RetrogeneDB ID: retro_ptro_1616

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 2A:77262931..77263536(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PNP
• Ensembl ID: ENSPTRG00000006095
• Aliases: PNP, NP
• Description: Purine nucleoside phosphorylase [Source:UniProtKB/TrEMBL;Acc:H2Q7W4]

Sequence

>retro_ptro_1616
ATGGAGAATGGATACATATATGAAGATTATCAGAGCACTGAGAATGGCTTCTGTTTCACACCAAGCACTGAACACAAGTG
ACAGTGATCTGTGGGTCTGAATTAGGAGATCTGACTGACAAATTAATAGAGGCCCAAATCTTTAACAACAGTGAGATGCT
CACCTTTTTCCAAAGTACAGTGCCAGGTCATGCTGGTTGACTGGTGTTTGGGTTCCTGAATGGCACAGCGTGTGTGATGA
TGCAAGGAGGGTTCTACTTGTATGATGGGTACCTGCTCTGGAACATGACATTTTTGCATGAGGTTTTCCAGCTTCTGGGT
GGGAACATCTTGGTGGCCACCGATGCAGCTGGAGGGCTCAACCCCAAGTCTGAGGTTGGAAGGATCATGCTTCTCTTTGA
TCACATCAAGCTACTTGGTTTCTGTGATCAGAACTCTCCCAAAGGGTCCAATGATGAAAGGTTTGGAGTTCATTTTCCTG
CCATGTCTGATGCCTACAACTGGACAATGAAGCAAAAGGCGCTCAATTCTTAGAACCAAATGGGGAAGCAGCAAGAGGTA
CAGAAAGACACCTATGTGATGGCAGTAAACTGCAACTTTGAGACT

Alignment

ORF - retro_ptro_1616 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.02 %
• Parental protein coverage: 69.9 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MENGYTYEDYKNTA-EWLLSHTKHRPQVAIICGSGLGGLTDKLTQAQIFDYSEIPNFPRSTVPGHAGRLV
          MENGY.YEDY..T..EWLL.HTKH..QV..ICGS.LG.LTDKL..AQIF..SE...F..STVPGHAG.LV
Retrocopy MENGYIYEDYQSTE<EWLLFHTKH*TQVTVICGSELGDLTDKLIEAQIFNNSEMLTFFQSTVPGHAG*LV

Parental  FGFLNGRACVMMQGRFHMYEGYPLWKVTFPVRVFHLLGVDTLVVTNAAGGLNPKFEVGDIMLIRDHINLP
          FGFLNG.ACVMMQG.F..Y.GY.LW..TF...VF.LLG...LV.T.AAGGLNPK.EVG.IML..DHI.L.
Retrocopy FGFLNGTACVMMQGGFYLYDGYLLWNMTFLHEVFQLLGGNILVATDAAGGLNPKSEVGRIMLLFDHIKLL

Parental  GFSGQNPLRGPNDERFGDRFPAMSDAYDRTMRQRALSTWKQMGEQRELQEGTYVMVAGPSFET
          GF..QN...G.NDERFG..FPAMSDAY..TM.Q.AL....QMG.Q.E.Q..TYVM.....FET
Retrocopy GFCDQNSPKGSNDERFGVHFPAMSDAYNWTMKQKALNS*NQMGKQQEVQKDTYVMAVNCNFET

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	12.48 RPM
SRP007412_cerebellum	0.00 RPM	11.04 RPM
SRP007412_heart	0.00 RPM	4.69 RPM
SRP007412_kidney	0.00 RPM	175.61 RPM
SRP007412_liver	0.00 RPM	62.29 RPM
SRP007412_testis	0.00 RPM	9.06 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1616 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1616 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1616 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2282
Gorilla gorilla	retro_ggor_1695

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Parental genes homology:

Parental genes homology involve 20 parental genes, and 33 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000005373	1 retrocopy	retro_amel_1666,
Bos taurus	ENSBTAG00000012317	1 retrocopy	retro_btau_1463,
Choloepus hoffmanni	ENSCHOG00000009274	5 retrocopies	retro_chof_1328, retro_chof_1595, retro_chof_1827, retro_chof_1933, retro_chof_348,
Callithrix jacchus	ENSCJAG00000009676	2 retrocopies	retro_cjac_1195, retro_cjac_1511,
Dasypus novemcinctus	ENSDNOG00000011630	1 retrocopy	retro_dnov_322,
Erinaceus europaeus	ENSEEUG00000002411	1 retrocopy	retro_eeur_541,
Felis catus	ENSFCAG00000006934	1 retrocopy	retro_fcat_1368,
Homo sapiens	ENSG00000198805	1 retrocopy	retro_hsap_2282,
Gorilla gorilla	ENSGGOG00000002126	1 retrocopy	retro_ggor_1695,
Macropus eugenii	ENSMEUG00000014512	3 retrocopies	retro_meug_1282, retro_meug_1560, retro_meug_211,
Macaca mulatta	ENSMMUG00000019126	1 retrocopy	retro_mmul_287,
Mustela putorius furo	ENSMPUG00000018119	2 retrocopies	retro_mputfur_420, retro_mputfur_822,
Nomascus leucogenys	ENSNLEG00000010969	1 retrocopy	retro_nleu_1964,
Otolemur garnettii	ENSOGAG00000013344	4 retrocopies	retro_ogar_1631, retro_ogar_2141, retro_ogar_3083, retro_ogar_594,
Pongo abelii	ENSPPYG00000005567	1 retrocopy	retro_pabe_1938,
Pan troglodytes	ENSPTRG00000006095	1 retrocopy	retro_ptro_1616 ,
Pteropus vampyrus	ENSPVAG00000010734	1 retrocopy	retro_pvam_1302,
Rattus norvegicus	ENSRNOG00000009982	1 retrocopy	retro_rnor_891,
Tupaia belangeri	ENSTBEG00000016378	1 retrocopy	retro_tbel_4632,
Tarsius syrichta	ENSTSYG00000000748	3 retrocopies	retro_tsyr_2057, retro_tsyr_2127, retro_tsyr_235,