RetrogeneDB ID: retro_ptro_371

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 1:177399901..177400367(-)
• Located in intron of: ENSPTRG00000001817

Retrocopy information

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

Parental gene information

• Parental gene symbol: PEBP1
• Ensembl ID: ENSPTRG00000005512
• Aliases: None
• Description: None

Sequence

>retro_ptro_371
GACCTCAGCAAGCGGTCCAGGCCCTTGAGCCTGCAGGAAGTGGATGGGCAGCCGCAGCACTCGCTGCATGTCACCTACGC
CAGGGCGACGGTGGACGAGCTGGGCAAAGTGCTGACGCCCACCTAGGTTAACAGACCCACCAGCATTTCATGGGATGATC
TTGAGTCAAGGAAACTCTACACCTTGGTCCTAACAGACCCGGATGCTCCTGGCAGGAAGAAGCCCCAATACACTGAATGG
CATCATTTCCTGGTGGTCAACATGAAGGGTAATGACGTTAGCAGTGGCCCAGTCCTCTCCATTACGTGGGCTCGGGCCTC
TGGAGGGCACAGATCTCCACCGCTATGTCTGGCTGGTTTACAAACAGGACAGGCTGCTGAAGTGTGACGAGCCCATCCTC
AGCAATGGATCTGGAGGCCACAGTGGCAAATTCAAAATGGCATCCTTCTGTCAAAAGTTCGAGCTT

Alignment

ORF - retro_ptro_371 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.87 %
• Parental protein coverage: 83.96 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  DLSKWSGPLSLQEVDEQPQHPLHVTYAGAAVDELGKVLTPTQVKNRPTSISWDGLDSGKLYTLVLTDPDA
          DLSK.S.PLSLQEVD.QPQH.LHVTYA.A.VDELGKVLTPT.V.NRPTSISWD.L.S.KLYTLVLTDPDA
Retrocopy DLSKRSRPLSLQEVDGQPQHSLHVTYARATVDELGKVLTPT*V-NRPTSISWDDLESRKLYTLVLTDPDA

Parental  PSRKDPKYREWHHFLVVNMKGNDISSGTVLS-DYVGS-GPPKGTGLHRYVWLVYEQDRPLKCDEPILSNR
          P.RK.P.Y.EWHHFLVVNMKGND.SSG.VLS..YVGS.GP..GT.LHRYVWLVY.QDR.LKCDEPILSN.
Retrocopy PGRKKPQYTEWHHFLVVNMKGNDVSSGPVLS<HYVGS<GPLEGTDLHRYVWLVYKQDRLLKCDEPILSNG

Parental  SGDHRGKFKVASFRKKYEL
          SG.H.GKFK.ASF..K.EL
Retrocopy SGGHSGKFKMASFCQKFEL

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	967.79 RPM
SRP007412_cerebellum	0.00 RPM	617.46 RPM
SRP007412_heart	0.06 RPM	390.50 RPM
SRP007412_kidney	0.05 RPM	1086.63 RPM
SRP007412_liver	0.00 RPM	478.02 RPM
SRP007412_testis	0.11 RPM	174.94 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_371 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_371 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_371 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_492
Gorilla gorilla	retro_ggor_461

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Parental genes homology:

Parental genes homology involve 20 parental genes, and 51 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016143	2 retrocopies	retro_amel_1355, retro_amel_754,
Bos taurus	ENSBTAG00000018115	2 retrocopies	retro_btau_1183, retro_btau_705,
Canis familiaris	ENSCAFG00000009910	1 retrocopy	retro_cfam_526,
Callithrix jacchus	ENSCJAG00000009314	2 retrocopies	retro_cjac_1410, retro_cjac_818,
Erinaceus europaeus	ENSEEUG00000003689	1 retrocopy	retro_eeur_292,
Felis catus	ENSFCAG00000002277	3 retrocopies	retro_fcat_1317, retro_fcat_1360, retro_fcat_299,
Homo sapiens	ENSG00000089220	3 retrocopies	retro_hsap_1456, retro_hsap_2288, retro_hsap_492,
Gorilla gorilla	ENSGGOG00000013281	3 retrocopies	retro_ggor_1121, retro_ggor_1701, retro_ggor_461,
Myotis lucifugus	ENSMLUG00000002259	7 retrocopies	retro_mluc_103, retro_mluc_1612, retro_mluc_1742, retro_mluc_2357, retro_mluc_2373, retro_mluc_984, retro_mluc_998,
Macaca mulatta	ENSMMUG00000005098	4 retrocopies	retro_mmul_1621, retro_mmul_2272, retro_mmul_328, retro_mmul_442,
Mustela putorius furo	ENSMPUG00000002861	3 retrocopies	retro_mputfur_1228, retro_mputfur_1361, retro_mputfur_223,
Mus musculus	ENSMUSG00000032959	4 retrocopies	retro_mmus_138, retro_mmus_1857, retro_mmus_2314, retro_mmus_542,
Oryctolagus cuniculus	ENSOCUG00000008395	2 retrocopies	retro_ocun_1329, retro_ocun_1900,
Otolemur garnettii	ENSOGAG00000001740	1 retrocopy	retro_ogar_2750,
Pongo abelii	ENSPPYG00000005011	2 retrocopies	retro_pabe_1202, retro_pabe_241,
Pan troglodytes	ENSPTRG00000005512	3 retrocopies	retro_ptro_1621, retro_ptro_371 , retro_ptro_992,
Rattus norvegicus	ENSRNOG00000001136	3 retrocopies	retro_rnor_1223, retro_rnor_46, retro_rnor_541,
Ictidomys tridecemlineatus	ENSSTOG00000004085	2 retrocopies	retro_itri_1603, retro_itri_961,
Tupaia belangeri	ENSTBEG00000000177	2 retrocopies	retro_tbel_272, retro_tbel_2728,
Tursiops truncatus	ENSTTRG00000000658	1 retrocopy	retro_ttru_1164,