GgaINT0067172 @ galGal3
Intron Retention
Gene
ENSGALG00000010697 | SEMA4D
Description
NA
Coordinates
chrZ:42877803-42879576:-
Coord C1 exon
chrZ:42879553-42879576
Coord A exon
chrZ:42878217-42879552
Coord C2 exon
chrZ:42877803-42878216
Length
1336 bp
Sequences
Splice sites
5' ss Seq
GCAGTTGGT
5' ss Score
-3.76
3' ss Seq
CTGATACTTTGCATATTTATTTT
3' ss Score
-2.69
Exon sequences
Seq C1 exon
TGGCAGCCTTTGACTATAGTTGCA
Seq A exon
GTTGGTTTTCTATCAGTCTTACCTTACCTTACCAAGATTTTTTTTTAACTTAATGTTTTCAAACATATACTTCTTATCCATTAATTGCCTACATAAAGAATGTCAGCTTGTGCTATTTAGATAAGATAAAATTTATCTTACGTTAGAGGATGGACTGACGTAGGAATAACATTTGAAGCTGTCATACTTGCACTATTTTTTACAGGAATTGGATTCAGAACATAGGTGGAGATGCATCTTCTTGTTCTGGTGAGTTACGTTCTGTGAAGAGCTACTTAACTTATTTAGGTGGAATAGGAAAGACTTGTGTTTGTGATTATCTAGATTTTCATTTATATTTTAATATGTATGAAGTTCTGTTTTTTTTTCATACTTGAGCATCTGTACAGCCTTCATCTTGTCTTGAAATGCTTGTATTTGTGTACATTTCAGTGAGCAGTGCACAAACTTCTGAAATGAATGGGAGTACCTCAACAGCATGTCGTGAATGAAAGTACTATTTACCAAGAGTACCTCTAGTACAGAGGTCTCTGTCTCTGATAAAATAACATTTGACATTCTACTGTGAGTCTTGATTAAGTGCTTGACTGTTGTTGCTAGATCGGATGAAATGGTTCTGAAAAATGCTGCTTTTATTATGAGAGGGGAGGGGTGCTCAATACATCATAGAGAGCAGCTGAAGTACCCTCCAGTGTACTTTAAGACAAGTAACTGCTGGTCCTTTCTTTCTTGTACATGTTGCTGCCATCAGATTATGGAGATCTTAAAGACTAGTGTTAGAGAAGATTTGTACTGCAGTAAATAGTACACTGCTTTATTCTTTTTTCATTTCTTATCTAAGCACAACGAGGGCCACCAGGAGAGTTTGACTTGTTAGTTATATCGCTCATTTATCATATTGTGTTTTGGGTGTGCAATGGGTACTGATGTTTTCAGAAGAGAGTTTAATTTGAGTACTGGTATTTGCATTTCTTAAAATTAAATTTCTTCTTGAACATTCTGTCATTACTTAAAATATACTAATTGGTTTGAAAGTAATACAAAGTTGAGCATCTTGTTTCAAATGATGACTTAGAGGCACACTCAATTTGGATCAACTAAGTCTCCCCCTACTTTTCTGGAAGTGGAAGCTGTTTTGGAGTTTGAGGTGTCTGATTTTGTAATCTGTTTTGATGTCCTGTATACATCTGTAGTTTAGTATTTCATGGAGACTTGCATGCTGTTATCTTGGTCTTGAGATAATCTTAACACCATAGTCTTTGCATTTCCATTATGACTCTTGAAACTGTGCAGATTAGATCAAACAGGAATCACTGCTGATACTTTGCATATTTAT
Seq C2 exon
TTTGGTGTTCCAGATAAAGTAAGAGAGAATTCGCTACAGCATACGTTCAAGCATGGGAGCACAGCAGAGCTCAAGTGTTCTCAGAAGTCCAATCTGGCACAGGTAGTTTGGAAGTTCAGAGATGACGTACTGAGAGTGGAGAGTCCCAAATACCGGCTACTGGAAAAGGCGCTACTCATCTTCAATTTATCAGAAGGAGACAGTGGTGTTTACCAGTGCCTGTCAGAAGAAAAAGTGAAGAATAAGAAATTCTCTCAGGTGTTGGCTAAGCATGTTTTGGAACTGAAGAAAGTCCAGCATACTACGGCAAGCCCATTGGTGGCAGCTGCATCAACAGAAGGTAATAGTGATGTACCAGAAGTGTCAGCTGTATCAACTGAGGGCTCTACTGCTCAAACCTCAACCACTCAGACT
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000010697:ENSGALT00000017396:13
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=0.116
Domain overlap (PFAM):
C1:
PF0143720=PSI=FE(14.6=100)
A:
NA
C2:
PF0143720=PSI=PD(0.1=0.0),PF138951=Ig_2=WD(100=58.7)
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Human
(hg38)
No conservation detected
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGCAGCCTTTGACTATAGTTGCA
R:
CCAATGGGCTTGCCGTAGTAT
Band lengths:
342-1678
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]