DreINT0049803 @ danRer10
Intron Retention
Gene
ENSDARG00000002831 | col4a4
Description
collagen, type IV, alpha 4 [Source:ZFIN;Acc:ZDB-GENE-101001-1]
Coordinates
chr15:36106398-36108489:-
Coord C1 exon
chr15:36108334-36108489
Coord A exon
chr15:36106506-36108333
Coord C2 exon
chr15:36106398-36106505
Length
1828 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAAA
5' ss Score
8.38
3' ss Seq
TTATTATTATTATTTTACAGGTG
3' ss Score
11.43
Exon sequences
Seq C1 exon
GGCCCATGGGGTTAATGGGGGATCCAGGCAATGCTTTTACAGTGTGTGGTGAATGTGGTGATCCGGGTGGTCCTGGGTCACTTGGGTTTAAAGGAGAGAAAGGATGCCATGGGTCTGGTGGCACCCCGGGGTGTCAAGGCCCACAAGGCCCAAAAG
Seq A exon
GTAAAATAAACAGCTTTAATTGAATGGTAAATTCACTGATTTTCAACCTGCTTTGTAGTGTGACAGTTTTGGGAGTGTATGTCAATTGTGAATGTTCTAGTATGGATGTTTCTTTCAGTTTTTAATACTAAGTCTGAAGCTGACACTGTCAAGTAGATTAGGGTTATTAAAACCAATCTCGTGTATATGATGACAAATATATAGTGGGGTAAGTATTAAACACGGTTTTCTCCAAAAACCTATTTCCAAAGGTCCTGTTGACCTGAAATATTCACAGATTATTAGTAACAACCAAAGAAATCCATATATGCAAATAAAACAATATTAAACAGTTTACAAATGAAGTTATGTTTAATAAAATAAAATGACACCTGAAAAAAAATTAAACACATGAAGAAAGGGAAGTGTAAAAAGGCAGGAAAAGCCCAGACAGCAGCTGAAATCTCTTAATAGCTATTCAGTAACCTTCTGCCCTTCGTCAGTGTAAATTAATATTAGCTGCTTCAGTCTAACATCTACATTAGCCGGATGATAAAGATGAAACCAAGATGGCCATTTCAGCAAGACAATGATCCAAAACAAAGCCAAGAAAACTTTAAAATGGTTTCAAAGAAATAAACTCAAGCTGTAGAATGGCCCAGCCTGTCACCTGAATTGAATCTATTCTAAAATACACATTAAAGATCAGATTTAATAGACAAGACCCACAGAACCATCAAGATTTACACTCTGTTGAAGTCTGTGAAAAACTCACACATGAGAGTTCATCAGCCAAAAACGGCTTTTATATAAAGTTTTAAATACATTAAATATTAGTTCAGTATTTCTCCTAGTGTCATTCTATTGTTATTACACATAACATTTTTTTCATATTTGTTTTGTTTTATTTTTATATTTGTATTGTTTGGGTTTTTACCAACATTTTTAGTTCAATTCCATGTCAACAGCTCCTTTAGACATATTTTTTTTCCAGAAAACAAACATAGCGTGTTGAATACCTCCCCCTCCCCTCATCACCAAGAATACTTAGAATAACTACATTTATAACTAACATAAATAACTGTGTGTCTCTCAAATAAATAGTTCTGTACAGTTTTATAATGCTGTGTTGATATTTAGACAGTATTTGAAAAAATGTTTTGCCTCATTCAAACAAAATACTTTAAAAAAATAATAATAATAATTTTACTCACTATTTTCTATCCTTCAAGTGGTTCCCAACCTTAATAAATTAGTGTCACACACACTCACACAAAGATATTATGAAGAATGTTGGAACCCAGTAGCCATTGACACACTGCAAAAAGGACTTTACTTACTTATATTTTTTCTCTTGTTTCTAGTCTAAATATCAAAAAATTCTTAAGTCAAAAAGCATTTTTCTAGACAAACAAATTTATTATGTTTTGTTTTAAGAAATAATATTCCAAAATTAAGTGAGTTTTTCTTTTTGACAATATTATTTTGCTTACAATTTTGGCACTTTATTTAGCTTGTCTGAATTAAAAACTCACTTCATTTTAACATATAATTTCTCAAAAAACAAGACAAGATGTTTTGCTTGTCCCGAAAATGCTTCTTTATTTAAGAACCTTTAGACATTTAGACTAAAAACAAGACAAAAATCTGACTAAGAAAAACATTGTTTTAGTGCATCATAGTCAAATTACTATGGAAGTCAAAGGCTGCTAGTTTCCAACAATTTTAAATATATAATAATTTGTGTTTTAAGAAAAGAAACTCACAAATGAGTAAATGGAAATGTTTAACTACACTTTTGTCATTCTGCTTGTTCTAGATTGTCATTATTATTATTATTATTTTACAG
Seq C2 exon
GTGAAAAGGGGCTGTGTGGACTTATGGGAATCCCGGGACTCCCTGGCCCTATGGGTGACTGTGGGCCTCTGGGTCCCAGTGGTGCAAAAGGAGATAAAGGGGACACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000002831:ENSDART00000154476:42
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(22.2=26.4),PF0139113=Collagen=FE(58.4=100),PF0139113=Collagen=PU(23.8=28.3)
A:
NA
C2:
PF0139113=Collagen=PD(21.3=51.4),PF0139113=Collagen=FE(57.1=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGCCCATGGGGTTAATGG
R:
GTGTCCCCTTTATCTCCTTTTGCA
Band lengths:
262-2090
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]