RetrogeneDB ID: retro_ptro_3280

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: X:156667372..156668364(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: AMD1
• Ensembl ID: ENSPTRG00000018501
• Aliases: None
• Description: S-adenosylmethionine decarboxylase proenzyme [Source:UniProtKB/TrEMBL;Acc:H2QTK1]

Sequence

>retro_ptro_3280
ATGGAAGCTGCAAAATTTTTTGAAGGGACCAAGAAGCTGCTGAAGGTTTGGTTCTCCTGGTAGCAGCCTGATACAAACGA
AGGATGTGGGGATCTTAGCAGTATTCCAAGATCTGAGTGGGACATATTTTTGAAGGATGTGTAATGTTCAATCATATGTG
TGACAAAAACTGACAAGCAGGAAGCTTATGTACTCAGTGAGAGTAGCATATTTGTCTCCAAGAGACGTTTCATTTTGAAG
ACATGTGGTACCACCCTCTTGCTGAAAGCACTGGTTCCCCTGCCGAAGCTTGCTGGGGATTACAGTGGGTTTGACTCTAT
TCAAAGCTTCTTTTATTCTCATAAGAATTTCATTAAGCCTTTTCACCAAGGGTACCCTAACCAGAATTTCCAGAAAGACA
TAGAGTTTCTTAATGCAGTTTTCCCAAATGGAGCAGCATATTGTATGGGATATATGAATTCTGACTGTTAGTACTTATAT
ACTCTGGAGTTCCCAGAGAGTTGGGTAATCAGTCAGCCAGATCAAACCCTGGAAATTCTGATGAAGTGAACTTGACCCAG
CAGTTACGGACCAGTTCTACGTGAAAGATGGTGTTACTGCAAAGAATGTCACTCATGAGAGTGGAATTTGTGACCTGATT
CCAGGTTCTGTCACTGATGACACAATATTTAATCCTTTTGAGCATTTGATAAATGGAATGAAATCAGACAAAACTTATTA
TTCACATCGCTCCAGAACCAGAATCCTCTTATGTTAGCTTTGAAACAAACTTAAGTCAGACCTCCTATGATGACCTGATC
AGAAAAGTTGTGGAACTCTTTAAGCGAGGAAAATTTGTGACGACGTTGTATGTTATTTAGAGGTCTAAATGTTGCACAGT
GCTTTCTTTGCCCCAGAAGATTTAAGGTTTTAAGTGTCTTGATTGTCAGAGTGCTATGTTCAATGATTACAATTTTGTTT
TTACCTGTTTTGCTAAAAATTTGCAACAGCAA

Alignment

ORF - retro_ptro_3280 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.64 %
• Parental protein coverage: 99.4 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MEAAHFFEGTEKLLEVWFSRQQPDANQGSGDLRTIPRSEWDILLKDVQCSIISVTKTDKQEAYVLSESSM
          MEAA.FFEGT.KLL.VWFS..QPD.N.G.GDL..IPRSEWDI.LKDV.CSII.VTKTDKQEAYVLSESS.
Retrocopy MEAAKFFEGTKKLLKVWFSW*QPDTNEGCGDLSSIPRSEWDIFLKDV*CSIICVTKTDKQEAYVLSESSI

Parental  FVSKRRFILKTCGTTLLLKALVPLLKLARDYSGFDSIQSFFYSRKNFMKPSHQGYPHRNFQEEIEFLNAI
          FVSKRRFILKTCGTTLLLKALVPL.KLA.DYSGFDSIQSFFYS.KNF.KP.HQGYP..NFQ..IEFLNA.
Retrocopy FVSKRRFILKTCGTTLLLKALVPLPKLAGDYSGFDSIQSFFYSHKNFIKPFHQGYPNQNFQKDIEFLNAV

Parental  FPNGAAYCMGRMNSDCWYLYTLDFPESRVISQPDQTLEILM-SELDPAVMDQFYMKDGVTAKDVTRESGI
          FPNGAAYCMG.MNSDC.YLYTL.FPES.VISQPDQTLEILM.SELDPAV.DQFY.KDGVTAK.VT.ESGI
Retrocopy FPNGAAYCMGYMNSDC*YLYTLEFPESWVISQPDQTLEILM>SELDPAVTDQFYVKDGVTAKNVTHESGI

Parental  RDLIPGSVIDATMFNPCGYSMNGMKSDGTYWT-IHITPEPEFSYVSFETNLSQTSYDDLIRKVVEVFKPG
          .DLIPGSV.D.T.FNP.....NGMKSD.TY...I...PE.....VSFETNLSQTSYDDLIRKVVE.FK.G
Retrocopy CDLIPGSVTDDTIFNPFEHLINGMKSDKTYYS>IAPEPESSY--VSFETNLSQTSYDDLIRKVVELFKRG

Parental  KFVTTLFVNQSSKCRTVLASPQKIEGFKRLDCQSAMFNDYNFVFTSFAKKQQQQ
          KFVTTL.V...SKC.TVL..PQKI.GFK.LDCQSAMFNDYNFVFT.FAK..QQQ
Retrocopy KFVTTLYVI*RSKCCTVLSLPQKI*GFKCLDCQSAMFNDYNFVFTCFAKNLQQQ

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	0.04 RPM	47.26 RPM
SRP007412_cerebellum	0.04 RPM	44.63 RPM
SRP007412_heart	0.03 RPM	33.84 RPM
SRP007412_kidney	0.00 RPM	50.08 RPM
SRP007412_liver	0.00 RPM	23.40 RPM
SRP007412_testis	0.00 RPM	32.67 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_3280 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_3280 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_3280 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4917
Gorilla gorilla	retro_ggor_3070
Pongo abelii	retro_pabe_3826
Macaca mulatta	retro_mmul_2648

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Parental genes homology:

Parental genes homology involve 23 parental genes, and 87 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000003500	1 retrocopy	retro_amel_797,
Bos taurus	ENSBTAG00000003342	1 retrocopy	retro_btau_1545,
Canis familiaris	ENSCAFG00000003905	2 retrocopies	retro_cfam_1526, retro_cfam_2056,
Choloepus hoffmanni	ENSCHOG00000009171	9 retrocopies	retro_chof_1327, retro_chof_2200, retro_chof_238, retro_chof_2691, retro_chof_332, retro_chof_425, retro_chof_628, retro_chof_74, retro_chof_968,
Callithrix jacchus	ENSCJAG00000005257	6 retrocopies	retro_cjac_1600, retro_cjac_1738, retro_cjac_2452, retro_cjac_3020, retro_cjac_631, retro_cjac_850,
Dasypus novemcinctus	ENSDNOG00000006867	10 retrocopies	retro_dnov_1736, retro_dnov_1796, retro_dnov_185, retro_dnov_2436, retro_dnov_2653, retro_dnov_315, retro_dnov_357, retro_dnov_63, retro_dnov_752, retro_dnov_770,
Equus caballus	ENSECAG00000011198	4 retrocopies	retro_ecab_1110, retro_ecab_173, retro_ecab_57, retro_ecab_681,
Felis catus	ENSFCAG00000028033	1 retrocopy	retro_fcat_1175,
Homo sapiens	ENSG00000123505	5 retrocopies	retro_hsap_3315, retro_hsap_3630, retro_hsap_3922, retro_hsap_4917, retro_hsap_547,
Gorilla gorilla	ENSGGOG00000006466	5 retrocopies	retro_ggor_1304, retro_ggor_2448, retro_ggor_2640, retro_ggor_3070, retro_ggor_498,
Loxodonta africana	ENSLAFG00000013203	2 retrocopies	retro_lafr_1040, retro_lafr_770,
Macropus eugenii	ENSMEUG00000010630	1 retrocopy	retro_meug_1558,
Myotis lucifugus	ENSMLUG00000005666	4 retrocopies	retro_mluc_1675, retro_mluc_1687, retro_mluc_2625, retro_mluc_538,
Macaca mulatta	ENSMMUG00000000535	6 retrocopies	retro_mmul_1606, retro_mmul_1742, retro_mmul_1841, retro_mmul_2076, retro_mmul_2383, retro_mmul_2648,
Mus musculus	ENSMUSG00000075232	1 retrocopy	retro_mmus_47,
Nomascus leucogenys	ENSNLEG00000012818	4 retrocopies	retro_nleu_2758, retro_nleu_2983, retro_nleu_720, retro_nleu_812,
Otolemur garnettii	ENSOGAG00000030150	7 retrocopies	retro_ogar_1108, retro_ogar_1152, retro_ogar_1608, retro_ogar_1962, retro_ogar_3163, retro_ogar_354, retro_ogar_366,
Pongo abelii	ENSPPYG00000016924	4 retrocopies	retro_pabe_2977, retro_pabe_3194, retro_pabe_3826, retro_pabe_505,
Pan troglodytes	ENSPTRG00000018501	5 retrocopies	retro_ptro_2157, retro_ptro_2453, retro_ptro_2667, retro_ptro_3280 , retro_ptro_411,
Rattus norvegicus	ENSRNOG00000000585	1 retrocopy	retro_rnor_1050,
Sorex araneus	ENSSARG00000014387	3 retrocopies	retro_sara_274, retro_sara_614, retro_sara_760,
Sus scrofa	ENSSSCG00000004392	1 retrocopy	retro_sscr_1042,
Ictidomys tridecemlineatus	ENSSTOG00000000205	4 retrocopies	retro_itri_1402, retro_itri_1859, retro_itri_598, retro_itri_943,