RetrogeneDB ID: retro_ggor_1065

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 14:59004069..59004607(+)
• Located in intron of: ENSGGOG00000011055

Retrocopy information

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

Parental gene information

• Parental gene symbol: ZMYND19
• Ensembl ID: ENSGGOG00000006875
• Aliases: None
• Description: None

Sequence

>retro_ggor_1065
ACACTGATAGATGCGCAAAGATATCCTGCTGGTGGAGAGATACTCCTCTGAGGTCCAAATGGAAGTAGATGCAGATAGAA
ATGGTCCTAAGATATTCAGGTATGCTTTCGACAAGCACTGAGGAAGAGGACTGGGAAGACTCCTTCATGAGTTGCTGTGG
GAGCACAGAAGAGGCATGACCCCTGGGTTCCAGGTGGTACATCTCAATGCCCTGACTGAGACAATTGCCTGGACAACCTG
TAGCTGGTGCTGTGGGGCTGGTGGCCCAAAGCCAAAGAGACCTCCAGAAGAGGTAGCAAAGCTTGTACTGGCTTGCAATT
CAGCAGCTTCCCATGGACCCCAAAGAAGAGCAGTGACCTGTCCTAACTGTGACCTGGTACTATAACACCAATGGAGACGT
GGTGGAAGAGTTGAATTCTTACACCTACTACAGTAGCATTACCCTTCCTGCACAGTGATTGAGAAGTAGCTCCAGGAGTT
CAAAATCTGTGGGTGCTGCCAGGTGGCCCAGTACTGAGGCTCTGAGTGCCAGCAGGAG

Alignment

ORF - retro_ggor_1065 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.78 %
• Parental protein coverage: 80.62 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  TLIDEQ-DIPLVESYSFEARMEVDADGNGAKIFAYAFDKNRGRGSGRLLHELLWERHRGGVAPGFQVVHL
          TLID.Q.DI.LVE.YS.E..MEVDAD.NG.KIF.YAFDK..GRG.GRLLHELLWE.HR.G..PGFQVVHL
Retrocopy TLIDAQ>DILLVERYSSEVQMEVDADRNGPKIFRYAFDKH*GRGLGRLLHELLWE-HRRGMTPGFQVVHL

Parental  NAVTV-DNRLDNLQLVPWGWRPKAEETSSKQREQSLYWLAIQQLPTDP-IEEQFPVLNVTRYYNANGDVV
          NA.T..DN.LDNL.LV.WGW.PKA.ET.S.........L.....P..P..EEQ.PVL.VT.YYN.NGDVV
Retrocopy NALTE<DNCLDNL*LVLWGWWPKAKET-SRRGSKACTGLQFSSFPWTP<KEEQ*PVLTVTWYYNTNGDVV

Parental  EEEENSCTYYEC-HYPPCTAIEKQLREFNICGRCQVARYCGSQCQQK
          .EE.NS.TYY...HYP.CT.IEK.L.EF.ICG.CQVA.Y.GS.CQQ.
Retrocopy -EELNSYTYYSS<HYPSCTVIEK*LQEFKICGCCQVAQY*GSECQQE

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	16.59 RPM
SRP007412_cerebellum	0.00 RPM	14.85 RPM
SRP007412_heart	0.03 RPM	4.44 RPM
SRP007412_kidney	0.00 RPM	6.58 RPM
SRP007412_liver	0.13 RPM	5.49 RPM
SRP007412_testis	0.10 RPM	36.36 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_1065 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_1065 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1367
Macaca mulatta	retro_mmul_2195

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000006644	2 retrocopies	retro_dnov_1389, retro_dnov_1468,
Dipodomys ordii	ENSDORG00000008360	1 retrocopy	retro_dord_390,
Equus caballus	ENSECAG00000012412	1 retrocopy	retro_ecab_903,
Echinops telfairi	ENSETEG00000005023	1 retrocopy	retro_etel_1068,
Homo sapiens	ENSG00000165724	1 retrocopy	retro_hsap_1367,
Gorilla gorilla	ENSGGOG00000006875	1 retrocopy	retro_ggor_1065 ,
Macropus eugenii	ENSMEUG00000011727	1 retrocopy	retro_meug_2010,
Macaca mulatta	ENSMMUG00000019610	1 retrocopy	retro_mmul_2195,
Monodelphis domestica	ENSMODG00000017172	1 retrocopy	retro_mdom_764,
Mus musculus	ENSMUSG00000026974	3 retrocopies	retro_mmus_1433, retro_mmus_2466, retro_mmus_942,
Nomascus leucogenys	ENSNLEG00000009236	1 retrocopy	retro_nleu_1071,
Tursiops truncatus	ENSTTRG00000010812	1 retrocopy	retro_ttru_900,