RetrogeneDB ID: retro_pabe_1258

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 15:62101770..62102358(+)
• Located in intron of: ENSPPYG00000006558

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMEM126A
• Ensembl ID: ENSPPYG00000003739
• Aliases: None
• Description: Transmembrane protein 126A [Source:UniProtKB/Swiss-Prot;Acc:Q5RAY9]

Sequence

>retro_pabe_1258
ATGGAAAATCATAAATCCAATACTATCAAGGAAAACTTAACAATCTTTGATATCATAACCAGAAAAATTAACCACCTTCC
ACAAGCAGAAAGGAATCTACCTGAAGAGGGATCAGCTTACGTTGGATTTAATGCTCTCTGTGGCCTCATAGCAAATAGTC
TTTTTCAATGCGTCTTGAACATGACACAGGCTCTTATAGCTGCTGGCTTACCAATGGCAGTGATCCCTTTTCTTACAACA
AACACAGCTTACAAGAGTTTTGTAAGTTTTCCTTCAAATACAGGTCATTTGAATTGTGAAACCTGTACCATAACACAGAC
TGGATTGGTTGGTCTTGCTTTTGGTGGTCTATACCCTGTTTTCTTGTCTATACCTGTGACTGGAGGCCTAGCAGCCTGAT
ATGAATCAACTCTGTTACCAGAGAAAGGGAACATCTTAAATTACTGGATTCAAATTTACAAGCCTGTCTTTAGAAAGATG
TTATTTCCTATTGTGTTCCAGACTGTGTTTGCAGCATACCTTGGGTTTAAACAACATAAACTACTTCTAAAGGCCCTTCA
GTTACCTGAACCTGGCAGAGAAATTCAT

Alignment

ORF - retro_pabe_1258 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.1 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MENHKSNNTKENITIVDI-SRKINQLPEAERNLLEHGSVYVGLNAALCGLIANSLFRRILNVTKARIAAG
          MENHKSN..KEN.TI.DI..RKIN.LP.AERNL.E.GS.YVG.N.ALCGLIANSLF...LN.T.A.IAAG
Retrocopy MENHKSNTIKENLTIFDIITRKINHLPQAERNLPEEGSAYVGFN-ALCGLIANSLFQCVLNMTQALIAAG

Parental  LPMAWIPFLTTDITYRCFVSFPLNTGDLDCETCTITRSGLIGLVIGGLYPVFLAIPVNGGLAARYQSALL
          LPMA.IPFLTT...Y..FVSFP.NTG.L.CETCTIT..GL.GL..GGLYPVFL.IPV.GGLAA.Y.S.LL
Retrocopy LPMAVIPFLTTNTAYKSFVSFPSNTGHLNCETCTITQTGLVGLAFGGLYPVFLSIPVTGGLAA*YESTLL

Parental  PHKGNILSYWIRTSKPVFRKMLFPIMLQTMFSAYLGSEQYKLLIKALQLSEPGKEIH
          P.KGNIL.YWI...KPVFRKMLFPI..QT.F.AYLG..Q.KLL.KALQL.EPG.EIH
Retrocopy PEKGNILNYWIQIYKPVFRKMLFPIVFQTVFAAYLGFKQHKLLLKALQLPEPGREIH

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	13.27 RPM
SRP007412_cerebellum	0.12 RPM	20.19 RPM
SRP007412_heart	0.00 RPM	31.28 RPM
SRP007412_kidney	0.00 RPM	18.89 RPM
SRP007412_liver	0.00 RPM	14.38 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1258 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1258 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1258 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1510
Pan troglodytes	retro_ptro_1022
Gorilla gorilla	retro_ggor_1157
Macaca mulatta	retro_mmul_2146

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Parental genes homology:

Parental genes homology involve 28 parental genes, and 80 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000008703	2 retrocopies	retro_amel_358, retro_amel_422,
Bos taurus	ENSBTAG00000000451	2 retrocopies	retro_btau_1849, retro_btau_223,
Canis familiaris	ENSCAFG00000030913	1 retrocopy	retro_cfam_725,
Callithrix jacchus	ENSCJAG00000014466	1 retrocopy	retro_cjac_4040,
Dasypus novemcinctus	ENSDNOG00000004391	7 retrocopies	retro_dnov_1741, retro_dnov_2634, retro_dnov_2676, retro_dnov_484, retro_dnov_549, retro_dnov_951, retro_dnov_984,
Dipodomys ordii	ENSDORG00000006408	2 retrocopies	retro_dord_120, retro_dord_656,
Erinaceus europaeus	ENSEEUG00000009105	3 retrocopies	retro_eeur_24, retro_eeur_340, retro_eeur_615,
Echinops telfairi	ENSETEG00000007180	2 retrocopies	retro_etel_1693, retro_etel_667,
Felis catus	ENSFCAG00000027606	3 retrocopies	retro_fcat_1015, retro_fcat_1320, retro_fcat_48,
Homo sapiens	ENSG00000171202	2 retrocopies	retro_hsap_1510, retro_hsap_3306,
Gorilla gorilla	ENSGGOG00000027742	2 retrocopies	retro_ggor_1157, retro_ggor_1308,
Macropus eugenii	ENSMEUG00000011625	1 retrocopy	retro_meug_1914,
Microcebus murinus	ENSMICG00000005510	3 retrocopies	retro_mmur_1382, retro_mmur_941, retro_mmur_956,
Myotis lucifugus	ENSMLUG00000005896	3 retrocopies	retro_mluc_1150, retro_mluc_1290, retro_mluc_1951,
Macaca mulatta	ENSMMUG00000016542	2 retrocopies	retro_mmul_2073, retro_mmul_2146,
Mustela putorius furo	ENSMPUG00000009968	2 retrocopies	retro_mputfur_1077, retro_mputfur_720,
Mus musculus	ENSMUSG00000030615	3 retrocopies	retro_mmus_1431, retro_mmus_1531, retro_mmus_3555,
Nomascus leucogenys	ENSNLEG00000016408	2 retrocopies	retro_nleu_1751, retro_nleu_2500,
Oryctolagus cuniculus	ENSOCUG00000016534	1 retrocopy	retro_ocun_1120,
Otolemur garnettii	ENSOGAG00000005403	12 retrocopies	retro_ogar_1020, retro_ogar_2016, retro_ogar_2083, retro_ogar_2118, retro_ogar_2379, retro_ogar_26, retro_ogar_2825, retro_ogar_2883, retro_ogar_3054, retro_ogar_3385, retro_ogar_661, retro_ogar_787,
Pongo abelii	ENSPPYG00000003739	2 retrocopies	retro_pabe_1258 , retro_pabe_2726,
Pan troglodytes	ENSPTRG00000004134	2 retrocopies	retro_ptro_1022, retro_ptro_2165,
Pteropus vampyrus	ENSPVAG00000006197	2 retrocopies	retro_pvam_1411, retro_pvam_254,
Rattus norvegicus	ENSRNOG00000022748	3 retrocopies	retro_rnor_1706, retro_rnor_2844, retro_rnor_918,
Ictidomys tridecemlineatus	ENSSTOG00000016101	2 retrocopies	retro_itri_108, retro_itri_165,
Tupaia belangeri	ENSTBEG00000009157	5 retrocopies	retro_tbel_3441, retro_tbel_3720, retro_tbel_3785, retro_tbel_4072, retro_tbel_4111,
Tarsius syrichta	ENSTSYG00000009071	6 retrocopies	retro_tsyr_1371, retro_tsyr_1457, retro_tsyr_1934, retro_tsyr_580, retro_tsyr_735, retro_tsyr_974,
Tursiops truncatus	ENSTTRG00000012008	2 retrocopies	retro_ttru_1091, retro_ttru_415,