DreINT0050356 @ danRer10
Intron Retention
Gene
ENSDARG00000021720 | col7a1
Description
collagen, type VII, alpha 1 [Source:ZFIN;Acc:ZDB-GENE-030131-2427]
Coordinates
chr6:40225334-40227378:-
Coord C1 exon
chr6:40227310-40227378
Coord A exon
chr6:40225370-40227309
Coord C2 exon
chr6:40225334-40225369
Length
1940 bp
Sequences
Splice sites
5' ss Seq
CCTGTAAGT
5' ss Score
7.52
3' ss Seq
GATTGTGTTTTTTCAATTAGGGA
3' ss Score
8.37
Exon sequences
Seq C1 exon
GTGGTCTATGTTAAAGGGGAGCCGGCAACACCGGGACCTCCAGGGCCTCAGGGCCCTCCAGGAACCCCT
Seq A exon
GTAAGTAACATCTACCAATGCTGGATCTTTAGTTCATTTCAGTTAGAGACTATGATCATACACCAGGCGCAATAAGGTGCAAGACATGTTTGGCACGATTTGTTGCTATTTTCAGACCAGTGCAACCCTAATTTTCACATTTTGCGACTCACTGTTTTAATAGCATATACTTCTGCGGCAATTTGTGGACTCATGGGTGTTCCGGTCTAAAAAGCAGGTGTATTAAGGTGCATTGTTGGTGCTTTGCTATTTTGAGGACCTAAAATAGACTACGTCATTAACCATCTAAAAGTCTAAAGTCCAGCGCAGAGGCATTAGTTATGCGCCTATGCAGGTCCAAGCACTTACACATTGCTTAATACACACAGGATGTACAGCAATACACAAATATCTTTACATATGAAAAAAAGTAATAGATTAAAGTGTTACAAAATTATTATTTTCTACATAAACATAAAAACCACTGCCTCCATGCCTTCATGTCGGAGGGCGTTTTTCAGTTTATTCATGACAATTTGCAATTGTATAATGTTATTATTATTTTTAGTTTTATTTATTAAAAACAAGTTAAAATTTGTCCTCCTGTCAAGGTTTGGAGACCTATGCATCACCACATAGGGGATAAGAATAGGACATGTGTTTGGATATAACTCAGTTTTTTGACCACACTTCATTATTATTGTCCCTTATTCATTTGCTGGAAATTAGAACAGAATTTAGAAATAGTTTTGAAACAAATCTTTGCACTTAACAAATGAAATTAAATATGTAGGCTAATGGATGTCTTCAGTGGAGTGCATACAACACAGTTTCCTTATTCATTTAAACTAAAGGAGTAAAGTAAAGAGTAAATGCAAAGAGAAAGTAAAGAGGTCGAATGGAGGAGGCTCATTCTTTATTCTCGCGCTGCAGATGGTCTATTGGTCGTTTTCTCGCTAGTGAAGTAATCAGTTTTTCCACATACAAAGTCGCCATGTAAATAGCAAATTTGCCATGGTGCGACGCAACTGACTCTTAAAGGTAATAGGAGATGAGACTATTTGGTTTAATGCATGTTATTCTCAAAACACACCCAGAACTCATTAAGAGAAAAGGCACTACCCTGTTAGGCCATGTGCCACAATTCAGAGCATATTTTCCAACCCGGGCTCATTGTGGGAACGTAGCCCCGCGGACGTTTCTGCGGACCGCAATTTATGTCCCGGGAGGTACGTATTCGAGCGTTTTTTTGTTTTCGCAGGTCCGCGAGAGGCCCGCGCCGTTCTCGCGCGAATAGCCGCCGGATTGAAAAAAAAAAAAAAAAGCAAAAGTCCCTGTCTTCGATTTCGACCGCGTTTTCAGATCCCGCCGCATTCTCGCCCTTATTTTCCGGATTCCGTTTTTCGTCTTACCTGATTTCCGGAACCCGCCGTTCCCCGGACTCGATCCCGGTCGTCGTCCACTGCGGCCGGCTCCGGCTCCGGCTCCGGCTCGTCCTCCTCCTCCGGGGCCTCCGCTCCGCCAACGCAACGCTGTGAGCTAGGCGGACAAACTGATTGCGTCGGGAAAGCCCTCCACTTGGAGGCGAGCCGTCGGCCGGCGAGCGCGAAGAGGAGGGGCGGAGCGGCGCCACACCGCCCCGCAGCATTCACTCGAAAAAAACCAAACGCGGCCTTTACGTACCTCCGGCCACGTAAATCGCGGTCTCCAGAAACGTCCGCGGGGCTACGTTTCCAGAATGAGCTTGGGTTGATATTTTCTATCCTTAAAATAGCAAAAGTGAACACATTCTTAATGCTTTTGCGCCATTCGCTTTAGACTTTGCGCCTAGATCATTAAAATAGAGCCATATGTCTTTTTGCCATATATTATTTAGTTTTTAAAAAAAGCATCACTTTATTTAAATGGAAAACTACAAAATAAATGCAGTATATTGTATTTGATTGTGTTTTTTCAATTAG
Seq C2 exon
GGAATACCTGGAGTTCCAGGAGCTGGTGGAGCAAGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000021720:ENSDART00000154878:68
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(0.1=0.0),PF0139113=Collagen=PU(32.2=82.6)
A:
NA
C2:
PF0139113=Collagen=FE(18.6=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:
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]