DreINT0049678 @ danRer10
Intron Retention
Gene
ENSDARG00000104110 | col4a2
Description
collagen, type IV, alpha 2 [Source:ZFIN;Acc:ZDB-GENE-070725-3]
Coordinates
chr9:8894246-8897319:+
Coord C1 exon
chr9:8894246-8894353
Coord A exon
chr9:8894354-8897127
Coord C2 exon
chr9:8897128-8897319
Length
2774 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAAT
5' ss Score
6.38
3' ss Seq
TAATCAATCTGAATTCTCAGGGA
3' ss Score
5.61
Exon sequences
Seq C1 exon
GTCCAAGTGGACACAAGGGGATGCCAGGTCTTCCTGGAATACCAGGAAGTCCAGGCTTCCGTGGAGAACCTGGATCAATGGGCCACTCTGGTCTGCAAGGCGAACAAG
Seq A exon
GTGAATGTTGTGCTTGTCTAAAAGTACTGTGAGGATTAAGAAATTCTGGGTTAGATTAGTGGATTAAAGATTGGGGGAAACTGGTTTATTTTAAATTTATTTCACATTTAAACTTTGTAACTGGAATCATTTTTTCATTTCATAATTTAGGAAAGTGTCACTAATTAAAACCTTTTCTTGGCTGCCAAAGTTATCAATTATTTAAGCCTATTTAAAATGATTTTATTAATTCCTTAAAGGATTAAGGGAAAAAAAAAATTGCAAGAACTTTGATCTGAGGTGAGTGACCATTTGTCCCAACTGTGCACCAGTAAACACATTAGAAGTGTTTCCAGATTTCCCATTTCTTTGAAACAGAGATGTTTACATCCTTATCTGGGATGCATCTGGAAAGTCTTCATAGCGCTTCACTTTTTTTCCTAATTTTTTATGTTACAGCTTTATTTATTTATTAAAATAAAAAAATCTGAAAAATCACATGTACATAAGTATTCACAGCCTTTGCTCAATACTTTGTTGATGCACCTTTGGCAGCAATCAACCCTGGGACCTTATATAGACAGGTGTGTGCCTTTTCAAATCATGTCCAATCAACTGAGGCCTACTCACACTAGGTACAGTTGCCTCGAACCGGGCCAAAGCACGCTTGTCCCCCCTCCCATGTCCCCCGACGGCCCTCGCTCACACCACAAACGGGCTTCGGCACGCTTACGTCATCGCTGCTGCGCTGTTCAATGAGAAGCACTCTCTCACTCAGCAGCACAGTGGAGATTTCTCTAGTTATATCGTTTCAGTCGTTTGATATGCCGTCAAATATTTCGCCAAACAGTCCTTAGGGATGCGGGGACACGCAGTCAGATATTTTGCCGAACAGATCCGCCACTTTTAAAGCTCTCGTGCTGCAGGAATGAGGAGGTCTGCTGAAGGCGCGCAGCTGTCGTGCAGTGATGGGTTTTTGCGTCTTTAATAAACTACGGCAGTTTGCGTTCACAGAAGAATACGAATTATTAATAAATCCATATGAAACAGTCCCTTAAAATTCACGTCTCGCTTTCAGTTTCGAGCTTTGGCGTGTTTTGCACTCACACACAAGCATACCGCGCCAAAGCCCAAGTGAACCGGGCTCAGGCACACCTCTTCCAACCGGGCCAGGGCCGGCCAAGTGAACCGTGCTTGAGCCCAATTCAGCGCACTCACACTTCTCAGACGATCCGGGAAACGGGACTGGGCACGGTACGGATGGCATAGTGTGAGTAGGCCCTGAATTTACCACAGGTGACTTCTAATTAGGCTGCTGAAACATCTAAAGAATGATCAGTGGAAACATAATAGAGCGTCACGGCAAAGGCTGGGAATACTTATGTGCATGTGATTTTTTTTATTTATTTATTTTTTTTAGAAATTTGCAACAATTTTTAATAAATATTTTTTCACATTGTCCTTATGGAGTTTTGAGAAAAAAAATTGAATCCATTTTGGAATAAGGCTATAACTTTAAAAATGTGGAAAAGTAAAGTGCTATGAATATTCCCGGATGCACTGTAAGTCTGTTAAAAGACACAGGGAGGAGAAAATATATTTTATCTGTGCAACATATGCACAGAGTCTCCAAACCCTTCACCACCAATATATGTATTTCTACAGTTAATCTTTCACCTAGAGATAAGATGTGCCCTCTATCATATACTCTTGCTCAGTCATATTCAGTTGGTCATATGATTTTAATTATGCACATTGAATCATGTGATGTTATTTCTGTTGCTGAGAAGGTACAATAACCACCTAAGAGTACAATGGCAAAGTTGTTTTTAACCATTGAGAAAAACATCATATGATACAAGTGATTTTGCATGACCAGAAACGTATATATGCTGAATACATACGATTGTTAAAAACCAAAGGGAAGCATTTCCCGTGAAAAAAGTTAGGAACTAATGGTAGAGCATAGGCCTCAAACTCAATTCGTGGAGGGCCGCAGGTTTGCTCAATTTAGCTCCAACCCTAATCGAACACAGCTGATCCAACTAATCAAGGTGTTCAAGACTACTAGAGACTACTATTAAGCAAGGGTGAGTTAGAGGTGGTTGGAGCTAAACTATGCAGAGCAGCGGCCCTCCAGGAATTGTGATTGAGACCATTGTAGTAGAGAAGTAACTAATATGAACAATAATATTTACATAATTAACTTAATATTAGCAACATTAAAGTCTTCGGGAACTCATTGGCTTGACTCATGTTTGGAAAACAGAGTAATGTTAATAATTTGCCACCACAGTGTTTGAAAACCTACAAACTGATTCAAAACCAGGCCAACTGATCTTCTTCAAGACAATTTCATGCTCCCAACTTTGTGTGAACAGTGGGGAAGACCCTTCCTGTTTCAGCATAACCAAGCACCAGTGTACAAAGCAATAACAAGCACAAGAAACATGGATAAATGAGTTTAATTTGGAGGAACTTGACTGGCCTGCATAGAGGCCTGATCTCAATCCGACTGAACATCTTTGGGTGAATTAGAGTAAAGACTGTGAGCCAGGTCATTTAATATCACTGCCTGATCTCACAAATGTGCATCTGAAAGAATGGTCAAAATTTTCCATAAACACACTCCTATACCTTGCAGAAAGCCTCTCCAAAAGGGTTCATGTGTGTGTAAAGGCAGATGCCCCAACACTTTTGCCAATATAGAGTACTAAAAGAAAGAACTGCAAATCATTTGATCGTGAATATCTGACTGCTCACATTATGAATTGATAATCAATCTGAATTCTCAG
Seq C2 exon
GGACTCGAGGACGACCTGGTATGCCCGGTCCTCTTGGAATGGCTGGCCGCAGTGTGAACGTTGGCTATCTGCTGGTGAAGCACAGTCAGTCTGAGGAGATCCCCATGTGTCCTCAGGGCATGTCCTTGTTATGGATGGGTTACAGTCTTCTGTACTTCGAGGGCCAGGAAAAGGCCCACAACCAAGACCTGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000104110:ENSDART00000160004:19
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=0.215
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PD(41.0=67.6),PF0139113=Collagen=FE(58.1=100)
A:
NA
C2:
PF0139113=Collagen=PD(37.3=33.8),PF0141314=C4=PU(39.8=66.2)
Main Inclusion Isoform:
NA
Other Inclusion 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]