DreINT0049826 @ danRer10
Intron Retention
Gene
ENSDARG00000052063 | col4a5
Description
collagen, type IV, alpha 5 (Alport syndrome) [Source:ZFIN;Acc:ZDB-GENE-030131-2281]
Coordinates
chr7:50887465-50889325:+
Coord C1 exon
chr7:50887465-50887656
Coord A exon
chr7:50887657-50889159
Coord C2 exon
chr7:50889160-50889325
Length
1503 bp
Sequences
Splice sites
5' ss Seq
CCTGTGAGT
5' ss Score
7.21
3' ss Seq
TTTAAGCCATTTTTTAACAGGGT
3' ss Score
5.79
Exon sequences
Seq C1 exon
GGAATACCTGGACCTCAGGGTTCCCCTGGACTCCCTGGAGAGAAGGGTGACCCAGGCGATACCCTCTCTGTTCTTGGCGTGAAGGGAGATAAAGGAGACACAGGTTTTCCTGGCTCTCCAGGTCTGCCGGGACTCGAAGGAAGACCTGGACGTGATGGAGTGCCTGGTCCACCTGGCCTCAGAGGACCACCT
Seq A exon
GTGAGTGTTTGTTCAATTTACTTTATGCCCAGCTCACACTGTGATTTCAGCCATGATTTGATTGTCTAAGACAAATTTGGGAAAAAAAACTCCAATAGTCCTAGGCTAAAACTCATGGTCTTTGATCATTGGTTTGACATGTTCGCTGATGGCCGTTCACTAATGGCCGTTGAGATTTTCCCTCCAATGAGGTTCTGTCAGTGTCTGAAGATTTTTGCAGTCCAACTTTAAACAAGAATCAAAAATGTAGGATTCCACACAATTCCTTCATGTTGTACCAACAGATATCGATTAAGTTAACTTATTTTTTTTTTTTACAAATTTAAGTTGATTGAACATAAAACAATTAAGTTATTCCAAAAAAATCTCAAGAATTGTGTTGATTCAGTTCTTTATAATTAGGTAGTTTGAATAAGCAGCAAAAAATTTTATTATTATAATTTTTTTGCATGGAGAAATGTCAAAAAATGTTGTTGTTTTTTTTGGTGTATTGAGGCAAGCAGTGAGTAAAATCATAGCTACAGGTTGTTTATGTATAGAGCAGTGATTCTTAACCATGTTCCTGGACCACCATTTTACCATGTCTCCTTAATCAAATACACCTGATTCAGATCATTAGCCCTATAGCAGAGACTGATAGACCTGTAATGGAAGAGACAGACAAAGGAGACATCCAAAACATGTAGTGTTGGTGGTCCTTCAGGAACGTGATTGAGAAACTCTGGGTTGAGTCATGGAAGGATGACTTTAAACTACGATGAGTTTTCTTGCATGTCTGTGTTTGATGCATCGTCATTGTTGCTCAGTCTGACATTATGATAACTGAGATCTTACAGGGTGACATGGAGATTGGATTTGTGCAGTCAGAAAAGTATTTGTTAAATAATGTTATTAATTACTCTCCCTCATTTGCTTTCAATCTCCCGAGACCTTTGTTCATCTTTGGATCACAAATGAATATGTAGGTGAAATCAGAGAGCTCTCTTTATCATACAAATCTCCAAAAAAAAATTTGTGCACCTAAAAACTTTTCAAATAACTTTGGTCACCAATATTAACCAATCAAACCAGGGTGCATTTTTACTACGGGTAAGAAAACGCTTGTGTGTTGTGCTGCTGAGTCTAATAGGAATATGTCATTCTGCCTCTAGTAAACCCAAACCCTGATATTATGAAATATAGGAGAAGAGAGTCATTTTTGTAGTTTTTTGCCACATAAAAGGGATCTCAGTGCTTTTGTATGATTACATTTGAACCACTGAAACTGAAATCTCTCCAATCAACTGAAAACTTAGTTCTGAAGATGAGCGAAGGACTCAGGGGATTGAAACGACTTGTGGATGATTAACCAGTGACAGATTTTTCTTTTTTGGGTGAACTTACCCTTGGTGGCTTTCACATGAAGCTAATTTTCACATCTAAAATGAGAAACCCTACTTTTACTTGACTTAACAGCTTTGCAAAACACTGATTCAGCACTGAATTTAAGCCATTTTTTAACAG
Seq C2 exon
GGTTTGGGACTGAAAGGTACACAAGGTCCCAACGGTGAACCTGGTTTGCCAGGACCTCCTGGAGACAGAGGTTTACCAGGTTCCCCAGGATTTGGTCCTCAAGGACCTTCTGGAGAAAAAGGTATTCAGGGTGTTTCAGGAAGACCAGGGGCACCTGGACTACCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000052063:ENSDART00000073827:24
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(33.9=31.2),PF0139113=Collagen=PU(75.5=62.5)
A:
NA
C2:
PF0139113=Collagen=PD(20.8=19.6),PF0139113=Collagen=PU(82.8=94.6)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGTTCCCCTGGACTCCCTG
R:
TGGTAGTCCAGGTGCCCCT
Band lengths:
339-1842
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]