RetrogeneDB ID: retro_ptro_1400

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 20:38269320..38269855(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ADI1
• Ensembl ID: ENSPTRG00000011624
• Aliases: None
• Description: 1,2-dihydroxy-3-keto-5-methylthiopentene dioxygenase [Source:UniProtKB/TrEMBL;Acc:H2R901]

Sequence

>retro_ptro_1400
ATGGTGCAGGCCTAGTACATGGATGAGTTCCCAGACTGCTGGAGGCAGCCCCACCACCCCGAGCCCCTGGCCACCCAGTG
GGCCAGAAACAGCCATGCTGGCTCAGGGTGTACTACTAAAGCTGGACACTGACAAATAAGAGAATGATCCAGAATTAGAA
AAGACTCAAAGAGAGAGAAGCTACTCCTGGATAGACATAATAACCATATGTAAAGATAAATTACCAAATTATGAAGAAAA
GATTAAGGTGTTTTATGAGGAGCATTTACACTTGGATGATCGGATCTGTTACATCCCGGGTGGCAGTGGATACTTTTGAT
ATGACAGATAAAGAGGACAAGTGAATCCACATCTTCATGGAGAAAGGAGACATAACTCTTCCCACAGGAATTCGTCACCA
CCTCACTCTGGATGAAAAGAAGTACGCGAAGGCCATATGGCCATTCAGGGAGACCCAGTGTGGACAGCATACAATGGGCC
AGCTGACCATTTCAATGTCCAGGGACAATACATGAAATTTCTGGCACAGACAGCA

Alignment

ORF - retro_ptro_1400 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.02 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  MVQAWYMDDAPGDPRQ-PHRPDP-GRPVGLEQLRRLGVLY-WKLDADKYENDPELEKIRRERNYSWMDII
          MVQA.YMD..P...RQ.P..P.P.G.PVG..Q...L.V.Y..KLD.DK.ENDPELEK..RER.YSW.DII
Retrocopy MVQA*YMDEFPDCWRQ>PTTPSP>GHPVGQKQPCWLRVYY<LKLDTDK*ENDPELEKTQRERSYSWIDII

Parental  TICKDKLPNYEEKIKMFYEEHLHLDDEIRYILDGSGY-FDVRDKEDQWIRIFMEKGDMITLPAGIYHRFT
          TICKDKLPNYEEKIK.FYEEHLHLDD.I.YI..GSGY.FD..DKED..I.IFMEKGD.ITLP.GI.H..T
Retrocopy TICKDKLPNYEEKIKVFYEEHLHLDDRICYIPGGSGY>FDMTDKEDK*IHIFMEKGD-ITLPTGIRHHLT

Parental  VDEKNYTKAMRLF-VGEPVWTAYNRPADHFEARGQYVKFLAQTA
          .DEK.Y.KA...F..G.PVWTAYN.PADHF...GQY.KFLAQTA
Retrocopy LDEKKYAKAIWPF<QGDPVWTAYNGPADHFNVQGQYMKFLAQTA

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	39.70 RPM
SRP007412_cerebellum	0.00 RPM	32.05 RPM
SRP007412_heart	0.00 RPM	56.95 RPM
SRP007412_kidney	0.00 RPM	152.54 RPM
SRP007412_liver	0.00 RPM	98.56 RPM
SRP007412_testis	0.00 RPM	8.33 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1400 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1400 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1400 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2427
Gorilla gorilla	retro_ggor_1510
Pongo abelii	retro_pabe_1789
Macaca mulatta	retro_mmul_622

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Parental genes homology:

Parental genes homology involve 21 parental genes, and 42 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000018432	2 retrocopies	retro_amel_1306, retro_amel_1350,
Canis familiaris	ENSCAFG00000003257	3 retrocopies	retro_cfam_1764, retro_cfam_554, retro_cfam_603,
Choloepus hoffmanni	ENSCHOG00000010496	8 retrocopies	retro_chof_1146, retro_chof_1212, retro_chof_1800, retro_chof_2067, retro_chof_2163, retro_chof_401, retro_chof_742, retro_chof_748,
Dasypus novemcinctus	ENSDNOG00000007523	3 retrocopies	retro_dnov_181, retro_dnov_1891, retro_dnov_2106,
Equus caballus	ENSECAG00000005765	1 retrocopy	retro_ecab_870,
Echinops telfairi	ENSETEG00000015860	1 retrocopy	retro_etel_1732,
Felis catus	ENSFCAG00000025763	2 retrocopies	retro_fcat_1465, retro_fcat_882,
Homo sapiens	ENSG00000182551	2 retrocopies	retro_hsap_165, retro_hsap_2427,
Gorilla gorilla	ENSGGOG00000034855	2 retrocopies	retro_ggor_1510, retro_ggor_250,
Loxodonta africana	ENSLAFG00000004902	1 retrocopy	retro_lafr_173,
Macaca mulatta	ENSMMUG00000019471	1 retrocopy	retro_mmul_622,
Monodelphis domestica	ENSMODG00000014484	2 retrocopies	retro_mdom_1128, retro_mdom_723,
Nomascus leucogenys	ENSNLEG00000007518	2 retrocopies	retro_nleu_1559, retro_nleu_237,
Oryctolagus cuniculus	ENSOCUG00000000530	1 retrocopy	retro_ocun_1236,
Otolemur garnettii	ENSOGAG00000007668	2 retrocopies	retro_ogar_2871, retro_ogar_535,
Pongo abelii	ENSPPYG00000012683	2 retrocopies	retro_pabe_1789, retro_pabe_463,
Pan troglodytes	ENSPTRG00000011624	2 retrocopies	retro_ptro_1400 , retro_ptro_157,
Pteropus vampyrus	ENSPVAG00000003660	1 retrocopy	retro_pvam_689,
Rattus norvegicus	ENSRNOG00000008950	1 retrocopy	retro_rnor_1316,
Tarsius syrichta	ENSTSYG00000004138	1 retrocopy	retro_tsyr_1271,
Tursiops truncatus	ENSTTRG00000005942	2 retrocopies	retro_ttru_1485, retro_ttru_1562,