RetrogeneDB ID: retro_ptro_981

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 14:70538969..70539389(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPTRG00000040068
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PDZD11
• Ensembl ID: ENSPTRG00000021995
• Aliases: None
• Description: None

Sequence

>retro_ptro_981
ATGGACAGCCAGATTCCTTATGATGACTACCCGGTGGTTTTCCTGCCTGCCTATGAGAATCCTCCAGGATGGATTCCTCC
TCATGAGAGGGTACCCCACCCAGACTACAACAATGAGTTGACCCAGTTTCCGCCCCAAACCATCACACTGAAGAAGCCTC
CTGGAGCTCAGTTGGGATTTAACATCTGAGGAGGAAAGGCCTCCCAGCTAGGCATCTTCATCTCCAAGGTGATTCCTGAC
TCTGATGCACATAGAGCAGGACTTCAGGAAGGGGACCAAGTTCTAGCTGTGAATGATGTGGATTTCCAAGATATTGAGCA
CAGCAAGGCTGCTGAGATCCTGAAGACAGCTCGTGAAATCAGCATGCATGTCCGCTTCTTTCCCTACAATTTTCATCGCC
AAAAAGAGAGGACTGTGCAC

Alignment

ORF - retro_ptro_981 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.57 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MDSRIPYDDYPVVFLPAYENPPAWIPPHERVHHPDYNNELTQFLPRTITLKKPPGAQLGFNIRGGKASQL
          MDS.IPYDDYPVVFLPAYENPP.WIPPHERV.HPDYNNELTQF.P.TITLKKPPGAQLGFNI.GGKASQL
Retrocopy MDSQIPYDDYPVVFLPAYENPPGWIPPHERVPHPDYNNELTQFPPQTITLKKPPGAQLGFNI*GGKASQL

Parental  GIFISKVIPDSDAHRAGLQEGDQVLAVNDVDFQDIEHSKAVEILKTAREISMRVRFFPYNYHRQKERTVH
          GIFISKVIPDSDAHRAGLQEGDQVLAVNDVDFQDIEHSKA.EILKTAREISM.VRFFPYN.HRQKERTVH
Retrocopy GIFISKVIPDSDAHRAGLQEGDQVLAVNDVDFQDIEHSKAAEILKTAREISMHVRFFPYNFHRQKERTVH

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	0.02 RPM	19.25 RPM
SRP007412_cerebellum	0.11 RPM	12.48 RPM
SRP007412_heart	0.06 RPM	12.24 RPM
SRP007412_kidney	0.03 RPM	21.47 RPM
SRP007412_liver	0.00 RPM	8.81 RPM
SRP007412_testis	0.11 RPM	2.74 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_981 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_981 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_981 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 24 parental genes, and 31 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009203	1 retrocopy	retro_amel_158,
Bos taurus	ENSBTAG00000012860	1 retrocopy	retro_btau_594,
Canis familiaris	ENSCAFG00000028800	1 retrocopy	retro_cfam_1549,
Callithrix jacchus	ENSCJAG00000012432	1 retrocopy	retro_cjac_138,
Cavia porcellus	ENSCPOG00000000210	1 retrocopy	retro_cpor_143,
Equus caballus	ENSECAG00000010771	1 retrocopy	retro_ecab_940,
Echinops telfairi	ENSETEG00000008626	3 retrocopies	retro_etel_1026, retro_etel_1863, retro_etel_921,
Felis catus	ENSFCAG00000008633	3 retrocopies	retro_fcat_1356, retro_fcat_1410, retro_fcat_263,
Homo sapiens	ENSG00000120509	1 retrocopy	retro_hsap_1439,
Gorilla gorilla	ENSGGOG00000006626	1 retrocopy	retro_ggor_1108,
Macropus eugenii	ENSMEUG00000012040	1 retrocopy	retro_meug_1858,
Macaca mulatta	ENSMMUG00000013938	1 retrocopy	retro_mmul_2265,
Mustela putorius furo	ENSMPUG00000004220	1 retrocopy	retro_mputfur_823,
Nomascus leucogenys	ENSNLEG00000000863	1 retrocopy	retro_nleu_1414,
Oryctolagus cuniculus	ENSOCUG00000017101	2 retrocopies	retro_ocun_1208, retro_ocun_1945,
Otolemur garnettii	ENSOGAG00000016423	1 retrocopy	retro_ogar_2975,
Ochotona princeps	ENSOPRG00000001811	1 retrocopy	retro_opri_374,
Pongo abelii	ENSPPYG00000020929	1 retrocopy	retro_pabe_1193,
Pan troglodytes	ENSPTRG00000021995	1 retrocopy	retro_ptro_981 ,
Rattus norvegicus	ENSRNOG00000002838	1 retrocopy	retro_rnor_615,
Sarcophilus harrisii	ENSSHAG00000005380	1 retrocopy	retro_shar_149,
Ictidomys tridecemlineatus	ENSSTOG00000027107	2 retrocopies	retro_itri_1264, retro_itri_1702,
Tupaia belangeri	ENSTBEG00000002767	2 retrocopies	retro_tbel_3155, retro_tbel_3203,
Tursiops truncatus	ENSTTRG00000007864	1 retrocopy	retro_ttru_953,