0009223=VWA=PU(46.2=89.9)
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]