RetrogeneDB ID: retro_ptro_2351

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 6:48262531..48263014(+)
• Located in intron of: ENSPTRG00000018244

Retrocopy information

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

Parental gene information

• Parental gene symbol: DNAJC17
• Ensembl ID: ENSPTRG00000006929
• Aliases: None
• Description: None

Sequence

>retro_ptro_2351
GAGGCCCAGGCCCAGGTGAGTGAGAAGGTGGAGGAAAGCTAGATCACCAGGACACTTGAGCAGGAGATTGAACATCTTAG
TGAATAGTGTTCATGGCAGCTGGAGGAACAGCAGATGATGTTCCAGGAGCAGATGTGCCAGGAACTTGACTTGAGATTAG
AAGTCAGAAAATACTGAAGACAAAGGAACCCAAAACTAAAACTGAAATGGAAGTACAGGAAGGATGAGTCAGAAGGCAGT
TACTCCAAAGGTGTCCTCTTGTGGCTTTTGCAAAAGTATGGTGGAATTCTCAACCTGGTGCTTTTGAGTAAGAAGGCAGG
TACTGGTGTCATGGAGTTTGGGACTGTCGAGGCTGCAGAGATGGCTGTCTGGAATAAAGTTGGCCTGGGTGATAATCCTT
GAAAGATTTCCTCTTTCAAAGGAGGACTCCAGGGTGCAGTGGGCCCCAGCCACCCAGGACAGTGAAGGGACCCAGTGGTG
TCT

Alignment

ORF - retro_ptro_2351 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.15 %
• Parental protein coverage: 53.95 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QAQAQESEEEEESRSTRTLEQEIERLREEGSRQLEEQQRLIREQIRQERDQRLRGKAENTEGQGTPKLKL
          .AQAQ.SE..EES..TRTLEQEIE.L.E..S.QLEEQQ....EQ..QE.D.RL.............KLK.
Retrocopy EAQAQVSEKVEES*ITRTLEQEIEHLSE*CSWQLEEQQMMFQEQMCQELDLRLEVRKY*RQRNPKLKLK-

Parental  KWKCKKEDESKGGYSKDVLLRLLQKYGEILNLVLSSKKPGTAVVEFATVKAAELAVQNEVGLVDNPLKIS
          .WK..K.DES.G.YSK.VLL.LLQKYG.ILNLVL.SKK.GT.V.EF.TV.AAE.AV.N.VGL.DNP.KIS
Retrocopy -WKYRK-DESEGSYSKGVLLWLLQKYGGILNLVLLSKKAGTGVMEFGTVEAAEMAVWNKVGLGDNP*KIS

Parental  WLEGQPQDAVGRSHSGVSKGSVLS
          ...G..Q.AVG.SH.G.....V.S
Retrocopy SFKGGLQGAVGPSHPGQ*RDPVVS

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	8.79 RPM
SRP007412_cerebellum	0.00 RPM	14.41 RPM
SRP007412_heart	0.00 RPM	2.94 RPM
SRP007412_kidney	0.05 RPM	10.62 RPM
SRP007412_liver	0.03 RPM	12.64 RPM
SRP007412_testis	0.00 RPM	2.00 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2351 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2351 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2351 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3468
Gorilla gorilla	retro_ggor_2340
Pongo abelii	retro_pabe_2864

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000020803	4 retrocopies	retro_cjac_1013, retro_cjac_4017, retro_cjac_738, retro_cjac_820,
Cavia porcellus	ENSCPOG00000014110	1 retrocopy	retro_cpor_693,
Homo sapiens	ENSG00000104129	2 retrocopies	retro_hsap_2363, retro_hsap_3468,
Gorilla gorilla	ENSGGOG00000000051	1 retrocopy	retro_ggor_2340,
Macropus eugenii	ENSMEUG00000005641	2 retrocopies	retro_meug_1387, retro_meug_2001,
Myotis lucifugus	ENSMLUG00000014835	1 retrocopy	retro_mluc_317,
Macaca mulatta	ENSMMUG00000013160	1 retrocopy	retro_mmul_1574,
Mus musculus	ENSMUSG00000034278	1 retrocopy	retro_mmus_3346,
Nomascus leucogenys	ENSNLEG00000003257	1 retrocopy	retro_nleu_343,
Pongo abelii	ENSPPYG00000006360	1 retrocopy	retro_pabe_2864,
Pan troglodytes	ENSPTRG00000006929	2 retrocopies	retro_ptro_1729, retro_ptro_2351 ,
Rattus norvegicus	ENSRNOG00000012368	2 retrocopies	retro_rnor_18, retro_rnor_2319,