Special

GgaINT0120884 @ galGal3

Intron Retention

Gene
ENSGALG00000008461 | F1P302_CHICK
Description
NA
Coordinates
chr1:11465548-11467521:+
Coord C1 exon
chr1:11465548-11465690
Coord A exon
chr1:11465691-11467400
Coord C2 exon
chr1:11467401-11467521
Length
1710 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAGG
5' ss Score
10.51
3' ss Seq
TATATATTTTTTGTTTCTAGTTG
3' ss Score
8.46
Exon sequences
Seq C1 exon
CTTTTTGCCTTCGAGCTATCGGGGTAAAGACCTGCGGGAAAACTACTGCCGAAACCCCCGAGGGGAAGAGGGAGGGCCATGGTGTTTCACCACCAGCCCACAGATGCGCCATGAAGTCTGTGACATCCCCCTCTGCTCTGAAG
Seq A exon
GTAAGGCAGGGCTCACGTCAAAAGGTGCTTTTTTTGTACAGAGAGCAGGTACACAGAACTTCCATTAGCTTCTGTAATACTCACCTGCAGACTCTGCAGTAAGGAAAGGTGACTTCTTAGCTAGAATGAATGCTAGAATGCTGCTGCACAAAAAGTAGTTAGAAGAAAAGATCTTGAACAAGCTTTCAGAATCACTAGTCTTGCTCATGTCACAGAGAATTTAGAACAATGCAGTTGTGCTGACTGCACAAATGTGTCTCTGATTTCATGGTGAAATACAGAGGGAATCTATTAACAATTTCATTACAACTGCTGATAAACTTATCTAGTATAAAAGCAGCTTTTCGTCTTTTTGATGAAAATATATAAGTACTGAATTACATGACAAATGCTTAAAGTAAAAACATATTTTGCTTTTCAAATGAATTACATAAATAAGGAAAACATTTAGGAAAGCCAGCCACATTCCACTTTCAAGTCTCAGAATCAGAAATTGAATTGATGTGCCTCATCACATCTGACTTTTACATTCTGTTAACTTCCAAACTGAGCTCTTACATCTTTCTAATCAGCCAATTCACTTCTAGTCAGTCAATTCATTTAAATTCTCAAGATAGGATGCCTTCAATTTTCCTGCTAATATGTTATGTGCAATAGGTACACAGTGAAGGGGGAATAAGAGGGAACGGAGAGAGAAAGGGAATTATTTATAAGTAGTTTGAAAATCTATTAAGAGCTAACATTTAATGATCAATTTAAGGCAGTTTCAAATGGGTTAAGACTTGGAGCTAACTGTGGGACCAAGACTTGAGCAGTGAATGTCTTGACTGAAGAATGAGATCTATAGTTGCATAAATTATTATTTACTAAATGCTTCTTAATTACAATTACTCTAATTAGGGGGCACTTGAGAAATGTGTCTGTAGTTAATTAGGGTGAATTTGTTATATTTTAAGATTTTCATTCCAAATTATGCAGCATATTTTATTTAATTGCAATTTCAGATCTTTTTTGTAGCTTTTACCCACTCTTCCTCCACCTTTCCACTTTCTTAAACCAAGAATGAAAACGTATAATTTTTTAAGCTACCAGAAAGAATTAGTATTGAAAAGAAACAATATTATACATAGCTGAAAGTGCTGCCAATTTAAAGACGGTACTTCCTGAAATTTGTAATTCAGGCATTATTCTGCACCTAAACTAGTGCTGCTATTCTACAGAGCTGTATGACTTAGAGTGATTTAGGATTATATCTACTACAGTAGAAAATATCACCTCCAAATAAGGCTCCTTCCTCTGCTGTGTCTCTCCCTGTCAGTAATCATAACACTTTCTACATGATATGCAGGGGATTAGAGACTAAAATCAGAACTCAAACAAATCTCTGTAATAGGTAAGATTAAAAAGCAACTAGGAACACAAATGGCTCTAGCAGCCAACACCTACCTGCTTCCCAACCGTGAGAGTGCTATGAAGTGGTACCAAATCTGGATTAGATCTGAGAAAGAGACGCAATTCAATTCCAAAGGAAATTTCCCATTTCAAGGAGCCAGCCCTGCCTTAAGAGATATCAACTTTTATACCTCTCTAAGTTGTTTTCAATTTATAACAGAAGGGATATAATTCATTATTATTATTATTATTTTTAATGCTGTAATTCACCAGCATAATAAATGACTAGAAAACTATATATATATTTTTTGTTTCTAG
Seq C2 exon
TTGAATGCATGACCTGCAATGGAGAGAGTTACAGAGGACCAATGGATCATACTGAGTCAGGCAAGGAGTGTCAGCGCTGGGACCTTCAGAGACCACACAAACACAAATTTCGTCCAGAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000008461:ENSGALT00000039793:6
Average complexity
IR
Mappability confidence:
NA
Protein Impact

ORF disruption upon sequence inclusion

No structure available
Features
Disorder rate (Iupred):
  C1=0.000 A=NA C2=0.161
Domain overlap (PFAM):

C1:
PF0005113=Kringle=PD(57.0=91.8)
A:
NA
C2:
PF0005113=Kringle=PU(48.7=92.7)


Main Inclusion Isoform:
NA


Main Skipping Isoform:


Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Human
(hg19)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CGAGCTATCGGGGTAAAGACC
R:
GGACGAAATTTGTGTTTGTGTGGT
Band lengths:
247-1957
Functional annotations
There are 0 annotated functions for this event


GENOMIC CONTEXT[edit]

INCLUSION PATTERN[edit]