GgaINT0046056 @ galGal3
Intron Retention
Gene
ENSGALG00000009287 | ATF2_CHICK
Description
NA
Coordinates
chr7:17803223-17804955:+
Coord C1 exon
chr7:17803223-17803341
Coord A exon
chr7:17803342-17804826
Coord C2 exon
chr7:17804827-17804955
Length
1485 bp
Sequences
Splice sites
5' ss Seq
AAAGTAAGT
5' ss Score
9.72
3' ss Seq
TTTTACACGATTACTTTTAGATG
3' ss Score
5.31
Exon sequences
Seq C1 exon
ATCAGACACCAACACCAACTCGATTCTTGAAGAACTGTGAAGAAGTGGGCTTATTCAATGAATTAGCAAGTCCTTTTGAAAATGAGTTTAAAAAGGCTTCTGAAGATGATATTAAGAAA
Seq A exon
GTAAGTTTATAGATGTTTTCTTCTCGGTCCTGCTGTTCAATTGAGAAAAGCAAACTTGAATTTATATCTTGTCTTTTGAGCTGTACCATTAGTCATTGGCCAGCTGTCAGCATATAGTCTTCTATGGAGAGAGTGCTAACTTAAGATTACTTTTCTGAAGGGTAGTTTGCCTCAGTTGACGTAAGTAGAATGGACACTGGAATACACTGACTTTTTCTGAACTCTGATTTTACTTTTGACTGATTATATGCTTTAACTTCCACAGGCAGTGACATTAAAAATAAATCAAGTCTCTTTTATACATATGGATATAGATTTTAAAGGATCAGTGTCTGGTTATTCTGTTTCAGTAAAGATTTTAGTAGACACTTCTGAATAGGACTCATTTCTGTGTGTTCTTGAGAAAACTCACCTTTGCTTTGTGCTCACAATTGTGCCAAATCTTTTTTAATTGGTGCATGGTAACTATTTATAAAATCATACATAAGATAATACAAATTCTGGTCTTGATTCTGACTTGATTTTCTGTGTAATTCACCACTTTCTTGGAGGAGGTTATAGTTATCGCAAAGTATTGAGAACACTTCAACAACTTTTAGAATTGATATTAGTTTTCCAAACTGACGAGAAGAAATGTGGTTGTGCTGGATATCTTTGGTAACATAAATAAACAAGAATGGCAAGGGGTAGAAAAAAATTACCCTAATAGCATTCTTCCTAAGGTGTTTTATTTTTTTAAACTGTTTTGCTTTTTCTGTAGTGTTTCACATTCAGCTGTCATGTGAAAAAAGGTTCCACCTTCAGCATTTTTCCCTTCTCTTTAATAAGCTTCTTCAGTAGAAAAACTAGAAATGAAATAGAAAAAAAGCACTTAGAAGATTATAAATGGAAGGTGAGCTCTGGGGGAACTCTCTTTCAAAGGTATTTGGACAACAGGTTAGACAGTTGTACAGGCTTTGTAGTCAATACATTGCTTTAAGTATCTTTATAACTGAATTTCTTTGCAGCATTTCATATGTCCTATCTGGACTATCTGTGTAGCAGTATAAAACTTTTTCAATAATTATTAGCTGCACTGAGTTTGAAATGACAAGTTCATTATAGCTTTTGTTCTACTTTGAAAATGAAGTTAAGATTTTACACTTGTGCGGCGTGTCATGTAATTTGTAGAAGGATGGTGTCCTAAGTGTAGCCTTTAAAAGTAGTTCTGTCCTTCCTCAATTACAACTTTCCTGTGAATCTTGAGAAAGAAATTAAGAAAAAAATTTAACCTGGCAACGGGAATATAAACACAAAGTCTTACTGAAAAATACTGATGCTGGAAGAAGTCGGCTTGGCTGCTAACACATCTGCATTAAGGTCTTCAAGATATCAGCACCTCACTATTATTATAATAAGGCTAATATTTCTCCTTAGTTACTTATACTTTCTTACATATTTTATTTCTTTAGTGATTGATATTTTTTTTTACACGATTACTTTTAG
Seq C2 exon
ATGCCTCTAGATCTGTCTCCTCTTGCAACACCAATTATAAGAAACAAAATTGAAGAACCTTCTGTTGTAGAGACGACTCATCAAGATAGTCCTTTACCTCATCCAGAGTCTACTACCAATGATGAAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000009287:ENSGALT00000015107:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.344 A=NA C2=0.814
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TCAGACACCAACACCAACTCG
R:
TTTTCATCATTGGTAGTAGACTCTGG
Band lengths:
246-1731
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]