GgaINT0032163 @ galGal3
Intron Retention
Gene
ENSGALG00000004946 | COL4A4
Description
NA
Coordinates
chr9:10381733-10383556:-
Coord C1 exon
chr9:10383270-10383556
Coord A exon
chr9:10382473-10383269
Coord C2 exon
chr9:10381733-10382472
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
CACACTGGATCTGGTGATCAGGGAGGTGGGCAGTCCCTTATGTCACCAGGAAGCTGCTTAGAAGACTTCAGATCAGCACCGTTCATTGAATGCCAGGGTCAGCGGGGAACTTGTCAGTTCTTTGCTAATGAATACAGCTTTTGGCTGACAACAGTGATGCCTGACTTGCAGTTTGCATCAGCCCCCTTGTCAGGAACTCTTAAAGAAGGACAAGAGCAGAGGAAAAAAATCAGTAGATGCCAGGTATGCCTGAAGCATGATTAACAAGCGAAACAAATTAATAGCTAGAGTGAGACGAAAAACATGCTAAAGACTTAAACAGTATTTAATATGTAAATATATTTTAAAGTGTGTAACTCTTTTTGCTTGAATGGATATATAAGATGGAAAGATGCATCTATTCAATTTCATTCACCCATGTGCACATATGTACAGGTAGTAAAATCCAGTGTAAACTACTGGAGTCCACTACCATAATGGGCAGGTAACAAGCTGAACTTGCAGGGTTGAATTAAGTCTGGAATACCAAGAACACAGTACATGATTATGCAAGATAGTGGATTTCCTGTTAAAAGTGGCATTTAGAACATAATATGGCATATTATAAAGAACTGTCTCTTAAAAAGTATATAGGTACAGATGTGCAAACACCCAAATGTCTTCAAGTCCTAGAGCTGAATTTCCCAAGCTAAAAGAAATTTTCCCATGCTGTTTCTGAGGGAAGGGGAAAATGTAATTGT
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=0.011
Domain overlap (PFAM):
C1:
PF0141314=C4=PD(59.3=66.7),PF0141314=C4=PU(25.6=31.2)
A:
NA
C2:
PF0141314=C4=PD(72.6=96.6)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping 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]