RetrogeneDB ID:

retro_pabe_1884

Retrocopy
location
Organism:Orangutan (Pongo abelii)
Coordinates:22:34352333..34352667(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:FUNDC2
Ensembl ID:ENSPPYG00000020897
Aliases:None
Description:FUN14 domain containing 2 [Source:HGNC Symbol;Acc:24925]


Retrocopy-Parental alignment summary:






>retro_pabe_1884
TCTGTCCCACGTGCCGGATGCCAATCGGTGGTGATGACTCTGTGTGCCACTCCGCGTCCTACAGCGCGGATCCTCTGCGT
GTGTCCTCGCGAGACAAGCTCGATGAAATGGCTGAGTCCAGTCAAGCAAACTTTGAGGGAAATTTTGAGTCACTGGACCT
TGTGGAATTTGCTAAGAAACAGCCATGGTGGTGTAAGCTGTTCGGGCAGGAATCTGGACCTTCGCCGAAAAGTAAAGGGT
GGCAACCCAGCCGTTCATTGGGGGTGTCACTGAATGGTGCACGGGTTTCGTATCCCAGAAGGTTGGAAAGTTGGCTGTAA
CAGTTGTGGGAGGT

ORF - retro_pabe_1884 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 78.95 %
Parental protein coverage: 58.73 %
Number of stop codons detected: 1
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalSAPRAGSQ-VVATTAR-HSAAYRADPLRVSSRDKLTEMAASSQGNFEGNFESLDLAEFAKKQPWWRKLFG
S.PRAG.Q.VV.T....HSA.Y.ADPLRVSSRDKL.EMA.SSQ.NFEGNFESLDL.EFAKKQPWW.KLFG
RetrocopySVPRAGCQSVVMTLCA<HSASYSADPLRVSSRDKLDEMAESSQANFEGNFESLDLVEFAKKQPWWCKLFG
ParentalQESGPS-AEKYSVATQLFIGGVTGWCTGFIFQKVGKLAATAVGG
QESGPS.AEK..VATQ.FIGGVT.WCTGF..QKVGKLA.T.VGG
RetrocopyQESGPS<AEK*RVATQPFIGGVTEWCTGFVSQKVGKLAVTVVGG

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)

Expression validation based on RNA-Seq data:
Library Retrocopy expression Parental gene expression
SRP007412_brain_prefrontal_cortex 0 .00 RPM 17 .47 RPM
SRP007412_cerebellum 0 .00 RPM 26 .75 RPM
SRP007412_heart 0 .00 RPM 34 .50 RPM
SRP007412_kidney 0 .07 RPM 22 .31 RPM
SRP007412_liver 0 .03 RPM 22 .28 RPM
Pongo abelii was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_pabe_1884 retrocopy.
Pongo abelii was not studied using FANTOM5 data.
retro_pabe_1884 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_pabe_1884 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Callithrix jacchus retro_cjac_651

Parental genes homology:
Parental genes homology involve 20 parental genes, and 51 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000169771 retrocopy
Choloepus hoffmanni ENSCHOG0000000430611 retrocopies
Callithrix jacchus ENSCJAG000000042873 retrocopies
Dipodomys ordii ENSDORG000000131561 retrocopy
Echinops telfairi ENSETEG000000138172 retrocopies
Homo sapiens ENSG000001657753 retrocopies
Loxodonta africana ENSLAFG000000152891 retrocopy
Myotis lucifugus ENSMLUG000000077761 retrocopy
Macaca mulatta ENSMMUG000000102481 retrocopy
Monodelphis domestica ENSMODG000000164841 retrocopy
Mus musculus ENSMUSG000000311982 retrocopies
Nomascus leucogenys ENSNLEG000000144435 retrocopies
Otolemur garnettii ENSOGAG000000334613 retrocopies
Pongo abelii ENSPPYG000000202682 retrocopies
Pongo abelii ENSPPYG00000020897 4 retrocopies
Pan troglodytes ENSPTRG000000418524 retrocopies
Pteropus vampyrus ENSPVAG000000135521 retrocopy
Rattus norvegicus ENSRNOG000000240662 retrocopies
Sus scrofa ENSSSCG000000128171 retrocopy
Ictidomys tridecemlineatus ENSSTOG000000078012 retrocopies



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