RetrogeneDB ID: retro_ggor_2259

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 5:54350274..54350717(-)
• Located in intron of: ENSGGOG00000010694

Retrocopy information

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

Parental gene information

• Parental gene symbol: NME4
• Ensembl ID: ENSGGOG00000004512
• Aliases: None
• Description: Nucleoside diphosphate kinase [Source:UniProtKB/TrEMBL;Acc:G3QPD1]

Sequence

>retro_ggor_2259
CCCGGCTCAGGAGGACCCTTCTTGATCCAGGAGTGGACCCTGGTCTCATTGAAGCCAGTTGGGGTCTTGTGGCGGCCTGT
TAGGGATGTGATCCAGCGCTTTGGAGGCAGGGCTTCAAGCTGGTAGGGATGAAGATCCTGTGGCCGGCCAGAAAGCGTCC
TTGCTGAACACTACCAGGACCTGTGAAAGAAGCCCCTCTACCCAGCCCTCCTTAGCTATGTGAGCTCCAGGCCTGTTGAT
GGCCATGGTCTGGGAAGGGTACAATGTGATCCACGCCTCGAGGGCCATGATAGATACACTGACAGGGTTGAGGCTGCCTC
TGTGACCATATGGGGAGACTTCAGCGACGTCCACATCAGCAGGAACATCATTCACACCAGCTATTCAGGGTAGGGGGTCA
GAAAGAGATCCAGCTATGGTTTGAAAGCAGTGAGCTGGTGAAC

Alignment

ORF - retro_ggor_2259 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.36 %
• Parental protein coverage: 91.88 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  PFEGGPSWTRERTLVAVKPDGVQRRLVGDVIQRFE-RRGFTLVGMKMLQA-PESILAEHYQDLRRKPFYP
          P..GGP....E.TLV..KP.GV..R.V.DVIQRF..R.GF.LVGMK.L...PES.LAEHYQDL..KP.YP
Retrocopy PGSGGPFLIQEWTLVSLKPVGVLWRPVRDVIQRFG<RQGFKLVGMKILWP>PESVLAEHYQDL*KKPLYP

Parental  ALIRYMSSGPV-VAMVWEGYNVVRASRAMIG-HTDSAEAAPGTIRGDFS-VHISRNVIHASDS-VEGAQR
          AL..Y.SS.PV..AMVWEGYNV..ASRAMI...TD..EAA..TI.GDFS.VHISRN.IH.S.S...G.Q.
Retrocopy ALLSYVSSRPV>MAMVWEGYNVIHASRAMID<YTDRVEAASVTIWGDFSDVHISRNIIHTSYS<RVGGQK

Parental  EIQLWFQSSELVS
          EIQLWF.SSELV.
Retrocopy EIQLWFESSELVN

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	59.37 RPM
SRP007412_cerebellum	0.12 RPM	75.37 RPM
SRP007412_heart	0.00 RPM	69.70 RPM
SRP007412_kidney	0.00 RPM	41.46 RPM
SRP007412_liver	0.00 RPM	58.40 RPM
SRP007412_testis	0.00 RPM	38.23 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_2259 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_2259 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 22 parental genes, and 37 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000007077	3 retrocopies	retro_amel_1271, retro_amel_216, retro_amel_238,
Canis familiaris	ENSCAFG00000019677	4 retrocopies	retro_cfam_1267, retro_cfam_2209, retro_cfam_447, retro_cfam_71,
Cavia porcellus	ENSCPOG00000006496	1 retrocopy	retro_cpor_1076,
Echinops telfairi	ENSETEG00000014875	1 retrocopy	retro_etel_1833,
Felis catus	ENSFCAG00000008300	3 retrocopies	retro_fcat_1013, retro_fcat_1512, retro_fcat_1672,
Homo sapiens	ENSG00000103202	1 retrocopy	retro_hsap_1740,
Gorilla gorilla	ENSGGOG00000004512	1 retrocopy	retro_ggor_2259 ,
Gorilla gorilla	ENSGGOG00000016526	1 retrocopy	retro_ggor_71,
Macropus eugenii	ENSMEUG00000005455	5 retrocopies	retro_meug_1027, retro_meug_1427, retro_meug_1981, retro_meug_1999, retro_meug_694,
Myotis lucifugus	ENSMLUG00000010061	1 retrocopy	retro_mluc_388,
Macaca mulatta	ENSMMUG00000000612	1 retrocopy	retro_mmul_1221,
Mustela putorius furo	ENSMPUG00000016017	3 retrocopies	retro_mputfur_1024, retro_mputfur_1067, retro_mputfur_846,
Mus musculus	ENSMUSG00000024177	1 retrocopy	retro_mmus_309,
Nomascus leucogenys	ENSNLEG00000008068	1 retrocopy	retro_nleu_2719,
Otolemur garnettii	ENSOGAG00000025808	1 retrocopy	retro_ogar_2689,
Pongo abelii	ENSPPYG00000006908	1 retrocopy	retro_pabe_1442,
Pan troglodytes	ENSPTRG00000007541	1 retrocopy	retro_ptro_1220,
Rattus norvegicus	ENSRNOG00000049152	1 retrocopy	retro_rnor_2679,
Sus scrofa	ENSSSCG00000007986	2 retrocopies	retro_sscr_1113, retro_sscr_852,
Ictidomys tridecemlineatus	ENSSTOG00000004798	1 retrocopy	retro_itri_1629,
Tursiops truncatus	ENSTTRG00000009157	2 retrocopies	retro_ttru_393, retro_ttru_688,
Vicugna pacos	ENSVPAG00000010316	1 retrocopy	retro_vpac_150,