DreINT0049827 @ danRer10
Intron Retention
Gene
ENSDARG00000052063 | col4a5
Description
collagen, type IV, alpha 5 (Alport syndrome) [Source:ZFIN;Acc:ZDB-GENE-030131-2281]
Coordinates
chr7:50889160-50890833:+
Coord C1 exon
chr7:50889160-50889325
Coord A exon
chr7:50889326-50890740
Coord C2 exon
chr7:50890741-50890833
Length
1415 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGA
5' ss Score
10.77
3' ss Seq
ATGTTTGTTTTTATGAATAGGTC
3' ss Score
8.91
Exon sequences
Seq C1 exon
GGTTTGGGACTGAAAGGTACACAAGGTCCCAACGGTGAACCTGGTTTGCCAGGACCTCCTGGAGACAGAGGTTTACCAGGTTCCCCAGGATTTGGTCCTCAAGGACCTTCTGGAGAAAAAGGTATTCAGGGTGTTTCAGGAAGACCAGGGGCACCTGGACTACCAG
Seq A exon
GTAAGAAACAATGCAATGTTTATTTAAAGTTTTCTTTACTTTAAAGAGCCCCTATTATACATTAAAAAGGTCATATTTTGTTTTTGGAGGTCTCCAAACATTGTCTTATAATATGCATTCATTTTTACCTAATTATCCCAGCGATTCATTTATTCCCAAACCCCTCCTAATCTGGGCTGATTGGACGGATGACAGTCTGTTGCGATTGGTCGACAGCGTTCAGTATGAGACAGAGTAAAATGCCCACCACGGCTTATCAACAATATTGAATTAGTCAGAGTGCGTAGTGTATGTGTGCGCATACCTGCCAACACTCCTGTTTTTTCCTAGAGTCTCCCGTATTTCAGACCCATCTCCCGCCTCCCTCCTGTTTTGGTATTTATCCCGGAAAACGCCCAAAATTTCAACCCCCACCACCCACGAGCTCTGACAAAGTCCCACTCACTAATAGTTTTTTCAGATCCTTCCTTTAACAAACGGCCGATGAATCCCCCTTTGTAAATGTGTAGACTGCAGAAGCACTCGTCAGAAAAATGACGGGAACACAGCACAAGGCTGGGGCTATAACGCTGAGGAATTTTTGCAAAAATAAACCTAAACCACTGACTCTTCACAGTTTCTTCTTTGGGTAGTGAAAATAACACTAACTTTACCTTACACTTCCGAATATATTCAGCAGAGCACAGCATCTTCACAACTTTATTTAACAGGGATCTGCTACAGTGCGTGTCTTCCTCTTTTTCTTTGCTACTGTATTTGTGGGCAGGGCTGAGGGTTTAAATTTTCCTAGGTTTGCGTGTGCAATAATTGAAATGGGCTTAAGTTTCGTAACAACATCACACTGACACTTGTTATCAAGACGATTCATTTGAAGCACTCTGAGTCAACTCTTTTTTAGACAAATGAAACACTGTGCACTTTCAGATTTAAGCCATAGCTGGATATTTCACTTCACTTAGAGGTGTGTTACCAATGCCATTTGTTATTTTGTTGTCATTTTAAAAAAATAATAATAGGGGCTCTTTAAGGATCTTATTCAGTTAAAATGCAGTTTATATAAAATGCATATAGGCTATTTTCTGCTCCATTCAAGGTAAATATCTACTGTAGATTAGTCTTGAAAATCTAGATGGCACAGAATGATTGCCCTCTGTATCCAATCAGATTTCTTGCTGAACATTTAAATACTATGATTGAGTTGTCATAGCCAATAGAGCAGTAGAGTAATCTGCTGTAGCTGCATGTGCAAATCTAATCCTACAAGGCTAAATGCATTTACATTGTCTTAATTATTAACATGACACACCCTTCAGAGTTTTTGACAGCTTATTTTCTTATGGAGTGCATTTTTTGTAGCTTTCAGTTTGGTAGTGTTCTACTATAGACATTATCTCAATGTTTGTTTTTATGAATAG
Seq C2 exon
GTCAGAAAGGTGAACCTGGGATGACTGTGCCAGAAGTTGGTGAACGTGGACCCCCAGGACAGGATGGAGATCCTGGTTCACAAGGACGTCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000052063:ENSDART00000073827:25
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PD(20.8=19.6),PF0139113=Collagen=PU(82.8=94.6)
A:
NA
C2:
PF0139113=Collagen=PD(15.6=31.2),PF0139113=Collagen=PU(46.9=71.9)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGGGACTGAAAGGTACACAAGG
R:
CTGGACGTCCTTGTGAACCAG
Band lengths:
255-1670
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]