RetrogeneDB ID: retro_ggor_1463

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 19:9535030..9535459(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: UBXN2A
• Ensembl ID: ENSGGOG00000002445
• Aliases: None
• Description: None

Sequence

>retro_ggor_1463
ATGAAAGACGTATATAATCTTGAAAGTATAAAAGACTGGGTTTGTGAAACAGGACCTGACAATCAACGTCTTGGTGATAA
TCAATAAACAAATTGTGAATAGTTTGTTGACAGCCTTTTTGAGGAAGCTCAGAAGGTTGGTTCCAAATGCTTGTCTCCCA
CTTAACAAAAGAAACAGGTAGACGTAAACATAAAATTATGGAAAAATGGATTCACCGTCAACAATTATTTTAGAAGTTAT
TCAAATGGTGCAAGTCAGCAGTTTTTGAACTCCATCAAAAAGGGGGAATTACCTTCAGAATTACAGGGAATTTTTGATAA
AGAAGAGGTGGGTGTTAAAGTTGAAGACAAGAAAAATGAAATATGTATGTCTACGAAGCCTGTCTTCCAGCCCTTTTCAG
GACAGGGTCACCAAGTAGGAAAGGTAAGC

Alignment

ORF - retro_ggor_1463 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.33 %
• Parental protein coverage: 55.6 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MKDVDNLKSIKEEWVCETGSDNQPLGNNQQSNCEYFVDSLFEEAQKVSSKCVSPAEQKKQVDVNIKLWKN
          MKDV.NL.SIK..WVCETG.DNQ.LG.NQ..NCE.FVDSLFEEAQKV.SKC.SP..QKKQVDVNIKLWKN
Retrocopy MKDVYNLESIKD-WVCETGPDNQRLGDNQ*TNCE*FVDSLFEEAQKVGSKCLSPT*QKKQVDVNIKLWKN

Parental  GFTVNDDFRSYSDGASQQFLNSIKKGELPSELQGIFDKEEVDVKVEDKKNEICLSTKPVFQPFSGQGHRL
          GFTVN..FRSYS.GASQQFLNSIKKGELPSELQGIFDKEEV.VKVEDKKNEIC.STKPVFQPFSGQGH..
Retrocopy GFTVNNYFRSYSNGASQQFLNSIKKGELPSELQGIFDKEEVGVKVEDKKNEICMSTKPVFQPFSGQGHQV

Parental  GSAT
          G...
Retrocopy GKVS

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	3.02 RPM
SRP007412_cerebellum	0.47 RPM	4.06 RPM
SRP007412_heart	0.03 RPM	1.25 RPM
SRP007412_kidney	0.12 RPM	4.46 RPM
SRP007412_liver	0.08 RPM	1.82 RPM
SRP007412_testis	0.10 RPM	3.73 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_1463 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_1463 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000001640	5 retrocopies	retro_chof_1096, retro_chof_1171, retro_chof_2641, retro_chof_961, retro_chof_964,
Callithrix jacchus	ENSCJAG00000007665	1 retrocopy	retro_cjac_2085,
Equus caballus	ENSECAG00000020144	1 retrocopy	retro_ecab_569,
Echinops telfairi	ENSETEG00000002623	1 retrocopy	retro_etel_1116,
Homo sapiens	ENSG00000173960	1 retrocopy	retro_hsap_2025,
Gorilla gorilla	ENSGGOG00000002445	1 retrocopy	retro_ggor_1463 ,
Gorilla gorilla	ENSGGOG00000013539	1 retrocopy	retro_ggor_2718,
Myotis lucifugus	ENSMLUG00000015640	1 retrocopy	retro_mluc_1195,
Macaca mulatta	ENSMMUG00000006487	1 retrocopy	retro_mmul_2068,
Mus musculus	ENSMUSG00000020634	1 retrocopy	retro_mmus_1007,
Nomascus leucogenys	ENSNLEG00000000751	1 retrocopy	retro_nleu_2612,
Oryctolagus cuniculus	ENSOCUG00000008783	1 retrocopy	retro_ocun_207,
Otolemur garnettii	ENSOGAG00000000025	1 retrocopy	retro_ogar_1909,
Procavia capensis	ENSPCAG00000011502	4 retrocopies	retro_pcap_169, retro_pcap_255, retro_pcap_271, retro_pcap_323,
Pan troglodytes	ENSPTRG00000011705	1 retrocopy	retro_ptro_1347,
Rattus norvegicus	ENSRNOG00000004950	2 retrocopies	retro_rnor_1746, retro_rnor_2966,
Sorex araneus	ENSSARG00000010108	1 retrocopy	retro_sara_272,
Sus scrofa	ENSSSCG00000026283	1 retrocopy	retro_sscr_537,
Tupaia belangeri	ENSTBEG00000012158	1 retrocopy	retro_tbel_3887,