RetrogeneDB ID: retro_pabe_2878

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 6:71138367..71139104(+)
• Located in intron of: ENSPPYG00000016763

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMEM192
• Ensembl ID: ENSPPYG00000015175
• Aliases: None
• Description: transmembrane protein 192 [Source:RefSeq peptide;Acc:NP_001125290]

Sequence

>retro_pabe_2878
GGTTTCTTGGGTATCACTCAAAGTATTGAAGATGACCCACCTCTGGATACCCAGCTTCTCTTAACATTACTCACTAGAAG
CTCATTTTAGACCCTGATTCTATCTTTTTCCTACAGTCATCATAGCAAATCTTCTTTTGTTTATTTATGTTGTGTTATTT
TTAGCATTTTTAACAGATGTGGTTTGTTCTTACCCTAATCTAAATGAAGACAGGTGCCCAGGAAACTATACCAACCCTCT
TGAAGTTCAAATGGTTGTAATCCTTTGGAAAGTTATTTTGTGGTGGATTTTCCGTTTACATCTTGAATGCTACATCCAGT
ATCACCACAGCAAAGTCAGAAATCGAGGCTATAACTTGATCTACTGACGGATAAGGCATCTCAAGAGATTTGCGTTAATG
ATACACTCCACTGGCAACACAGTAATTCTCTTCATACTGTGTTGCAGCATTCCTTCCTGGAACCTAGCAGATCAGATTAT
ATCTTGATCTCCTTCTGGCCATCCTGGCCCTGGAGCTGATCTGTTTTCTGATGTGTCTGCTCATTTACACAGTGAAAATC
TGGAAGTTTAATAAAGCTAAGCCATATCCTGATGTACTTGAAGAAGGAAAAATCTATACTTAACCTAGCAGTATTACCTC
AGAGACTGGATTCAGGACTATTTGAAACCTAGAAGAAGTTGTTGAAAAGCAAGGAGACATAATAGTATATATGAAGCGAC
ACAATGAAGTGTTGAGT

Alignment

ORF - retro_pabe_2878 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.4 %
• Parental protein coverage: 90.04 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  GSLDITQSIEDDPLLDAQLLP-HHSLQAHFRPRFHPLPTVIIVNLLWFIHLVFVILAFLTGVLCSYPNPN
          G.L.ITQSIEDDP.LD.QLL..H.SL.AHFRP.F...PTVII.NLL.FI..V...LAFLT.V.CSYPN.N
Retrocopy GFLGITQSIEDDPPLDTQLLL>HYSLEAHFRP*FYLFPTVIIANLLLFIYVV-LFLAFLTDVVCSYPNLN

Parental  EDKCPGNYTNPLKVQTVIILGKVILW-ILHLLLECYIQYHHSKIRNRGYNLIYRSTRHLKRLALMIQSSG
          ED.CPGNYTNPL.VQ.V.IL.KVILW.I..L.LECYIQYHHSK.RNRGYNLIY...RHLKR.ALMI.S.G
Retrocopy EDRCPGNYTNPLEVQMVVILWKVILWWIFRLHLECYIQYHHSKVRNRGYNLIY*RIRHLKRFALMIHSTG

Parental  NTVLLLILC-MQHSFPEPGR-LYLDLILAILALEL--ICSLICLLIYTVKIRRFNKAKPEPDILEEEKIY
          NTV.L.ILC..QHSF.EP.R...L.L.L....L.L..IC.L.CLLIYTVKI..FNKAKP.PD.LEE.KIY
Retrocopy NTVILFILC<LQHSFLEPSR<IRLYLDLLLAILALELICFLMCLLIYTVKIWKFNKAKPYPDVLEEGKIY

Parental  AYPSNITSETGFRTISSLEEIVEKQGDTIEYLKRHNALLS
          ..PS.ITSETGFRTI..LEE.VEKQGD.I.Y.KRHN..LS
Retrocopy T*PSSITSETGFRTI*NLEEVVEKQGDIIVYMKRHNEVLS

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	0.06 RPM	21.23 RPM
SRP007412_cerebellum	0.24 RPM	20.06 RPM
SRP007412_heart	0.00 RPM	10.36 RPM
SRP007412_kidney	0.07 RPM	112.00 RPM
SRP007412_liver	0.03 RPM	29.81 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2878 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2878 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2878 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3483
Pan troglodytes	retro_ptro_2357
Macaca mulatta	retro_mmul_1769

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000009198	1 retrocopy	retro_cjac_2346,
Homo sapiens	ENSG00000170088	1 retrocopy	retro_hsap_3483,
Macaca mulatta	ENSMMUG00000021912	1 retrocopy	retro_mmul_1769,
Nomascus leucogenys	ENSNLEG00000006475	1 retrocopy	retro_nleu_2203,
Pongo abelii	ENSPPYG00000015175	1 retrocopy	retro_pabe_2878 ,
Pan troglodytes	ENSPTRG00000016571	1 retrocopy	retro_ptro_2357,
Ictidomys tridecemlineatus	ENSSTOG00000000402	1 retrocopy	retro_itri_1414,