RetrogeneDB ID: retro_ggor_2340

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 6:49110733..49111216(+)
• Located in intron of: ENSGGOG00000009343

Retrocopy information

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

Parental gene information

• Parental gene symbol: DNAJC17
• Ensembl ID: ENSGGOG00000000051
• Aliases: None
• Description: None

Sequence

>retro_ggor_2340
GAGGCCCAGGCCCAGGCGAGTGAGAAGGTGGAGGAAAGCTAGAGCACCAGGACACTTGAGCAGGAGATTGAACATCTTAG
TGAATAGTGTTCATGGCAGCTGGAGGAACAGCAGATGATGATCCAGGAGCAGATGTGCCAGGAACTTGACTTGAGATTGG
AAGTCAGAAAATACTGAAGACAAAGGAACCCAAAACTGAAACTGAAATGGAAGTACAGGAAGGATGAGTCAGAAGGCAGT
TACTCCAAAGGTGTCCTCTTGTGGCTTTTGCAAAAGTATGGTGGAATTCTCAACCTGGTGCTTTTGAGTAAGAAGGCAGG
TACTGGTGTCGTGGAGTTTGGGACTGTCGAGGCTGCAGAGATGGCTGTCTGGAATAAAGTTGGCTTGGGTGATAATCCTC
GAAAGATTTCCTCTTTCAAAGGAGGACTCCAGGGTGCAGTGGGCCCCAGCCACCCAGGACAGTGAAGGGACCCAGTGGTG
TCT

Alignment

ORF - retro_ggor_2340 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.37 %
• Parental protein coverage: 53.95 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QAQAQESEEEEESRSTRTLEQEIERLREEGSRQLEEQQRLIREQIRQERDQRLRGKAENTEGQGTPKLKL
          .AQAQ.SE..EES.STRTLEQEIE.L.E..S.QLEEQQ..I.EQ..QE.D.RL.............KLK.
Retrocopy EAQAQASEKVEES*STRTLEQEIEHLSE*CSWQLEEQQMMIQEQMCQELDLRLEVRKY*RQRNPKLKLK-

Parental  KWKCKKEDESKGGYSKDVLLRLLQKYGEVLNLVLSSKKPGTAVVEFATVKAAELAVQNEVGLVDNPLKIS
          .WK..K.DES.G.YSK.VLL.LLQKYG..LNLVL.SKK.GT.VVEF.TV.AAE.AV.N.VGL.DNP.KIS
Retrocopy -WKYRK-DESEGSYSKGVLLWLLQKYGGILNLVLLSKKAGTGVVEFGTVEAAEMAVWNKVGLGDNPRKIS

Parental  WLEGQPQDAVGRSHSGLSKGSVLS
          ...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	0.05 RPM	6.43 RPM
SRP007412_cerebellum	0.04 RPM	12.73 RPM
SRP007412_heart	0.00 RPM	3.53 RPM
SRP007412_kidney	0.20 RPM	8.95 RPM
SRP007412_liver	0.11 RPM	10.76 RPM
SRP007412_testis	0.10 RPM	5.49 RPM

ChIP-Seq

Gorilla gorilla was not studied using ChIP-Seq data.

EST

Gorilla gorilla was not studied using EST data.

TSS

Gorilla gorilla was not studied using FANTOM5 data.

Lab

retro_ggor_2340 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_2340 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3468
Pan troglodytes	retro_ptro_2351
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,