GgaINT0005585 @ galGal3
Intron Retention
Gene
ENSGALG00000005824 | SUSD2
Description
NA
Coordinates
chr15:8084641-8086568:-
Coord C1 exon
chr15:8086470-8086568
Coord A exon
chr15:8084843-8086469
Coord C2 exon
chr15:8084641-8084842
Length
1627 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGT
5' ss Score
10.67
3' ss Seq
TTGATGTGTTCTCTAACAAGGAG
3' ss Score
6.48
Exon sequences
Seq C1 exon
CAGTCAGCTGCCCTGAATCACCCGAACAAAACATGGAGTGTGTTGGTGCAGGTGTTCCTTTATTCATCCTCTTCTCCCTCGCTGCCCTTTGGAATACAG
Seq A exon
GTGAGTGCCCTTCATTTGTTTTTCTGCTTTCCTTCCAACACAATCAGGTGTTCTAGGAGAGAATTAAGGATCCACATCCACATATTATCTCAGGATGAAGGATGGAGGTCAGCAAAAAGAGGCAGAAATAGTGGTATTTTACTGCCTTTTCATTCTCTTGCTCTCTCCACCCTACAAAAAACAAACAGCCCCCTTTTCACCTTCACCTCCCCCAGTACACAAAAGAAAACCCAGTGACATTTTCTTCTCCTTTTGGCAGAAAGTGTCACACCTGAAGCTATGACCGTAACCCTTTCTTCCTCTCCTAGTCTTACTCACATGTTGCCGATGACCTTTGGGAAGTGTGTCAGTCTGCTGAATTATGGAATGCAGTTGATTTCTCCTCCCTGATCTGCTACTGCCAGCTCTTCTGTGCTCCCACATGCAGGAAATTCCTCCTGCCTCAGTCCCACACATGTGGTTACTGCTGTTGTGGATACAACCAGTACTGAAGATAAGCCTCTGCTCCAAAGAGGCAAATACAGATACTGTACTGACAGTGTTAGCTCAGCAAGCCACACAGTCTTACACAGCCTGTAACTGCGTTAGTAACCCTCCCCTAATTATATGTTTATCAATGGCCCCAGTTTTGTTGCATTCATGGCCAAATTTAGAATTTCTGATACTCAGTGAGGTCATCTCAACTTTATGTGAAGTTATTGACATAGGTAACAAAGTGTTGCTCTTACAAGACTCAGCTATCAGAAGATTCCACTCCACTGTGTTCCATATTAGCAGTGCAGCTTGTCCGTCTCACTCAAATCCCTCTTCACTCTGAAATCCAGCCATTACTCTGTCAACTTTTTACTGCTTTATTTGTTGTATTCAGCAGTTTTTCATGTCCAATAATAACTCATGGTCTACTCAGTTAGCTCTCAGCCAAGGCCTGGGCATCTGTCCACCTACCTATTTATATTAACAGCTATGTTGTTAAGGTTAAATTCAAATAAAATGCATGGCAGGAAGAAATCTCAGCTTTCTGTAACCTCACGTTGGATCACACCTTGTCACTAATGTTAGTTTCTCATTTATCCAAGAGCATTGGCCTGTTATCATAGATTCCTGTTATCGTTGATAAGGAAGAAGTGTTTACACTGAGGGCAGTGAGGCACTGGCACAGGGTGCACAGAGAGGTGGTGGTGCCCCATCCCTGCAGACACACACGGTCAGGGGATGGGGCTGTGGGTGTCCCTGTGCACTGCAGGCAGTGCGAACAGATGGCCTTTGGGGGTCCCTTCTGACTCCAACCATTCTATGGCTCTGTGATGATTCTATGATACTCCTAGGAATAACTATGACTAGTGACACTACTTGGGTGACAGGGGGCAGGCTGCTCTTGAGATTTACCTTTTTATTAGATATAAAAACACCCACAGAATTGCTGAAATTACATATGAGTGAATTTTTCTAAACAAAACAGAGTAACATTAATGCACAGGTGATTGCTGCCTTCATTTGACATAAACAGCCAACCTCACTTACTTATGGCAATTCTTTAGACGTTGTATTGCTGCTTCAGAGAAGGGCTCAATGACATTCCTGACAACGTGTTGTTTGTTTGTTTTTCTTTGATGTGTTCTCTAACAAG
Seq C2 exon
GAGCTCAAGACTCCTGCTCAAGCCAGTGTGGGAAGCTGCTTGGTGCCTGTTCATGCCAGGAGATCTGCCAGTCCTTGGGGACCTGCTGTCCTGATTACAATGAATTTTGTCTCCACATTTCTCCATACTCAGGATCTCTGATGGGAGGCAAAGATTTTTTGATAGAGAATACAGCATTTAATACTTCTGTGTTAATGTGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000005824:ENSGALT00000009356:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0103312=Somatomedin_B=WD(100=60.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Rat
(rn6)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CAGCTGCCCTGAATCACCC
R:
AAAAATCTTTGCCTCCCATCAGAGA
Band lengths:
254-1881
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]