RetrogeneDB ID: retro_ggor_2349

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 6:70423702..70424078(+)
• Located in intron of: ENSGGOG00000011243

Retrocopy information

• Ensembl ID: ENSGGOG00000024049
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: NDUFAB1
• Ensembl ID: ENSGGOG00000006320
• Aliases: None
• Description: Acyl carrier protein, mitochondrial [Source:UniProtKB/TrEMBL;Acc:G3QTY8]

Sequence

>retro_ggor_2349
CTGTGCTCTGTGGGGACTCTGATGAGGCTGGGGCTTTGCAGCTGGCTCCACAGCGGGCTTTGGTGCTTGCGCACATGCTG
GGTAGAAGTTACACAGTCGTGCTGTCAGTATAGTGACTTGCCCCCTTTGACGTTAGAGGGAATCGAAGACTGTCTTCTTT
ATATCTTGAAACCCTGTGACAGGATTGACCCAGAGAAGCTCTCAGTGAATTCTTACTTTATGAAAGACCTGTGCTTGGAC
AGTTTGGACCAAGTAGAGAGTAAGCATGGTCATGGAAGATAAATTTGGGTTTGAAATTCCTGATATAGATGTGGAAAAGT
TAATATGTCCACAAGAAATTGTAGATTATATTGCAGATAGGAGAGATGTGTATGAA

Alignment

ORF - retro_ggor_2349 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.32 %
• Parental protein coverage: 77.56 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LCSAGTQTRLGT---LQPALVLAQTESRSVTQAGMQWRDLSPLTRQGIVKQILALLK-IHKLDSHKLSVN
          LCS.GT..RLG....L...L....T....VTQ...Q..DL.PLT..GI....L..LK.....D..KLSVN
Retrocopy LCSVGTLMRLGLCSWLHSGLWCLRTCWVEVTQSCCQYSDLPPLTLEGIEDCLLYILKPCDRIDPEKLSVN

Parental  SHFMKDLGLDSLDQVE-IIMAMEDEFGFEIPDIDAEKLMCPQEIVDYIADKKDVYE
          S.FMKDL.LDSLDQVE...M.MED.FGFEIPDID.EKL.CPQEIVDYIAD..DVYE
Retrocopy SYFMKDLCLDSLDQVE>VSMVMEDKFGFEIPDIDVEKLICPQEIVDYIADRRDVYE

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	19.47 RPM
SRP007412_cerebellum	0.04 RPM	16.82 RPM
SRP007412_heart	0.03 RPM	22.42 RPM
SRP007412_kidney	0.00 RPM	28.87 RPM
SRP007412_liver	0.08 RPM	16.86 RPM
SRP007412_testis	0.10 RPM	12.54 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_2349 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_2349 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3484
Pan troglodytes	retro_ptro_2358
Pongo abelii	retro_pabe_2879

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 35 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000014304	1 retrocopy	retro_amel_1692,
Canis familiaris	ENSCAFG00000017667	3 retrocopies	retro_cfam_1738, retro_cfam_1821, retro_cfam_450,
Callithrix jacchus	ENSCJAG00000020616	2 retrocopies	retro_cjac_2635, retro_cjac_3099,
Cavia porcellus	ENSCPOG00000012038	2 retrocopies	retro_cpor_728, retro_cpor_767,
Felis catus	ENSFCAG00000013241	3 retrocopies	retro_fcat_1104, retro_fcat_1181, retro_fcat_2012,
Homo sapiens	ENSG00000004779	1 retrocopy	retro_hsap_3484,
Gorilla gorilla	ENSGGOG00000006320	1 retrocopy	retro_ggor_2349 ,
Macropus eugenii	ENSMEUG00000012681	3 retrocopies	retro_meug_1780, retro_meug_303, retro_meug_830,
Microcebus murinus	ENSMICG00000007778	2 retrocopies	retro_mmur_1193, retro_mmur_120,
Macaca mulatta	ENSMMUG00000020522	1 retrocopy	retro_mmul_101,
Monodelphis domestica	ENSMODG00000016352	1 retrocopy	retro_mdom_389,
Mus musculus	ENSMUSG00000030869	6 retrocopies	retro_mmus_1724, retro_mmus_2073, retro_mmus_2188, retro_mmus_2947, retro_mmus_3094, retro_mmus_3332,
Oryctolagus cuniculus	ENSOCUG00000008457	1 retrocopy	retro_ocun_1712,
Otolemur garnettii	ENSOGAG00000005562	2 retrocopies	retro_ogar_2916, retro_ogar_325,
Pongo abelii	ENSPPYG00000007192	1 retrocopy	retro_pabe_2879,
Pan troglodytes	ENSPTRG00000007889	1 retrocopy	retro_ptro_2358,
Rattus norvegicus	ENSRNOG00000018129	2 retrocopies	retro_rnor_1353, retro_rnor_2058,
Ictidomys tridecemlineatus	ENSSTOG00000024657	2 retrocopies	retro_itri_281, retro_itri_916,