RetrogeneDB ID: retro_ptro_3290

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: Y:11744156..11745812(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GLUD2
• Ensembl ID: ENSPTRG00000002711
• Aliases: None
• Description: Pan troglodytes glutamate dehydrogenase 2 (GLUD2), nuclear gene encoding mitochondrial protein, mRNA. [Source:RefSeq mRNA;Acc:NM_001009004]

Sequence

>retro_ptro_3290
GGCGAAGCCCTGCTGCTCTCCTGGGTTGGCCCGGTGCCCTGGGTTCGGCGGCCGCCCACTCAGCCGCGTTGCTGGGCCGG
GCCGGGGGATAGCCCACCGCCGCCCGCAGCCGGGGCTCGTATTGGCCGCCCGGCGCCACTACAGCGAAGAGGTGGCCGAA
CGCGAGGATGACCCCAGCTTCTTCAAAACGGTGGAGGGCTTCTTCAATCGTGGCGCCAGCATCGTGCAGGACAAGCTGGT
GGAGGACCTGAGGACCCGGGAGAGTGAGGAGCAGAAGCGGAACCGGGTGGGCGGCATCTTTCGGATCATCAATCCCTGCA
ACCACATGCTGAGTGTCTCCTTCCGCATCCGGCGCGACGACAGCTCCTGGGAGGTCACCAAAGGCTACCCGGCCCAGCAC
AGCCAGCACCGCATGCCCTGCAATGGAGGTGTCCATTACAGCACTGATGTGAGTATAGATGAAGTAAAAGCTTTGGCTTC
TCTGATGACATGCAAGTGTGCAGTGGTTGGTGTGTTGTTCTGGGGTGCTAAAGCTGGTGTTAAGATCAGTCCCAAGTACT
ATACCAATAATGAATTGGAAAAGATCACAAGGAGGTTCACCATAGAGCTAGCAAAGAAAGGCTTTATTGGTTGTGGCATT
GATGTGCCTGCTCCAGACAAGAGCACAGGTGAGCTGGAGATGTCCTGGATCGCTGATGCCTATGCCAGCACCATAGGGCA
CTACGATATTAATGCACACGCCTGTGTTATTGGTAAACCCATCAGCCAAGGGGGAATCCATGGACGCATCTCTGCTACTG
GCCATGGTGTCTTCCATGGGATTGAAAACTTCATCAATGAAGCTTCTTACATGAGCATTTTAGGAATGACATCAGGGTTT
GGAGGTAAAACATTTTTCGTTCAGGGATTTGGTAATGCGGGCCTCCACTCTATGAGATATTTACATCGTTTTGGTGCTAA
ATGTATTGCTGTTGGTGAGTCTGATGGGAGTATATGGAATCCAGATGGTATTGACCCAAAGGAATTGGAAGACTTCAAAT
TGCAACATGGGTCCATTGTGGGCTTCCCCAAGGTAAAGCCCTATGAAGGAAGCATCTTGGAGCCCTACTGTGACATACTG
ATCCCAGCTGCCAGTGAGAAGCAGTTGAGCAAATCCAATGAATCCAGAGTCAAAGCCAAGATCATTGCTGAAGGTGACAA
TGGGCCAACAACCCCAGAAGCTGACAAGATCTTCCTGGAGAGAAACATTATGGTTATTCCAGATCTCTACATGAATGCTG
GAGGAGTGACAGTATCTTACTTTGAGTGGCTGAAGAATCTAAAGCATGTCAGCTATGGCCGTTTGACCTTCAAATATGAA
AGGAATTCTAACTACCACTTGTTCATGTCTGTTGAAGAGACTTTAGAAAGAAAATGTGGAAAGCATGGTGGAGCTATTCC
CATTGTACCCACGGCAGAGTTCCAAGACAGGATATCAGGTGCATCTGAGAAAGACATCATGCACTCCGGCTTGGTGTGCA
CAATGGAGCATTCTGCCAGGCAAATCATGCACACAGCCAGGAAGTATAAACTGGGATGGACCTGAGAGCAGCTGCCTATG
TCAATACCATTGAGAAAGTCTTCAAAGTGTACAATGAAGCTGGTGCGACCTTCACA

Alignment

ORF - retro_ptro_3290 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.61 %
• Parental protein coverage: 99.1 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  GEALLLSRAGPA-ALGSASADSAALLGWARGQPAAA-PQPGLALAARRHYSEAVADREDDPNFFKMVEGF
          GEALLLS..GP..ALGSA.A.SAALLG.A.G.P.AA.PQPGL.LAARRHYSE.VA.REDDP.FFK.VEGF
Retrocopy GEALLLSWVGPV<ALGSAAAHSAALLGRAGG*PTAA<PQPGLVLAARRHYSEEVAEREDDPSFFKTVEGF

Parental  FDRGASIVEDKLVEDLRTRESEEQKRNRVRGILRIIKPCNHVLSLSFPIRRDDGSWEVIEGYRAQHSQHR
          F.RGASIV.DKLVEDLRTRESEEQKRNRV.GI.RII.PCNH.LS.SF.IRRDD.SWEV..GY.AQHSQHR
Retrocopy FNRGASIVQDKLVEDLRTRESEEQKRNRVGGIFRIINPCNHMLSVSFRIRRDDSSWEVTKGYPAQHSQHR

Parental  TPCKGGIRYSTDVSVDEVKALASLMTYKCAVVDVPFGGAKAGVKINPKNYTDNELEKITRRFTMELAKKG
          .PC.GG..YSTDVS.DEVKALASLMT.KCAVV.V.F.GAKAGVKI.PK.YT.NELEKITRRFT.ELAKKG
Retrocopy MPCNGGVHYSTDVSIDEVKALASLMTCKCAVVGVLFWGAKAGVKISPKYYTNNELEKITRRFTIELAKKG

Parental  FIGPGIDVPAPDMSTGEREMSWIADTYASTIGHYDINAHACVTGKPISQGGIHGRISATGRGVFHGIENF
          FIG.GIDVPAPD.STGE.EMSWIAD.YASTIGHYDINAHACV.GKPISQGGIHGRISATG.GVFHGIENF
Retrocopy FIGCGIDVPAPDKSTGELEMSWIADAYASTIGHYDINAHACVIGKPISQGGIHGRISATGHGVFHGIENF

Parental  INEASYMSILGMTPGFGDKTFVVQGFGNVGLHSMRYLHRFGAKCIAVGESEGSIWNPDGIDPKELEDFKL
          INEASYMSILGMT.GFG.KTF.VQGFGN.GLHSMRYLHRFGAKCIAVGES.GSIWNPDGIDPKELEDFKL
Retrocopy INEASYMSILGMTSGFGGKTFFVQGFGNAGLHSMRYLHRFGAKCIAVGESDGSIWNPDGIDPKELEDFKL

Parental  QHGSILGFPKAKPYEGSILEADCDILIPAASEKQLTKSNAPRVKAKIIAEGANGPTTPEADKIFLERNIM
          QHGSI.GFPK.KPYEGSILE..CDILIPAASEKQL.KSN..RVKAKIIAEG.NGPTTPEADKIFLERNIM
Retrocopy QHGSIVGFPKVKPYEGSILEPYCDILIPAASEKQLSKSNESRVKAKIIAEGDNGPTTPEADKIFLERNIM

Parental  VIPDLYLNAGGVTVSYFEWLKNLNHVSYGRLTFKYERDSNYHLLMSVQESLERKFGKHGGTIPIVPTAEF
          VIPDLY.NAGGVTVSYFEWLKNL.HVSYGRLTFKYER.SNYHL.MSV.E.LERK.GKHGG.IPIVPTAEF
Retrocopy VIPDLYMNAGGVTVSYFEWLKNLKHVSYGRLTFKYERNSNYHLFMSVEETLERKCGKHGGAIPIVPTAEF

Parental  QDRISGASEKDIVHSGLAYTMERSARQIMRTAMKYNL-GLDLRTAAYVNAIEKVFKVYNEAGVTFT
          QDRISGASEKDI.HSGL..TME.SARQIM.TA.KY.L.G.DLR.AAYVN.IEKVFKVYNEAG.TFT
Retrocopy QDRISGASEKDIMHSGLVCTMEHSARQIMHTARKYKL<GMDLRAAAYVNTIEKVFKVYNEAGATFT

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	140.90 RPM
SRP007412_cerebellum	0.00 RPM	104.43 RPM
SRP007412_heart	0.00 RPM	109.18 RPM
SRP007412_kidney	0.00 RPM	315.57 RPM
SRP007412_liver	0.00 RPM	455.56 RPM
SRP007412_testis	0.00 RPM	31.30 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_3290 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_3290 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_3290 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 20 parental genes, and 28 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000007540	2 retrocopies	retro_btau_1413, retro_btau_1741,
Canis familiaris	ENSCAFG00000016095	1 retrocopy	retro_cfam_747,
Choloepus hoffmanni	ENSCHOG00000001101	1 retrocopy	retro_chof_2002,
Callithrix jacchus	ENSCJAG00000011633	1 retrocopy	retro_cjac_2830,
Dipodomys ordii	ENSDORG00000009767	1 retrocopy	retro_dord_400,
Equus caballus	ENSECAG00000007371	2 retrocopies	retro_ecab_886, retro_ecab_919,
Echinops telfairi	ENSETEG00000019638	2 retrocopies	retro_etel_141, retro_etel_2024,
Homo sapiens	ENSG00000148672	1 retrocopy	retro_hsap_31,
Gorilla gorilla	ENSGGOG00000015770	1 retrocopy	retro_ggor_2954,
Loxodonta africana	ENSLAFG00000012059	1 retrocopy	retro_lafr_504,
Microcebus murinus	ENSMICG00000016526	1 retrocopy	retro_mmur_524,
Monodelphis domestica	ENSMODG00000002756	1 retrocopy	retro_mdom_124,
Nomascus leucogenys	ENSNLEG00000011658	1 retrocopy	retro_nleu_36,
Otolemur garnettii	ENSOGAG00000003641	1 retrocopy	retro_ogar_2757,
Procavia capensis	ENSPCAG00000008662	1 retrocopy	retro_pcap_11,
Pongo abelii	ENSPPYG00000002827	3 retrocopies	retro_pabe_3109, retro_pabe_3213, retro_pabe_79,
Pan troglodytes	ENSPTRG00000002711	4 retrocopies	retro_ptro_3162, retro_ptro_3283, retro_ptro_3285, retro_ptro_3290 ,
Ictidomys tridecemlineatus	ENSSTOG00000012843	1 retrocopy	retro_itri_737,
Tarsius syrichta	ENSTSYG00000001578	1 retrocopy	retro_tsyr_313,
Tursiops truncatus	ENSTTRG00000008145	1 retrocopy	retro_ttru_950,