DreINT0050314 @ danRer10
Intron Retention
Gene
ENSDARG00000021720 | col7a1
Description
collagen, type VII, alpha 1 [Source:ZFIN;Acc:ZDB-GENE-030131-2427]
Coordinates
chr6:40283799-40285805:-
Coord C1 exon
chr6:40285625-40285805
Coord A exon
chr6:40283956-40285624
Coord C2 exon
chr6:40283799-40283955
Length
1669 bp
Sequences
Splice sites
5' ss Seq
CAGGTCTGT
5' ss Score
6.84
3' ss Seq
GTGAATTTTCTGACTATAAGGGT
3' ss Score
3.67
Exon sequences
Seq C1 exon
GCCAGTGCAATGATGTTGTTGCAGCAGACGTTGTTTTCCTAGTTGATGGGTCATCCAGTATTGGCCGGGCCAATTTTATGTTGGTCAAGAGTTTCATGGCAGGCATTGTCAAACCCTTTGCCAAAGCAGTAGGACCGAATGGCATCCGCTTTGGAGCTGTACAGTACAGCGATACCGCCAG
Seq A exon
GTCTGTGTGTGTGTCCTTGTGTACCTAAAGGCATACTATTATCTTTTTACAAGAATTAAAATTAGTTGGTCTCATGTGTCCCCAAAAAGTTCAGCTTAAAATATGAAATGGATGAATTTGATACCATACTGTATATAACCCTTTTCTGGTGTTTTGTGCTTTTTCTCATTCAAGAGAGAAATTTTTAATTCTGTCATCATTTAGTCACCCTATACTTGTTCAAAACTCATTTGAGTGTCTTTCATCTGTTGAACACAAATGAAGATATTGTGATGAATGTTGGTTGCTGGCAACACTGACTTCTGTAGTATTTATTATGGAGGTCAATGGGTGCCAGCAACCAGCTTTCTTTAAAAATTTCTTTCTTGCGTCTTTAACAAAAGAAAGAAACTCATAAAGGCTTAAAACCACATGAGGGAGAATTAATGAAGATGTCGTTTTCATTTTGGGGTGAACTATTTCTTTAAATGCATATAAGCTGTCTCTTTAAATGCAAATAAAAGCCTTTTTAGTTTAAGCTTATATCATTTTCGCAGAGTGCTTACACAGAAAGCTGACTGTCTGAGCAAATAATTTCTTTTTCATGTTGTCTATCTAATATTTCAGCTGTTTAGTCTTTGTCCAAAGCACACACAAACACAAGTTCACATTATTCTGATTATGTCTGTAAATGTAAACACTCGGGGAAGAAATTGCATGTGCATCAGTACGATACCTGACAAAAGGCATCGATTCCAGTTGTAAAAGCAACAAATACTAACTTGATTTCTAGTTGATTGTTTGGAGAAGTGACAGAAGGTAGATTTTTCTGATGAATCATCTGTTAAGCTGCATCCCAATCATCACAAATACTGCAGAAGACCCATTGGAACCTGCATGGACCCAAGATTCTCATAGAAATCAATCAAGTTTGGTGAAGGAAAAATCATGGTTTGGAGTTACATTCAGTATGGGAGTGTGCAAGAGATCTGCAGAATAAATGGCAACATCAACAGCCTGAGGTATCAAGACATTTGTGCTGCCCATTACATTACAAACCACAGGAGAGGGCAAATTCTTCAGCAGGATAGCGCTCCTTAGATATTCTATGCTGTGCATTCTTTCTGTTAAGTGACAAGATTTTTGTCAAATCAAAGTCAGACCGTACTGTCCTATTAAAATCATTTAAAAAATCAAGAAATGATCATATTACATTTTGGTAAAATAAGCTTAGTCTTGAGGTCTTTGCCTTTCATATTAGCCACTTTTGATATCAAATAATCAACTATAGAAGTCAAGTTATTATTTGTGGTTCTTAAAACTTGAATATGCAACAAGAGTTTTGTCAGGTAGTATGTGTTAGATCCGTGAAACAGCATCTCTCGGACAACACACTACTACCAACATAACTCAGACAGGTCTTGAGTCTGGAGTGTGGAGAAGTTATTTTATTTAAATGTAAAGGTTGAAAATGTAAAATATATTTATAAGAGATGCTTTATTTGACAATATGTACAATTTTCTAATATATTTGATTTAATTATTAGTTTAATTTTAAGAAACAGTTCAGATGCTGGTTGTTTTGATGGACTGCATTTGTTACAGTATGAACAGGAAAGGTGGATGTTTGTGTGTGTGATAGATTATTGGTATGTTTGTTAATTATAGTTGTGAATTTTCTGACTATAAG
Seq C2 exon
GGTGGAGTTTACATTCACTGCATACCTGAATGGCACTGAGCTCATTACTGCTGTAGAGAATATCAATTATAAAGGGGGAAACACACGCACTGGAGCTGGTCTCAAATACATCGCAGACAACTTCTTCAGCCCGGCCTCTATCAGAGATGTACCCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000021720:ENSDART00000154878:3
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0009223=VWA=PU(29.5=83.6)
A:
NA
C2:
PF0009223=VWA=FE(30.1=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCCAGTGCAATGATGTTGTTG
R:
TGGGTACATCTCTGATAGAGGCC
Band lengths:
336-2005
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]