RetrogeneDB ID: retro_ggor_2065

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 4:139851363..139851866(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ENSG00000234125
• Ensembl ID: ENSGGOG00000013557
• Aliases: None
• Description: None

Sequence

>retro_ggor_2065
CTGGCTGCTGAGCTCAAGGTCAAAGACCTCTTCACTCACTTGCTCAAGAGTACCTTTGTGTTGGATGAATTTAAGCGCAA
GTACTCCAATGAGGACACGCTCTCTGTGGTGCTGCCCTATTTCTGGGAGCACTTTGATAAGGATGGCTGGTCCCTGTGGT
ACTCACAATATCGCTTTCCTAAAGAACTCACTCAGACCTTTATGACTTGCAATCTCATCACTGGAATGTTCAAGCGACTG
GACAAGCTGAGGAAGATGCCTTTGCCAGTGTCATCCTCTTTGGAACCAACAACAGTAGCTCTATTTCTGGAGTCTGAGGC
TTCTGAGGTCAGGAGCTTGCCTTTCTGCTGAGTCCAGATTGGCAGATGGACTACCAGTCATACACATGGCAAAAACCGGC
TCCTGGCAGCGACGAGCCCCAGACCCTGATTGGAGCGTAGTTTTCCTGGGAGGAGGGTTTCCAGAATATGGGCAAAGCCT
TCAATCAGGGCGAGATCGTCAAG

Alignment

ORF - retro_ggor_2065 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.88 %
• Parental protein coverage: 81.46 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LAAEPKAKDPFAHLPKSTFVLDEFKRKYSNEDTLSVALPYFWEHFDKDGWSLWYSEYRFPEELTQTFMSC
          LAAE.K.KD.F.HL.KSTFVLDEFKRKYSNEDTLSV.LPYFWEHFDKDGWSLWYS.YRFP.ELTQTFM.C
Retrocopy LAAELKVKDLFTHLLKSTFVLDEFKRKYSNEDTLSVVLPYFWEHFDKDGWSLWYSQYRFPKELTQTFMTC

Parental  NLITGMFQRLDKLRK-NAFASVILFGTNNSSSISGVWVFRGQELAFPLSPDWQVDYESYT-RKLDPGSEE
          NLITGMF.RLDKLRK..AFASVILFGTNNSSSISGV..F.GQELAF.LSPDWQ.DY.SYT..K..PGS.E
Retrocopy NLITGMFKRLDKLRK<DAFASVILFGTNNSSSISGV*GF*GQELAFLLSPDWQMDYQSYTWQKPAPGSDE

Parental  TQTLVREYFSWEGAFQHVGKAFNQGKIFK
          .QTL....FSWE..FQ..GKAFNQG.I.K
Retrocopy PQTLIGA*FSWEEGFQNMGKAFNQGEIVK

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	186.35 RPM
SRP007412_cerebellum	0.00 RPM	209.48 RPM
SRP007412_heart	0.03 RPM	245.22 RPM
SRP007412_kidney	0.04 RPM	553.39 RPM
SRP007412_liver	0.00 RPM	308.31 RPM
SRP007412_testis	0.00 RPM	350.06 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_2065 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_2065 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2982
Pan troglodytes	retro_ptro_2017
Macaca mulatta	retro_mmul_1905

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 44 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000015834	6 retrocopies	retro_cfam_1241, retro_cfam_1398, retro_cfam_1862, retro_cfam_478, retro_cfam_638, retro_cfam_653,
Erinaceus europaeus	ENSEEUG00000001231	1 retrocopy	retro_eeur_575,
Gorilla gorilla	ENSGGOG00000013557	12 retrocopies	retro_ggor_1935, retro_ggor_1936, retro_ggor_1991, retro_ggor_1992, retro_ggor_2064, retro_ggor_2065 , retro_ggor_2214, retro_ggor_243, retro_ggor_2542, retro_ggor_2633, retro_ggor_2946, retro_ggor_2947,
Latimeria chalumnae	ENSLACG00000014700	1 retrocopy	retro_lcha_82,
Loxodonta africana	ENSLAFG00000003339	1 retrocopy	retro_lafr_381,
Macaca mulatta	ENSMMUG00000006598	5 retrocopies	retro_mmul_1447, retro_mmul_1905, retro_mmul_2528, retro_mmul_736, retro_mmul_802,
Monodelphis domestica	ENSMODG00000007691	1 retrocopy	retro_mdom_68,
Mus musculus	ENSMUSG00000071644	7 retrocopies	retro_mmus_1447, retro_mmus_1839, retro_mmus_2350, retro_mmus_2765, retro_mmus_3080, retro_mmus_425, retro_mmus_989,
Rattus norvegicus	ENSRNOG00000020075	8 retrocopies	retro_rnor_1312, retro_rnor_2126, retro_rnor_2235, retro_rnor_2269, retro_rnor_2468, retro_rnor_2617, retro_rnor_2928, retro_rnor_979,
Ictidomys tridecemlineatus	ENSSTOG00000002851	2 retrocopies	retro_itri_852, retro_itri_886,