GgaINT0124315 @ galGal3
Intron Retention
Gene
ENSGALG00000003187 | SURF1_CHICK
Description
NA
Coordinates
chr17:7535553-7536361:-
Coord C1 exon
chr17:7536280-7536361
Coord A exon
chr17:7535990-7536279
Coord C2 exon
chr17:7535553-7535989
Length
290 bp
Sequences
Splice sites
5' ss Seq
CTGGTAAGC
5' ss Score
8.69
3' ss Seq
TTTTTTACTTCTTGTCACAGGTA
3' ss Score
9.74
Exon sequences
Seq C1 exon
GAAGCACAGTCCCAGGAGGGCCCATTGGAGGCCAAACAAGAGTGAGCCTGAGAAACGAGCACATGCAGTACATCGTTACCTG
Seq A exon
GTAAGCTACCCAGCCAACGTCTGACCTTTGTTTTCTGTACATGAAGCCTTAAAATGCTTTCTGTTGAATCCACTGAAAGCAAGGAAATAATTTTTCCCCAGCATTCTTGCTCCTGCATCAGGGAGACTGATGAGATCTTTAGCTGCAAACTGTTTGGCCCTAAGTAGTATTTCCCAGATAGTTTGAAATAACTTTATTACTGAACTGCAGCTGATTTAGGGAACATTAATCAATCTTGGAAATACCATGTAAATGTTTTGCATCATTTACTTTTTTACTTCTTGTCACAG
Seq C2 exon
GTATGGCTTGTGTGCTGCAACTTCCTTCTTGTGGTACAGAAAATTTATACAGAAAATACCTCTGTGAGGGGAAAGATTAATTTCTGCTCTCCTGTGCTACAGTCAAGACTGCAGCCTGATCAATCAAGAACTTAATCTCAGGGCACGGGACTTACCAGCTGATGCTGGCAGCAGTTTGGAAGCACTGAACTTCAGAATTAGTGGTGGGTATTGACATGCTTGCTTACATCTGCTTTCTGGACCTGAAGGATGCATTTTTCTATTGTAGTTGGACAGTTTGGTCACAAGCTACAAAGCCTCTTCTTCTCCACTGCTATATTTTCTATATTCAATCTAAGCAAATGAGGCCAAGGGATTTTTCACGTAGCAGTCATTCCTAAAGCTAAGATGGGGACACTGCAGTGCCATCAGGATAAATAAAACAGGCCTGTTTAGTA
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000003187:ENSGALT00000005056:8
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.071 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0210410=SURF1=FE(12.3=100)
A:
NA
C2:
PF0210410=SURF1=PD(2.7=26.1)
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:
GAGTGAGCCTGAGAAACGAGC
R:
TCCTTCAGGTCCAGAAAGCAGA
Band lengths:
293-583
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]