RetrogeneDB ID: retro_pabe_1011

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 13:76232180..76232929(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: RIOK3
• Ensembl ID: ENSPPYG00000009062
• Aliases: None
• Description: RIO kinase 3 [Source:HGNC Symbol;Acc:11451]

Sequence

>retro_pabe_1011
AATCTGGCAGAAGTGACATTGCCTAAGCCCAAGCCAGCAGTGGCCTGGGGACCCAGTAAGTGTCCATGGGCTACCCTTCA
AATGACAATATCTTGTTCTTTGGCTGATATAATGAGTGAACGGTCAAAGAACTGCAGTTAGGGGAAGAAACTGTCACTTT
TCCTCAAGTAGCTGTTGCTAAAAGACCATTTATTATTGAAGAAAACATTGATACTTCCAGCGACCTAATGTTGGCTCAGA
TATTATAGATGGAATTTGGCAAAGAATATGATGCACAATTAGACATAAAGAAAAGAAAATTCAATAGAGATAGAAAAGTT
TCCATGTCCTTTGAAAACTATTGAAAAGTGCATCCTGATGAAGACAGTGATAGCTCCGAAGATGAGGCTGACTGGCAGGA
TACTCATGATGATCTCTACTGACTAGCAAAACCAGTTCCCACTCCCAAAAAGGGTTTTATTGGAAAAGGAAAAGGCATTA
CCACCAAACGTCATGAAGTAGTATGTGGGAGAAAGAATCCAGCAAGAATGGAAAATTTTGCACCTGCATTTCAGGTAGAA
GACAGAATGGATCTAAAACTACCAAACAAAGTTTTTGATGCTTCAAAAACGCCATGCCTACTCAGAAGAACAGCAAAGTT
CCTGCCTCCACAAGAAAAAGGAGCATTCTACGGAAGAAAATGCCATTGATCCTGAGACATGTTTTCTTATGTAAAAATGG
TCAACTCTGGAATGTTTGAGACAATCACT

Alignment

ORF - retro_pabe_1011 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.36 %
• Parental protein coverage: 51.84 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  DLVGVASPEPGPAAAWGPSKCPWAIPQNTISCSLADVMSEQLAKELQLEEEAAIF-PEVAVAEGPFITGE
          .L..V..P.P.PA.AWGPSKCPWA..Q.TISCSLAD.MSE...K..........F.P.VAVA..PFI..E
Retrocopy NLAEVTLPKPKPAVAWGPSKCPWATLQMTISCSLADIMSER-SKNCS*GKKLSLF<PQVAVAKRPFIIEE

Parental  NIDTSSDLMLAQMLQMDYDREYDAQLRREEKKFNGDSKVSISFENYRKVHPYEDSDSSEDEVDWQDTRDD
          NIDTSSDLMLAQ.L.M....EYDAQL.....KFN.D.KVS.SFENY.KVHP.EDSDSSEDE.DWQDT.DD
Retrocopy NIDTSSDLMLAQIL*MEFGKEYDAQLDIKKRKFNRDRKVSMSFENY*KVHPDEDSDSSEDEADWQDTHDD

Parental  PYRPAKPVPTPKKGFIGKGKDITTKHDEVVCGRKNTARMENFAPEFQVGDGIGMDLKLSNHVFNA-LKQH
          .Y..AKPVPTPKKGFIGKGK.ITTK..EVVCGRKN.ARMENFAP.FQV.D...MDLKL.N.VF.A..K.H
Retrocopy LY*LAKPVPTPKKGFIGKGKGITTKRHEVVCGRKNPARMENFAPAFQVED--RMDLKLPNKVFDA>QKRH

Parental  AYSEERRSARLHEKKEHSTAEKAVDPKTRLLM-YKMVNSGMLETIT
          AYSEE..S..LH.KKEHST.E.A.DP.T..LM..KMVNSGM.ETIT
Retrocopy AYSEEQQSSCLHKKKEHSTEENAIDPETCFLM<VKMVNSGMFETIT

Legend:

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

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain_prefrontal_cortex	0.00 RPM	21.45 RPM
SRP007412_cerebellum	0.00 RPM	31.13 RPM
SRP007412_heart	0.00 RPM	23.18 RPM
SRP007412_kidney	0.00 RPM	42.26 RPM
SRP007412_liver	0.00 RPM	49.33 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1011 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1011 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1011 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Macaca mulatta	retro_mmul_1291

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000008343	1 retrocopy	retro_chof_1788,
Callithrix jacchus	ENSCJAG00000020556	1 retrocopy	retro_cjac_2617,
Echinops telfairi	ENSETEG00000003689	1 retrocopy	retro_etel_2181,
Macropus eugenii	ENSMEUG00000006292	1 retrocopy	retro_meug_1278,
Macaca mulatta	ENSMMUG00000021478	1 retrocopy	retro_mmul_1291,
Ochotona princeps	ENSOPRG00000004803	2 retrocopies	retro_opri_1034, retro_opri_946,
Pongo abelii	ENSPPYG00000009062	1 retrocopy	retro_pabe_1011 ,