GgaINT0124313 @ galGal3
Intron Retention
Gene
ENSGALG00000003187 | SURF1_CHICK
Description
NA
Coordinates
chr17:7536640-7537181:-
Coord C1 exon
chr17:7537109-7537181
Coord A exon
chr17:7536803-7537108
Coord C2 exon
chr17:7536640-7536802
Length
306 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGA
5' ss Score
10.77
3' ss Seq
TTTTCTCCTCTGCGTTTTAGATT
3' ss Score
10.85
Exon sequences
Seq C1 exon
GGTCACCATTTTAGTCAACCGAGGATTTGTGCCCAAAAAGAAACTGAAACCAGAGACCAGGCTGAAGGGACAG
Seq A exon
GTAAGAGGGACACAGGGAAATCTTGCACGTTACTTTCTAACCTCTTACCCAGAGACACTTTTGACAAACTAAGAAAGGCAGCAGCCACGTTCAGCTTCATGAGTCGCTGCACTTCTGAAAGGTGCCTTTTCTTGATGCCTTTGATAAAGTAAATAAAGCATCTGCCTTTTTCCCTGCTGTGTTACAGCACTGTATAGCACAACCTGCTGATTTACTTATAACCAGACCTGCAGGTGATGTACTACCAGGTCCTGGTACGCTACAAATGAATCTTGAGAGATTCCTTTTTTCTCCTCTGCGTTTTAG
Seq C2 exon
ATTGAAGAAGAAATCGATCTGACGGGGGTAGTGAGGCTGTCAGAAAAACGGAAACCTTTCGTGCCTGAAAATAACATTGAAAAAAACCGCTGGCACTATCGTGACCTGGAGGCCATGGCGAAGGTGACCGGTGCTGAGCCCATCTTCATTGATGCAGATTTCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000003187:ENSGALT00000005056:6
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=0.000
Domain overlap (PFAM):
C1:
PF0210410=SURF1=FE(11.0=100)
A:
NA
C2:
PF0210410=SURF1=FE(24.7=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:
GTCACCATTTTAGTCAACCGAGGA
R:
TCTGCATCAATGAAGATGGGCT
Band lengths:
230-536
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]