RetrogeneDB ID: retro_ggor_1618

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 22:20185611..20186751(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NDUFA9
• Ensembl ID: ENSGGOG00000006076
• Aliases: None
• Description: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrial [Source:UniProtKB/Swiss-Prot;Acc:Q0MQB3]

Sequence

>retro_ggor_1618
ATGGCGGCCGCTGCACAATCCCGGGTTGTCTGGGCCCTGCCAGTGTCACATTCTGCCATTACTGCAATAGCCACATCCAT
GTGTCACAGCCCACTCCATTGCCAGCTTCATCATGCCCTCATACCTCATGGGAAAGGTGGATGTTCCTCAAGTCAGTGGG
ATTGTGGCCACTGGGTTTGGAGCAACAGGATTCCTGGGCCGATGTGTTGTCAACCACCTTGGACGTGTGGGGTCACAGGT
GATCATACCCTATCAGTGTGATACATGTGACATCGTGCACCTTCATCCCATGGGAGACCTGGGCTAGCTTCTGTTTCTGG
AATGGGACGCGAGAGATGAAGATTCTATCCGACGAGTAGTGGAACACAGCAATGTGGTCATAAATCTTGTTGGACGAGAC
TGGGAAACCAAAAACTTTGATTTTGAGGATGTTTTTGTGAAGATTCCCCAAGCAATTGCTCAGGTGTCCAAGGAAGCTGA
AGTTGGAAAATTCATTCATGTTGCACATCTGAATGTGAATATTAAAAGCTCTTCTAGATATTTGAGAAAGAAGGCTGTTG
GAGAGAAAGCAGTCAGAGACACATTTCCAGAAGCCATTATCGTAAAGCTGTTGGACATCTTTGGAAGAGAGGATAGATTC
CTTAATTATTTTGCAAATATGTGTTGGTTTGGTGCTATACCCCTTGTTTCCTTGGGCTGGAAGGCAGTTAAACAACCAGT
ATATGTCGTAGATGTATCCAAAGGAATTGTTAATGCAGTTAAGGATCCTGATGCCAATGGGAAAACCTTTGCTTTCGTTG
GGCCAAATCAGTACCTCCTCTTTGACCTGGTGAAGTACATCTTTGCTGTGGCTCACAGCAAAGGGGTACTTCCTCCTGTA
CCCCTTGCCACCTTTTGCCTATCAGTGGGTAGCAAGAGACTTTGAAATAAGCCTATTTGAGTCCTGGACAACAAGGGATA
AAGTGGAGCGTTATTCACATCACAGACATGACCTTGTCTCACCTGCCCAGCTTAGAAGACCTTGGTATTCAGGCAACACC
ACTGGAACTCAAGGCCATTGAGGTGCTGCGGCTTCATCACACTTACTGCTGGCTGTCTGCTGAAATTGAGGATGTGAAGC
CGGCCAAGACCGTCAACATT

Alignment

ORF - retro_ggor_1618 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.94 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MAAAAQSRVVRVLSMSRSAITAIATSVCHGPPCRQLHHALIPHGKGGRSS-VSGIVATVFGATGFLGRYV
          MAAAAQSRVV..L..S.SAITAIATS.CH.P...QLHHALIPHGKGG.SS.VSGIVAT.FGATGFLGR.V
Retrocopy MAAAAQSRVVWALPVSHSAITAIATSMCHSPLHCQLHHALIPHGKGGCSS>VSGIVATGFGATGFLGRCV

Parental  VNHLGRMGSQVIIPYRCDKYDIMHLRPMGDLGQLLFLEWDARDKDSIRRVVQHSNVVINLIGRDWETK-F
          VNHLGR.GSQVIIPY.CD..DI.HL.PMGDLG.LLFLEWDARD.DSIRRVV.HSNVVINL.GRDWETK.F
Retrocopy VNHLGRVGSQVIIPYQCDTCDIVHLHPMGDLG*LLFLEWDARDEDSIRRVVEHSNVVINLVGRDWETKNF

Parental  DFEDVFVKIPQAIAQLSKEAGVEKFIHVSHLNANIKSSSRYLRNKAVGEKVVRDAFPEAIIIKPSDIFGR
          DFEDVFVKIPQAIAQ.SKEA.V.KFIHV.HLN.NIKSSSRYLR.KAVGEK.VRD.FPEAII.K..DIFGR
Retrocopy DFEDVFVKIPQAIAQVSKEAEVGKFIHVAHLNVNIKSSSRYLRKKAVGEKAVRDTFPEAIIVKLLDIFGR

Parental  EDRFLNSFASMHRFGPIPLGSLGWKTVKQPVYVVDVSKGIVNAVKDPDANGKSFAFVGPSRYLLFHLVKY
          EDRFLN.FA.M..FG.IPL.SLGWK.VKQPVYVVDVSKGIVNAVKDPDANGK.FAFVGP..YLLF.LVKY
Retrocopy EDRFLNYFANMCWFGAIPLVSLGWKAVKQPVYVVDVSKGIVNAVKDPDANGKTFAFVGPNQYLLFDLVKY

Parental  IFAVAHR--LFLPFP-LPLFAYRWVARVFEISPFEPWITRDKVER-MHITDMKLPHLPGLEDLGIQATPL
          IFAVAH......P.P.LP.FAY.WVAR.FEIS.FE.W.TRDKVER..HITDM.L.HLP.LEDLGIQATPL
Retrocopy IFAVAHSKGVLPPVP>LPPFAYQWVARDFEISLFESWTTRDKVER>IHITDMTLSHLPSLEDLGIQATPL

Parental  ELKAIEVLRRHRTYRWLSAEIEDVKPAKTVNI
          ELKAIEVLR.H.TY.WLSAEIEDVKPAKTVNI
Retrocopy ELKAIEVLRLHHTYCWLSAEIEDVKPAKTVNI

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	1.20 RPM	34.96 RPM
SRP007412_cerebellum	0.83 RPM	18.71 RPM
SRP007412_heart	0.41 RPM	25.52 RPM
SRP007412_kidney	1.14 RPM	41.22 RPM
SRP007412_liver	0.84 RPM	17.17 RPM
SRP007412_testis	0.93 RPM	39.58 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_1618 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_1618 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2585
Pan troglodytes	retro_ptro_1511
Pongo abelii	retro_pabe_1905
Macaca mulatta	retro_mmul_648

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000009588	1 retrocopy	retro_acar_16,
Danio rerio	ENSDARG00000070723	1 retrocopy	retro_drer_1,
Homo sapiens	ENSG00000139180	1 retrocopy	retro_hsap_2585,
Gorilla gorilla	ENSGGOG00000006076	1 retrocopy	retro_ggor_1618 ,
Macaca mulatta	ENSMMUG00000020813	1 retrocopy	retro_mmul_648,
Monodelphis domestica	ENSMODG00000018283	1 retrocopy	retro_mdom_209,
Nomascus leucogenys	ENSNLEG00000003252	1 retrocopy	retro_nleu_1520,
Otolemur garnettii	ENSOGAG00000005225	1 retrocopy	retro_ogar_2244,
Pongo abelii	ENSPPYG00000004171	1 retrocopy	retro_pabe_1905,
Pan troglodytes	ENSPTRG00000004557	1 retrocopy	retro_ptro_1511,
Ictidomys tridecemlineatus	ENSSTOG00000006504	1 retrocopy	retro_itri_543,