GgaINT0099740 @ galGal3
Intron Retention
Gene
ENSGALG00000023195 | F1NCZ0_CHICK
Description
NA
Coordinates
chr2:24408019-24409829:+
Coord C1 exon
chr2:24408019-24408212
Coord A exon
chr2:24408213-24409557
Coord C2 exon
chr2:24409558-24409829
Length
1345 bp
Sequences
Splice sites
5' ss Seq
CAGGTAATT
5' ss Score
8.55
3' ss Seq
TCGCCGCCTTTCGCTTGCAGGTG
3' ss Score
11.81
Exon sequences
Seq C1 exon
ATCAGCAGAAAACGACGGTGATCGAAAACGGCGAGATCAGATTCAACGGGAAAGGGAAAAAGATCCGGAAGCCCCGAACCATTTACTCCAGCCTTCAGCTGCAGGCGTTAAACCACCGCTTCCAGCAGACTCAGTACCTGGCGCTCCCGGAGCGAGCCGAGCTGGCGGCCTCCCTCGGCCTGACCCAGACGCAG
Seq A exon
GTAATTGCGGCGGCCCCGCACCGCCCGCTGCCCCGGGCCCGGCCCCGCACCGCCGCGCTCGGATCTGTGCGCGCCGCGCAGCGCTCCGCCGCCGGAGGAGCCGAGCGGGGCCCTTCCCTCTGCCCTTCCGCCGCCACAATAAAGTGCTGGAGTTGCCTCTCCGTTCGGATGGGAGCGATCGCGGCGCCGGCGCTGCCCGGCCGGAGGAGGAGAACAAAGCGGAGGCGCTGGGCCCGGTGCGGGGCCGAGAGCGGGGCCACGCAGCGACCTATAGGCGGAGGGGAAGCGGGAACACGTTAGGAGATACCCGGGAGCTCGATGGTTAATTGCGCCTGGATGGAGAACGCCAACGCGGTGCTCGCCGCCGGGCAAAATGTGCGGAGGTGATAAGAGATGCGGGCACCGGAGCGGCCGTGCGCGGAGCGGTGGCGCCGGGCCGGGGCCGAGCGCGGGGCGCAGCCGGGCCGGGCCCACCTCGGCCTCGGGGAGCGGGGCTGGAGGGCCCCGAGCGGTGGCTCAGCGGGAAAGCCGGGCAGATGGCTTTGGGCCGGGGAAGCGGTGGCGAGTAGAGCCCGCGCTTCGCCGTGGCCGGCGGCAGCAGCCGCTTCCAGGCGGCGGGTTTGAAACGCGCCGCAAACGTGCAGCGCGGACGCAGAGCCGGTGGCCGCGGCGATGGGCGCGGGGCGCTCTGCTTCCCCAGCGCAGGTGTACGGGCCCGAGCCCACGGTGCGGATAGACGTAGTCCTAACGGTGCGTCTGCCGAGCCCGTGAGGTCAGATTCACGCCGGGAGCCGCCTTCGTTCGATTTTTGAGACGTACGGCTTCGTAGATACATTTGCCTTCCCTTTCGGTGATTTCTATAATAACTGTGAGTTCCGCGGCCCGACCCGAGTGCTGATCCCAGCCGGGGAGGTGGGACGGGGCCCAGGGCCGTTCCCACAGCCGGCAGTTCTCTGAGAAACGAGGGTTTGCATTTCCTGATGGAGAACTGTGCCAATAAAGCCGCTGCCCGGCCCCGCTGTGCCCCCCCTCCTCCCCCCCCGAGGACCCGCGCACGCTTTGGGATGCGCGATGCGCTCACGGCGCCCTTTGTCCATTGGCTCCTCTCTCCTGGCACCAAACCAGGCGGATGCCCGGGGCTGACAACGGCCGCCAGGTGACGGAATCACCCCGAAATTCGGGACGAGGCGCCGGCAGAGCGCTCTGACTCCCGCCCCACGCGTAGCGCACCCCATCCCCGGGCCGTCCCGGCGCTGCCCCCGCACCCGTCGCCCCCGCGCTCGCACCGCAGCCCCGCACGGCCCCGGTTCCCGCAGCCCTAACGCTCGCCGCCTTTCGCTTGCAG
Seq C2 exon
GTGAAGATCTGGTTCCAGAACAAGCGCTCCAAGTTTAAGAAGCTGCTGAAGCAGGGCAGCAACCCCCACGAGAGCGACCCTCTGCCCGGCTCCGCCGCGCTGTCCCCGCGCTCCCCGGCGCTGCCGCCCGTCTGGGACGTTTCGGCGTCTGCCAAGGGGGTCAACATGCCCCCCAACAGCTACATGCCCGGCTATTCCCACTGGTACTCCTCTCCACACCAAGACACAATGCAGAGACCGCAGATGATGTGAACTGTCCGAGACGACCCACG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000023195:ENSGALT00000038006:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.367 A=NA C2=0.591
Domain overlap (PFAM):
C1:
PF0004624=Homeobox=PU(73.7=64.6)
A:
NA
C2:
PF0004624=Homeobox=PD(22.8=15.5)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCCGAACCATTTACTCCAGCC
R:
TGTGTCTTGGTGTGGAGAGGA
Band lengths:
350-1695
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]