RetrogeneDB ID: retro_ggor_2912

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: X:56825897..56826596(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GOT2
• Ensembl ID: ENSGGOG00000005767
• Aliases: None
• Description: Aspartate aminotransferase [Source:UniProtKB/TrEMBL;Acc:G3QSK6]

Sequence

>retro_ggor_2912
TCCTGGTGGACCTATGTGGAGATGGGACTTCCAGATCCCATCCTGGGAGTCACCAAAGCCTTTAAGAGGGACACCGATAG
CAAAAAGATGAATCTGGGAGTTTGTGTCTACTGGGATGATAATGGAAAGCCTTACATGCTGCTTAATGTCAACAAGGAAG
AGGCCCAGATTGCCACAAAAAATCTGGACAAAGAATACCTGCCCATTGGGGGTCTGGCTGAATTTTGCACGGCATCTGCA
GAACTAGCCCTGGGTGAGAATAGTGAAGTGTTGAAAAATGTCCAGTTATTCACTGTGCATACCATTTCTGGAACTGTGAC
CTTAACCATCAGAGCCTGTTTTCTGCAAAGATTTTTTAAGCTCAGCCAGGATGTCCAAACCATCCTGGGGAAATCACATA
CCCATCTTCAGGGATGCTGGCATGCAGCTACAAATTTATTGTTACTACGACCCCAAGACTTGGTGTTTGACTTCACAGGT
CGTATGGAGGACATTTCAAAAATACCAGAGCAAAGTGTTTTTCTGCATGCCTGTGCCTATAATCCCATGGGAGTGGAACC
TCGTCTAGAGCAGTGGAAAGAAATAGCAACAGTGATGAAGAAAAATAATCTCTTTGCATTCTTTGACATGGCCTAGCAAG
GGTTTGCTAGTGATGATTGTAACAAGGATGCCTGGGCTGTGCACCACTTCATCAAAGAG

Alignment

ORF - retro_ggor_2912 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.06 %
• Parental protein coverage: 55.12 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SWWTHVEMGPPDPILGVTEAFKRDTNSKKMNLGVGAYRDDNGKPYVLPSVRKAEAQIAAKNLDKEYLPIG
          SWWT.VEMG.PDPILGVT.AFKRDT.SKKMNLGV..Y.DDNGKPY.L..V.K.EAQIA.KNLDKEYLPIG
Retrocopy SWWTYVEMGLPDPILGVTKAFKRDTDSKKMNLGVCVYWDDNGKPYMLLNVNKEEAQIATKNLDKEYLPIG

Parental  GLAEFCKASAELALGENSEVLKSGRFVTVQTISGTGALRIGAS-FLQRFFKFSRDVFLPKPTWGNHTPIF
          GLAEFC.ASAELALGENSEVLK.....TV.TISGT..L.I.A..F...F....R.....KP.WGNH.PIF
Retrocopy GLAEFCTASAELALGENSEVLKNVQLFTVHTISGTVTLTIRAC>FCKDFLSSAR---MSKPSWGNHIPIF

Parental  RDAGMQLQGYRYYDPKT-CGFDFTGAVEDISKIPEQSVLILHACAHNPTGVDPRPEQWKEIATVVKKRNL
          RDAGMQLQ.Y.YYDPKT...FDFTG..EDISKIPEQSV..LHACA.NP.GV.PR.EQWKEIATV.KK.NL
Retrocopy RDAGMQLQIYCYYDPKT<LVFDFTGRMEDISKIPEQSVF-LHACAYNPMGVEPRLEQWKEIATVMKKNNL

Parental  FAFFDMAYQGFASGDGDKDAWAVRHFIEQ
          FAFFDMA.QGFAS.D..KDAWAV.HFI..
Retrocopy FAFFDMA*QGFASDDCNKDAWAVHHFIKE

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	135.85 RPM
SRP007412_cerebellum	0.00 RPM	78.64 RPM
SRP007412_heart	0.03 RPM	210.01 RPM
SRP007412_kidney	0.04 RPM	123.16 RPM
SRP007412_liver	0.00 RPM	271.77 RPM
SRP007412_testis	0.00 RPM	78.94 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_2912 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_2912 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4687

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 34 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017346	3 retrocopies	retro_amel_1805, retro_amel_815, retro_amel_846,
Canis familiaris	ENSCAFG00000008357	2 retrocopies	retro_cfam_586, retro_cfam_816,
Callithrix jacchus	ENSCJAG00000011234	1 retrocopy	retro_cjac_2916,
Equus caballus	ENSECAG00000016504	1 retrocopy	retro_ecab_694,
Felis catus	ENSFCAG00000025552	3 retrocopies	retro_fcat_1068, retro_fcat_1888, retro_fcat_381,
Homo sapiens	ENSG00000125166	4 retrocopies	retro_hsap_4687, retro_hsap_473, retro_hsap_960, retro_hsap_971,
Gorilla gorilla	ENSGGOG00000005767	3 retrocopies	retro_ggor_2912 , retro_ggor_449, retro_ggor_774,
Macropus eugenii	ENSMEUG00000012574	1 retrocopy	retro_meug_2109,
Microcebus murinus	ENSMICG00000008954	1 retrocopy	retro_mmur_480,
Macaca mulatta	ENSMMUG00000006000	1 retrocopy	retro_mmul_1337,
Mustela putorius furo	ENSMPUG00000004862	1 retrocopy	retro_mputfur_567,
Mus musculus	ENSMUSG00000031672	1 retrocopy	retro_mmus_2701,
Oryctolagus cuniculus	ENSOCUG00000003871	1 retrocopy	retro_ocun_1516,
Otolemur garnettii	ENSOGAG00000000551	2 retrocopies	retro_ogar_2182, retro_ogar_827,
Pongo abelii	ENSPPYG00000007413	3 retrocopies	retro_pabe_3640, retro_pabe_823, retro_pabe_901,
Pan troglodytes	ENSPTRG00000008185	4 retrocopies	retro_ptro_3115, retro_ptro_354, retro_ptro_665, retro_ptro_670,
Rattus norvegicus	ENSRNOG00000011782	1 retrocopy	retro_rnor_2695,
Tupaia belangeri	ENSTBEG00000001808	1 retrocopy	retro_tbel_3799,