RetrogeneDB ID: retro_ptro_556

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 11:78810355..78810643(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: COX6A1
• Ensembl ID: ENSPTRG00000005532
• Aliases: None
• Description: cytochrome c oxidase subunit VIa polypeptide 1 [Source:HGNC Symbol;Acc:2277]

Sequence

>retro_ptro_556
AGTCATCCCCAGAGCTGGGGGCCTCTGTTGAGTGGTGCCCAAGGCAAGGAGGGCTCAGCTCGCCTATGGAATGCCCTCAT
CTACTGTGTGGCTCCTGGGATGGGACTGAGCTTGCTAAATGTGTTCCTGAAGTCGCACCACAGAGAGCATGAGAGGCCCG
AGTTCATTGAGTTCATTGCCTACTCTCATCTCCCGATCAAGTTCAAGTCCTTTCCCTGCAGAGATGGTAACCACACTTTA
TTCCATAACCTTCATGTGAATCGGCCTCCAACTAGCTATGAAAGTGAA

Alignment

ORF - retro_ptro_556 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.89 %
• Parental protein coverage: 86.24 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SRPQLGRPMSSGAHGEEGSARMWKTLTFFVALPGVAVSMLNVYLKSHHGEHERP---EFIAYPHLRIRTK
          S.PQ...P..SGA.G.EGSAR.W..L...VA.PG...S.LNV.LKSHH.EHERP...EFIAY.HL.I..K
Retrocopy SHPQSWGPLLSGAQGKEGSARLWNALIYCVA-PGMGLSLLNVFLKSHHREHERPEFIEFIAYSHLPIKFK

Parental  PFPWGDGNHTLFHNPHVNPLPTGYEDE
          .FP..DGNHTLFHN.HVN..PT.YE.E
Retrocopy SFPCRDGNHTLFHNLHVNRPPTSYESE

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	186.88 RPM
SRP007412_cerebellum	0.00 RPM	75.78 RPM
SRP007412_heart	0.00 RPM	15.24 RPM
SRP007412_kidney	0.00 RPM	144.67 RPM
SRP007412_liver	0.00 RPM	116.44 RPM
SRP007412_testis	0.00 RPM	38.25 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_556 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_556 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_556 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Callithrix jacchus	retro_cjac_912

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Parental genes homology:

Parental genes homology involve 22 parental genes, and 74 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000012788	1 retrocopy	retro_btau_229,
Canis familiaris	ENSCAFG00000031458	1 retrocopy	retro_cfam_506,
Choloepus hoffmanni	ENSCHOG00000009222	2 retrocopies	retro_chof_2085, retro_chof_2579,
Cavia porcellus	ENSCPOG00000006426	1 retrocopy	retro_cpor_1265,
Equus caballus	ENSECAG00000012512	2 retrocopies	retro_ecab_578, retro_ecab_845,
Echinops telfairi	ENSETEG00000016826	1 retrocopy	retro_etel_1482,
Felis catus	ENSFCAG00000031188	9 retrocopies	retro_fcat_1049, retro_fcat_1399, retro_fcat_1505, retro_fcat_1518, retro_fcat_1653, retro_fcat_1891, retro_fcat_318, retro_fcat_753, retro_fcat_886,
Homo sapiens	ENSG00000111775	1 retrocopy	retro_hsap_25,
Gorilla gorilla	ENSGGOG00000014101	2 retrocopies	retro_ggor_176, retro_ggor_2527,
Myotis lucifugus	ENSMLUG00000010330	4 retrocopies	retro_mluc_1127, retro_mluc_1405, retro_mluc_1879, retro_mluc_465,
Macaca mulatta	ENSMMUG00000016000	2 retrocopies	retro_mmul_127, retro_mmul_2535,
Nomascus leucogenys	ENSNLEG00000015644	4 retrocopies	retro_nleu_1116, retro_nleu_412, retro_nleu_484, retro_nleu_985,
Oryctolagus cuniculus	ENSOCUG00000009873	6 retrocopies	retro_ocun_1320, retro_ocun_1668, retro_ocun_1700, retro_ocun_174, retro_ocun_1898, retro_ocun_1928,
Otolemur garnettii	ENSOGAG00000003561	18 retrocopies	retro_ogar_1068, retro_ogar_111, retro_ogar_1150, retro_ogar_1466, retro_ogar_188, retro_ogar_1904, retro_ogar_2063, retro_ogar_2312, retro_ogar_2933, retro_ogar_3021, retro_ogar_3106, retro_ogar_3190, retro_ogar_3227, retro_ogar_3240, retro_ogar_346, retro_ogar_852, retro_ogar_871, retro_ogar_872,
Pongo abelii	ENSPPYG00000005028	4 retrocopies	retro_pabe_2905, retro_pabe_3087, retro_pabe_3206, retro_pabe_713,
Pan troglodytes	ENSPTRG00000005532	3 retrocopies	retro_ptro_311, retro_ptro_54, retro_ptro_556 ,
Pteropus vampyrus	ENSPVAG00000002226	3 retrocopies	retro_pvam_1060, retro_pvam_790, retro_pvam_910,
Rattus norvegicus	ENSRNOG00000001170	2 retrocopies	retro_rnor_2581, retro_rnor_2680,
Tupaia belangeri	ENSTBEG00000008018	4 retrocopies	retro_tbel_2490, retro_tbel_3010, retro_tbel_3167, retro_tbel_395,
Tarsius syrichta	ENSTSYG00000011541	1 retrocopy	retro_tsyr_1025,
Tursiops truncatus	ENSTTRG00000000142	2 retrocopies	retro_ttru_1873, retro_ttru_889,
Vicugna pacos	ENSVPAG00000010359	1 retrocopy	retro_vpac_218,