RetrogeneDB ID: retro_ptro_204

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 1:133686985..133687707(+)
• Located in intron of: ENSPTRG00000001425

Retrocopy information

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

Parental gene information

• Parental gene symbol: POU5F1
• Ensembl ID: ENSPTRG00000017953
• Aliases: POU5F1, OTF-3, oct-3
• Description: Pan troglodytes POU class 5 homeobox 1 (POU5F1), mRNA. [Source:RefSeq mRNA;Acc:NM_001252041]

Sequence

>retro_ptro_204
GGTGCCGTGAAACTGGAGAAGGAGAAGCTGGAGCAAAACCCGCAGGAGTCCCAGAACATCAAAGCTCTGCAGAAAGAACT
CGAACAATTTGCCAAGCTCCTGAAGCAGAAGAGGATCACCCTGGGATATACACAGGCCGATGTGGGGCTCACCCTGGGGG
TTCTGTTTGGGAAGGTGTTCAGCCAAACGACCATCTGCCGCTTTGAGGCTCTGCAGCTTAGCTTCAAGAACATGTGTAAG
CTGCGGCCCTTGCTGCAGAAGTGGGTGGAGGAAGCTGACAACAATGAAAATCTTCAGGAGACATGCAAAGCAGAAACCCT
CTTGCAGGCCCGAAAGAGAAAGCGAACCAGTATCGAGAATCGAGTGAGAGGCAACCTGGAGAATTTGTTCCTGCAGTGCC
CGAAACCCACACTGCAGCAGATCAGCCACATCGCCCAGCAGCTTGGGCTCGAGAAGGATGTGGTCCGAGTGTGGTTCTGT
AACCGGTGCCAGAAAGGCAAGCAATCAAGCAGCGACTATGCATAACGAGAGGATTTTGAGGCTGCTGGGTCTCCTTTCTC
AGGGGTACCAGTGTCCTTTCCTCTGGCCCCAGGGCCCCATTTTGGTACCCCAGGCTATGGGAGCCCTCACTTCACTGCAC
TGTACTCCTCGGTCCCTTTCCCTGAGGGGGAAGCCTTTCCCCCGTCTCCGTCACCACCCTGGGCTCTCCCATGCATTCAA
AC

Alignment

ORF - retro_ptro_204 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.28 %
• Parental protein coverage: 66.94 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GAVKLEKEKLEQNPEESQDIKALQKELEQFAKLLKQKRITLGYTQADVGLTLGVLFGKVFSQTTICRFEA
          GAVKLEKEKLEQNP.ESQ.IKALQKELEQFAKLLKQKRITLGYTQADVGLTLGVLFGKVFSQTTICRFEA
Retrocopy GAVKLEKEKLEQNPQESQNIKALQKELEQFAKLLKQKRITLGYTQADVGLTLGVLFGKVFSQTTICRFEA

Parental  LQLSFKNMCKLRPLLQKWVEEADNNENLQEICKAETLVQARKRKRTSIENRVRGNLENLFLQCPKPTLQQ
          LQLSFKNMCKLRPLLQKWVEEADNNENLQE.CKAETL.QARKRKRTSIENRVRGNLENLFLQCPKPTLQQ
Retrocopy LQLSFKNMCKLRPLLQKWVEEADNNENLQETCKAETLLQARKRKRTSIENRVRGNLENLFLQCPKPTLQQ

Parental  ISHIAQQLGLEKDVVRVWFCNRRQKGKRSSSDYAQREDFEAAGSPFSGGPVSFPLAPGPHFGTPGYGSPH
          ISHIAQQLGLEKDVVRVWFCNR.QKGK.SSSDYA.REDFEAAGSPFSG.PVSFPLAPGPHFGTPGYGSPH
Retrocopy ISHIAQQLGLEKDVVRVWFCNRCQKGKQSSSDYA*REDFEAAGSPFSGVPVSFPLAPGPHFGTPGYGSPH

Parental  FTALYSSVPFPEGEAFP-PVSVTTLGSPMHSN
          FTALYSSVPFPEGEAFP.PVSVTTLGSPMHSN
Retrocopy FTALYSSVPFPEGEAFP<PVSVTTLGSPMHSN

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	0.11 RPM	1.05 RPM
SRP007412_cerebellum	0.22 RPM	0.79 RPM
SRP007412_heart	0.03 RPM	0.15 RPM
SRP007412_kidney	0.21 RPM	0.76 RPM
SRP007412_liver	0.00 RPM	0.26 RPM
SRP007412_testis	0.00 RPM	0.00 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_204 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_204 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_204 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Gorilla gorilla	retro_ggor_295

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Parental genes homology:

Parental genes homology involve 25 parental genes, and 63 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000010377	3 retrocopies	retro_amel_1057, retro_amel_1213, retro_amel_1616,
Bos taurus	ENSBTAG00000021111	2 retrocopies	retro_btau_1576, retro_btau_951,
Canis familiaris	ENSCAFG00000000485	1 retrocopy	retro_cfam_1538,
Callithrix jacchus	ENSCJAG00000019789	1 retrocopy	retro_cjac_123,
Dipodomys ordii	ENSDORG00000009549	1 retrocopy	retro_dord_65,
Equus caballus	ENSECAG00000008967	1 retrocopy	retro_ecab_301,
Erinaceus europaeus	ENSEEUG00000015357	2 retrocopies	retro_eeur_196, retro_eeur_558,
Felis catus	ENSFCAG00000001078	3 retrocopies	retro_fcat_1372, retro_fcat_1422, retro_fcat_275,
Gorilla gorilla	ENSGGOG00000027662	3 retrocopies	retro_ggor_2275, retro_ggor_295, retro_ggor_852,
Macropus eugenii	ENSMEUG00000013221	3 retrocopies	retro_meug_1146, retro_meug_1475, retro_meug_692,
Microcebus murinus	ENSMICG00000001511	1 retrocopy	retro_mmur_1423,
Myotis lucifugus	ENSMLUG00000011028	3 retrocopies	retro_mluc_1465, retro_mluc_2382, retro_mluc_515,
Mustela putorius furo	ENSMPUG00000001202	2 retrocopies	retro_mputfur_253, retro_mputfur_96,
Mus musculus	ENSMUSG00000024406	2 retrocopies	retro_mmus_2201, retro_mmus_250,
Oryctolagus cuniculus	ENSOCUG00000017160	3 retrocopies	retro_ocun_1175, retro_ocun_1696, retro_ocun_463,
Otolemur garnettii	ENSOGAG00000000621	3 retrocopies	retro_ogar_1406, retro_ogar_1436, retro_ogar_2229,
Ochotona princeps	ENSOPRG00000003926	2 retrocopies	retro_opri_1213, retro_opri_556,
Pongo abelii	ENSPPYG00000017210	3 retrocopies	retro_pabe_2761, retro_pabe_3294, retro_pabe_898,
Pan troglodytes	ENSPTRG00000017953	5 retrocopies	retro_ptro_1798, retro_ptro_204 , retro_ptro_2132, retro_ptro_2721, retro_ptro_733,
Pteropus vampyrus	ENSPVAG00000007334	2 retrocopies	retro_pvam_724, retro_pvam_74,
Rattus norvegicus	ENSRNOG00000046487	4 retrocopies	retro_rnor_1474, retro_rnor_2186, retro_rnor_2968, retro_rnor_921,
Sus scrofa	ENSSSCG00000001393	2 retrocopies	retro_sscr_252, retro_sscr_678,
Ictidomys tridecemlineatus	ENSSTOG00000026103	3 retrocopies	retro_itri_1076, retro_itri_1705, retro_itri_951,
Tupaia belangeri	ENSTBEG00000013044	4 retrocopies	retro_tbel_3628, retro_tbel_3718, retro_tbel_3779, retro_tbel_4614,
Tarsius syrichta	ENSTSYG00000007340	4 retrocopies	retro_tsyr_1508, retro_tsyr_1630, retro_tsyr_814, retro_tsyr_817,