GgaINT0032163 @ galGal4
Intron Retention
Gene
ENSGALG00000004946 | COL4A4
Description
collagen, type IV, alpha 4 [Source:HGNC Symbol;Acc:HGNC:2206]
Coordinates
chr9:8788722-8790709:-
Coord C1 exon
chr9:8790423-8790709
Coord A exon
chr9:8789626-8790422
Coord C2 exon
chr9:8788722-8789625
Length
797 bp
Sequences
Splice sites
5' ss Seq
ATGGTAAGT
5' ss Score
11.01
3' ss Seq
TCTTTCATTGTTCCTTCCAGCAC
3' ss Score
9.14
Exon sequences
Seq C1 exon
GTCTGGCAGGATCTTGTCTTCCTGTATTTAATACCATGCCCTTTGCTTACTGTAACATCAACCAAGTTTGTTACTATGCCAGCCGAAATGATAAGTCCTACTGGTTGTCAAGTGCCGCTCCCTTACCAATGACACCACTGTCTGAGGAAGAAATACAACCATATATAAGCAGATGTGCTGTATGTGAGGCCCCAGCCCAAGCAGTAGCAGTTCACAGCCAAGATCAGTCAATTCCTCCCTGCCCAATGAACTGGAGAAGTCTTTGGATAGGATATTCTTTTCTGATG
Seq A exon
GTAAGTTTCTGGGCATATGAATTCTTTAATACAGCCTTTGTGTTCTAAAGATTGAAACGAAAAAACTTCACAAAATGAAGGTCAGTTTCAAAACGTGTCTGTAGCTATCTCTATTATGCTAAAGTCATAGCCTTGAGCTATACATTTCTTAAAATTGCCAGGATTTTTGCGTACTTGTCCCATAAACAGTGGAATTTTCATGTACAAAGACACTTCAGGACAGCGTAGAAACAGGACAGGGAATAATGGTTTTAAACTAAAAAAAAAAAGGTAATTTAGATTAGATACAAGGAAGAAACTCCTTATTCAGAGGGCGGTGAGGCACCAGAACAGGCTGCCCTGAGGAGCTGTGGATGCACCATCCCAGGAAATGTTCAGAGGCCAGGCTGGATGGGGTTTTGAGCAACCTGACATAGGGGAATGTATCTGTCCCCATAGCAGGGGGGGGGGGGAGTGAAGTTAAATCTTCAAGGTCTCTTTCAACTCCAAACATTCTATGATGCTGTGAATTAGAAGTCCAGGTCTTTTCAGTGCTGTCTTCTAGTCACATTAGAAGCAGTTTAGATTGAAGAACTGCATTTAGAATCCACTTGGATTACTCTTCAGCTTGGTAAGTACTACAAAAGTAAGAGAGCTGGTCCCAGACTTTTGAGATTAGAGATTTTGTCCAACAATCGAAGTTGACTGCAACCTGAGATCACAAAACAAAATTGAAAGCAGTTAAAGAAAAAGAAAAATTAAAATCATATACATATTCTCCACACACAGTTAACAAGTTCTTTCATTGTTCCTTCCAG
Seq C2 exon
CACACTGGATCTGGTGATCAGGGAGGTGGGCAGTCCCTTATGTCACCAGGAAGCTGCTTAGAAGACTTCAGATCAGCACCGTTCATTGAATGCCAGGGTCAGCGGGGAACTTGTCAGTTCTTTGCTAATGAATACAGCTTTTGGCTGACAACAGTGATGCCTGACTTGCAGTTTGCATCAGCCCCCTTGTCAGGAACTCTTAAAGAAGGACAAGAGCAGAGGAAAAAAATCAGTAGATGCCAGGTATGCCTGAAGCATGATTAACAAGCGAAACAAATTAATAGCTAGAGTGAGACGAAAAACATGCTAAAGACTTAAACAGTATTTAATATGTAAATATATTTTAAAGTGTGTAACTCTTTTTGCTTGAATGGATATATAAGATGGAAAGATGCATCTATTCAATTTCATTCACCCATGTGCACATATGTACAGGTAGTAAAATCCAGTGTAAACTACTGGAGTCCACTACCATAATGGGCAGGTAACAAGCTGAACTTGCAGGGTTGAATTAAGTCTGGAATACCAAGAACACAGTACATGATTATGCAAGATAGTGGATTTCCTGTTAAAAGTGGCATTTAGAACATAATATGGCATATTATAAAGAACTGTCTCTTAAAAAGTATATAGGTACAGATGTGCAAACACCCAAATGTCTTCAAGTCCTAGAGCTGAATTTCCCAAGCTAAAAGAAATTTTCCCATGCTGTTTCTGAGGGAAGGGGAAAATGTAATTGTTAAAAACACATGATTACACATAATAAAACCAACAAAGATCAAAGTCTTTTACTGCTGCTGTACCTAACAAAACTGTGAAAGAGCTTAATTGAGATTTCATAAGTAACAGTAAGTTGCAAATCCATTTGACAGCAGATTATGTAAGAAAATAAAATTAGATGAGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000004946:ENSGALT00000007918:46
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=NA
Domain overlap (PFAM):
C1:
PF0141314=C4=FE(35.3=100)
A:
NA
C2:
NA
Main Inclusion Isoform:
NA
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CGCTCCCTTACCAATGACACC
R:
CTGCAAGTCAGGCATCACTGT
Band lengths:
343-1140
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]