DreINT0050294 @ danRer10
Intron Retention
Gene
ENSDARG00000021720 | col7a1
Description
collagen, type VII, alpha 1 [Source:ZFIN;Acc:ZDB-GENE-030131-2427]
Coordinates
chr6:40186699-40188429:-
Coord C1 exon
chr6:40188256-40188429
Coord A exon
chr6:40188151-40188255
Coord C2 exon
chr6:40186699-40188150
Length
105 bp
Sequences
Splice sites
5' ss Seq
AAGGTACAT
5' ss Score
7.87
3' ss Seq
CTATATATTCTGCATTATAGAAT
3' ss Score
6.25
Exon sequences
Seq C1 exon
ATCCGTGCATCTTGCCTATGGAAGAGGGTGATTGTTCCCGCTATACCCTGCGCTGGTACTTTAACTCTCAGGTGGACGCCTGTAGACCTTTTATCTACAGCGGCTGTGGAGGAAACGCTAACCGCTATTTACAGAAGGAAGAGTGTGAGAAACTCTGTCTACAGCAGTAAGAAG
Seq A exon
GTACATTACCACTCAGCTCCGAAGATGAAAAACATACGCATTAATGCATGTGGACCGGATAGAGATGGGATTTTTCACACTGTATCTATATATTCTGCATTATAG
Seq C2 exon
AATCGTGAAGGCAAGAGGATTTCCAACTCATTAATGATATGAAACCCCTAAACCTCAGTGTTGACCAATGCCATCATGCACAGGAGATTGATGGCAACACTTTTTCCTTGACGGGATGAGCAAATTTTAATTATTGATCCCATTTTATTTTATTTATTTGTTTGTCTGTTGAGCTGACAAACATCTGTCAATCTTGCCGCCAGACTAAATCTGCCTACATTTGCATCAAAGACAAAAAGTCAAACAGGAATTTTCCTCATGAACATCTTGTACATTAGTCCAGCCAGTAACAGCACAGCATTATCTTTCATTTCTCACTTAATCCTGGATGTCGCATATTTACACCCACTGACATTTTCTCAGGTGCTAAAAACAGACACGAGAACACACAATGTAATATTCCAGTTCCTTAAGACCTGTTCTTAGAATAAGCCTACGCTGTACAGAATTGTACTGTAAATGTAGATCTGTATTTTTATCAGCCTTAAAATGAGAATGAATGTTCTTCTATTATTAAATGTTGCATGTTGTGTACAGTACATGGACAAACGGTGCTATTTTTTAAAGATATTTTTATATTGTTGATTGGATTTGTATTGCTTTTTGGTTAAATTCCGTGTTTGTTCCATTACAGTTTACATTTTCTTTGCACAAGATGCAGTTTTGATAGCACATGTAGTCATTTTCCATATGTTGTAATGTGATCGGTCTCTTTTTCACATGTTCATTATTTACTTAGGAATAAACTTCGGAATTTAAAGGGAAAATAAACATGAAAACAATACAAAATGTCTGAATTGTCTCATTTTAACTATAAATATTAACAAGTACAGATCTACATTTGACTGGTCTCACGTCAACCGAAAGGTCCATTTGTGGTTCACTATCAGAACTAAAGTCACTGCAATCTGCTTTATCAATTTGCAGTTGCTCTGCGTTGTTGTCTTTTGGAGGGGATTTGTGTTGCGCATCAATCCTAGTCACACATCTGATGATTCAGTAATGGTTCTGGAGCGTCTTGTTAAGATGCCAACGTACACTCATTACTACTCTTCCAGAACTGTCACTCAAGCGCTGTTTTCATATTCATTTCTACTCATATTTATTCATTGACTGCATTTTGGCCAGTCCATCTGTTAGGGTATTTTGTTTTATATTCTTACGCCTGCTTAATAGCGCATTGTTTGAGTGCCAGCGTGTATTTTTATTCTGTTCACTCTTGAGATGAATCCGCCATTGTGCCTTTTAATGAGTTTGTTGCATTGTCGGTCTCTGAATAGCGTGCATCAAATTTTCTGTGGTGCTCCAGATGTCAAACAGTGTCTTAATCTATATCAGATGGTGCATTGAATATTAATATAAATGGATGCTTTCTTCATTCTCTAGGATTGTTGCGCATGCTTTTAAAATGGCTCTTTCCATACCTACTAATCTTTGGGAAGGAAGGAGTGT
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000021720:ENSDART00000154878:117
Average complexity
IR
Mappability confidence:
NA
Protein Impact
3' UTR
No structure available
Features
Disorder rate (Iupred):
C1=0.018 A=NA C2=NA
Domain overlap (PFAM):
C1:
PF0001418=Kunitz_BPTI=WD(100=93.0)
A:
NA
C2:
NA
Main Inclusion Isoform:
NA
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCGTGCATCTTGCCTATGGAA
R:
TGTGCATGATGGCATTGGTCA
Band lengths:
254-359
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]