DreINT0050386 @ danRer10
Intron Retention
Gene
ENSDARG00000021720 | col7a1
Description
collagen, type VII, alpha 1 [Source:ZFIN;Acc:ZDB-GENE-030131-2427]
Coordinates
chr6:40209333-40211727:-
Coord C1 exon
chr6:40211692-40211727
Coord A exon
chr6:40209393-40211691
Coord C2 exon
chr6:40209333-40209392
Length
2299 bp
Sequences
Splice sites
5' ss Seq
AAGGTATGT
5' ss Score
9.79
3' ss Seq
TCATTTTCCTCCACATTCAGGGT
3' ss Score
9.37
Exon sequences
Seq C1 exon
GGTGCTGCAGGCCTTCCAGGACTTAAGGGTGATAAG
Seq A exon
GTATGTCATGTGTGGCTTGCAGAGCTTCTAGCCTACAATTTTTCTTTTTAATTTAAAAAATTCAGAAGCACTGTCAAAAATTTAGCAGCTGATGTCATGCAGATGAAAAGGGAGCTTACAGTACCCATTATGACAGAAAAATATGGGAGACATGATAAAGCAATGATGAACCAATGTAGGTAATTTAACAGTTGATGAAATGAAATAGATGAAATTAAACATGCTCGTCTTCATTTCTTGGTTTTGAACCGTTAAACTAGAACTTTTATTAACTGCATGGTAATTTTAAACATCTAGTTTGCTGGCAACATAGAGTTCTCATTAACAGATGGTTGGCACATGTAATGTTGCATTTTCAAACGCACGTCATTCAGTAACTGACCCAAATTCGCAGCCCTTTCAGAGATGGAGTTTGTGTGTAGCAGCATTTTCTGCAAACCGAACCACTTTGAGCTGCCAAAAATACAGAATCATGAGCTGTTGTTAATTTATATGTAAATTAACAAAATGACACTATTCAATTGGAAACACATATTTTGGATTATAAAGGAGCTTAATTTTGGTCTTTGCAATTTTTACTCACATTTTGCTTTGACAAATGTTTATTTATTGATGACCTTCACTTGGTTCTGTCTAATCGGGTCATGATAGTTTTTTTTCTTATTTGGTTCATGATGATTTTCCCCACTGATTCTGGTAACAATTTATGGAGTGTGTCTCAGCCCAAATGCATATTATCACTAGAGCAAAATATGAATTTGCAGAGGCAGTGATTCAGTTCACTTGCCTTTTTTTTTACCTATCAATTGATATGATAATTACATTTAGGGCTCTATTTTAACGATCTGGGGCAAAGTCTAAAGTGCATGGCGCAAAAGCATTAAGGGCGTGTCCGAATCCACTTTTGCTATTTTAAGGACGGAAAAATACACTTTGCGCCCCAGCGCATGCTCTAACAGGGTTGTGCTAATTTTTTATTGAGTAATGGGTAGACCCACATGGAATCTGTGCATGCAGAAATCTGCAGATTTTTAGCCCATCATTGAGTCTATGTATTTACTTATGTAAATGTGTGTAAATGTATATTTATTCAGTTTTTATATTCATTTCAGAAATATTATTGACTAATATGAAAATGTTTAAATGATTTATTTACAATACAGTTTGTAAAGTGTTTCAGTAGATATATCATTTGAGATTTGCTTTGCTTACCAATTTAGTAGATCTAATTAGATTTGCTTTGGAGACATTAAATAAAAGTTTAGCCACAATGCTCACAAAATCATTCCGCATAAATCCACAGATTTTTACAAAATTCTCCACAAAAATACCAAAAAATGTCAATAGATTCCGTCTAGCCCTAGTTATGGGTGTGTTTTAGCATAACGTGCATTAAAACAATCAGAGTCTCATCTCCTATCGCCTTTAAGATTCAGGTGCTTCAAGCCATGGTGCATTTGCTATTTACATGTCGGACCTTGTAAGTGTAAAAACTCAAAGCTTTACAAGCCAGAAAGCAGTTAACAAACCATGAGCAGTGCGAGTGAGGATAAAGAACGAATCTCCTCAATTCAGCCTCTTTACTTTACTTTTACTCTTTACTCCTTAACTTTCATGCATCATCTCACTACATTTCACTCCACTGAAGATATCCATTAGCCTACATATTTAATTTTGTTTGTTAAGCGCAAAGATTTGTTTCAAAACTATTTCTATATTCTGTTCCGATTTCCAGCAAACGAATAAATGTAACAAAGTTTGGTCAAAAACTGAGTTTGTATATTGCTGTACATTCTCTGTACATCATCCTCTTTAGATTTGCTTTTAGTTGGTCAGTGGCGCAGTCTATTTCAGTTCCTTAAAATAGCAACGGTCAACAATGTACATTAACACACCTCCTTTTTAGACCAGCACACACATGAGTCTACAAAGTGGTGCAAATTGATTTGCTATCTAAACAACATGGCACAAAACATTAAAAAAGGGGTTGCGCTGGTCTAAAAAAAGCAACAAATCGTGTCAAACATGTCCTGCATCTTATTGCGCCTGGTGTATGATAGGTGTTTAAGTAAGTGTTACAGTAAGAAATTAAAAATACTATGATTTTACAAAAGTGCTCTCCGACCTTTAGGCCGCATTGGATATGAGCTTTTTATTTTAGAATGAAGAAAGCAGGCCATCGCAAAAGCTAAAACTCCATAACCAGCTTGTCTCTGTCAGTCAGAGCCACTTTTATGAGATTCTATCGGACAAAATGAAGTCATTACCCTTCTTCTTTCTCATTTTCCTCCACATTCAG
Seq C2 exon
GGTGAAATTGGTGTTGGAGTGCCAGGTCAAAGAGGGGAGCGGGGAGACCCAGGACCTCGT
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000021720:ENSDART00000154878:95
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=FE(18.3=100)
A:
NA
C2:
PF0139113=Collagen=PD(8.3=25.0),PF0139113=Collagen=PU(26.2=80.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
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]