GgaINT0032160 @ galGal4
Intron Retention
Gene
ENSGALG00000004946 | COL4A4
Description
collagen, type IV, alpha 4 [Source:HGNC Symbol;Acc:HGNC:2206]
Coordinates
chr9:8793343-8795538:-
Coord C1 exon
chr9:8795393-8795538
Coord A exon
chr9:8793460-8795392
Coord C2 exon
chr9:8793343-8793459
Length
1933 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAGA
5' ss Score
10.57
3' ss Seq
CATACTTCACATTTATCTAGGAA
3' ss Score
7.24
Exon sequences
Seq C1 exon
ATTGCATGCAACAGGTGAGCCTGGTGAACCAGGAAAAACAGATGACTCATGTCCTGCAATCCCAGGGCCTCCAGGGGAAGCAGGACATAGAGGAGATGATGGTTCTATAGGATTACCAGGGCCAATAGGTCACCCTGGACCCCAAG
Seq A exon
GTAAGATTGTGTTTTGAAATCTTAGATGTTTGTTTTCAGCCATTTAGACAAGGAGTTGGAAAGGGTCACTGCACCTTCTCTACCTTTTACCCTTAAAACAGTGGTCTGCAGAAAAAGGTAGTGTGTTGGTTAATGCTGAGGATGATAGGCCAGTATGGCTAGACCGGGCTACTTGAGTCTGCCTACACTACATTCCTCTTTTCCTAGGCCATGGAAGGCAAAAGCATCATGAGGCACTGAGAAAAATAAATTCTTCAGATGGTATTTTTCCTTTTACCAGCAAATAAAAAGCAATGCCTAGAATCCCCACTACCATTTAATATTAAGTGGTGGCTTGGCCCAGACAGGTTATATTCAGATGTTAAACATATCTTTAAATTTCAGCAAAACACAGATTCATAAAGCCATGCTATGCTAACCAAAGTCCTAAAAAGATGTACCAGTGATTCCAACAGAGTTGCCATCTTCTCAGAAAAACCACAGCAAATCTGTACTGTGTCTTCAGTTTAGGTTGTATCTAAATGTAGTGTCCTCAATTTAGGTAGTGGGATCCCTCCTACGGTTTGAGACATTTCTTACTTGGACAAGTTTGTTGTGGTAACTGCACTGAACATACGATATCTCCAAAGGAAAAAAATAAAAAAATAAGAATGTGTCATGTGCTCCCAGTAGATTCCCTGCAGGGGTCATTGCTCTCATGAAAGTGAGCATAAGGCAGTTTTCAATGAACTATATCATTTTATACAGCTTAATTGATTTGCCAACAAAGAGGTGTTTCTAAGTTGAATTTCTGTTTTCATTCTGTATATCCTTAAAACAGTTTCTGTAAAATCAGACAGTGCAATGATACTTATTTGCACTGGTTTTTACAAAAACCACTCTAGTAATGCTTTTTCTTTCATTAACACAGCAGAATTCCAAACGTTCCTGCTGCGAAAGCTACATAGATCAGAAACAGAGGTTTTACTGGCAGAATCAGTGTATATTACTAAACTTCCGTTACTTGAACCTTGGCAAAACAGCTATGCAACAGCAATTGAAAAGCTGTTCAATTGCTTTCCAATTTTCATAATGAAAAGGTAACATGGGGAATGGTTGAATGCTGTAAAGCAGTCTCAAAAAACAGTCTGCAGGTTAAATAGTATAGCTTGCAAGGAATTATAACCATTAATTATAACCAACTCCTATGCTAGAGAAAGTTGTTTTTCACAAAAATTGGAAAAACACAGCCAAGTACAACAATATCTGACAAGTTCAGATTGCGTTTAAAGTAGTCAGAGGGGTATCGTTATCTGTGCCCTACATATGAGATATCTATTACTGTGTGACCACGCTTTATTATCTGCTAATGTGTACAAATGTGTTTGTATGTGAGAAATATAAAAAAGCCTTTGCTCTTCCCCACTGAATGTAATCCAGTTCAGCTGTCTCTCTCTTTTCTATTAATACTTGAATACAAGCATTGCTTCACAGGAAGTTCAGTAATGTTTAAAAGCTTTGTTGAATCAAGTCCTAAAAGATGAAGGACTCCCATAGTATGAGTTATAACACATTACATAGAAGAAATACTAATGGCAATTCTGCAATAGGCTTGTCATAGTAATGTTTGTCACTGGTTTTACTTCAACTGTAAATCATACATATTCCATAGAGAGAATATAAAACCTTATCAGCAGTTACTGTTATTAAATTCTCACCTCTGAGCTACCACTGCAGTCACCAGGAGAATAAGTTGTAAAGAGAATTCCCAGCAGAAAGCATTTCTGCACCTCTCTGTTCCTTAGGTGATGTTCCTTTGTGGCATCATTTCTGCTGACCTTTTGCATACTGTGTACGTTTGGACAATGTACTAACATTAAAAGGAGTTACACTGAGTTATACTGAGTTATATAAAAGCGTTATATTAATGTGAACATACTTCACATTTATCTAG
Seq C2 exon
GAAGGAAAGGTGAAGAAGGGTCATGTGGCCTGCCAGGTCAAGATGGCTTACCAGGAGCACCTGGACCACCAGGTGACCAAGGGCATGTGGGAGAACAAGGATATGCTGGACCACAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000004946:ENSGALT00000007918:43
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=0.909
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PD(28.8=38.0),PF0139113=Collagen=PU(54.8=68.0),PF0139113=Collagen=PU(1.7=2.0)
A:
NA
C2:
PF0139113=Collagen=PD(43.5=67.5),PF0139113=Collagen=FE(67.2=100)
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:
ATTGCATGCAACAGGTGAGCC
R:
TTGTGGTCCAGCATATCCTTGT
Band lengths:
262-2195
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]