RetrogeneDB ID: retro_ptro_2361

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 6:73367023..73367776(+)
• Located in intron of: ENSPTRG00000018339

Retrocopy information

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

Parental gene information

• Parental gene symbol: PGAM1
• Ensembl ID: ENSPTRG00000002807
• Aliases: None
• Description: Pan troglodytes phosphoglycerate mutase 1 (brain) (PGAM1), mRNA. [Source:RefSeq mRNA;Acc:NM_001246485]

Sequence

>retro_ptro_2361
ATGGCCACCTACAAACTGGTGCAGATCCGGCACAGCGAGAGTGCGTGGAACCTGGAGAACCACTTCAGCGGCTGGTACGA
CGCCATCCTGAGCCCGGCGGGCCATGAGGCGGCAAAGCAGGCACTGTGAGATGCTGGCTATGAGTTTGACATCTGCTTCA
CCTCAGTGCAGAAGAGAGCGATCCCGACCTTCTGGACAGTGCTAGATGCCATTGATCAGATGTAGCTGCCGATAGTGAGG
ACTTGGCGCCTCAATGAGCAGCACTATGGGGCTCTAACCAGTCTCAATAAAGCAGAAACTGCTGCAAAACATAGTGAGGC
CCAGGTGAAGATCTGCAGGTGCTCCTGTGATGTCCCACCACCTCCGATGGAGCCCTACCATCCTTTTTACAGCAACATCA
GTAAGGATCACAGGTATGCAGACCTCACAGAAAATCACCTACCCTCCTGTGAGAGTCTGAAGGACACTATTGCCAGAGCT
CTGCCCTTCTGGAATGAAGAAGTATTTCCCCAGATCAAGGAGGGGAAATGGGTACTGATTGCAGCCCATGGCAACAGCCT
CTGGGGCACTGTCAAGCATCTGAAGGGTCTCTCTGAAGAGGCTATCATGGAGCTGAACCTGCCAACTGGCATTCCCATTG
TCTATGAATTGGACAAGAACTTGAAGCCCATCAAGCCCACGCAGTTCCTAGGGGATGAAGAGACCATGTACAAAGCCATG
GAAGTTGTGGCTGCCCAGGGGAAAGCCAAGAAG

Alignment

ORF - retro_ptro_2361 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.22 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAAYKLVLIRHGESAWNLENRFSGWYDADLSPAGHEEAKRGGQALRDAGYEFDICFTSVQKRAIRTLWTV
          MA.YKLV.IRH.ESAWNLEN.FSGWYDA.LSPAGHE.AK...QAL.DAGYEFDICFTSVQKRAI.T.WTV
Retrocopy MATYKLVQIRHSESAWNLENHFSGWYDAILSPAGHEAAK---QAL*DAGYEFDICFTSVQKRAIPTFWTV

Parental  LDAIDQMWLPVVRTWRLNERHYGGLTGLNKAETAAKHGEAQVKIWRRSYDVPPPPMEPDHPFYSNISKDR
          LDAIDQM.LP.VRTWRLNE.HYG.LT.LNKAETAAKH.EAQVKI.R.S.DVPPPPMEP.HPFYSNISKD.
Retrocopy LDAIDQM*LPIVRTWRLNEQHYGALTSLNKAETAAKHSEAQVKICRCSCDVPPPPMEPYHPFYSNISKDH

Parental  RYADLTEDQLPSCESLKDTIARALPFWNEEIVPQIKEGKRVLIAAHGNSLRGIVKHLEGLSEEAIMELNL
          RYADLTE..LPSCESLKDTIARALPFWNEE..PQIKEGK.VLIAAHGNSL.G.VKHL.GLSEEAIMELNL
Retrocopy RYADLTENHLPSCESLKDTIARALPFWNEEVFPQIKEGKWVLIAAHGNSLWGTVKHLKGLSEEAIMELNL

Parental  PTGIPIVYELDKNLKPIKPMQFLGDEETVRKAMEAVAAQGKAKK
          PTGIPIVYELDKNLKPIKP.QFLGDEET..KAME.VAAQGKAKK
Retrocopy PTGIPIVYELDKNLKPIKPTQFLGDEETMYKAMEVVAAQGKAKK

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	0.20 RPM	300.77 RPM
SRP007412_cerebellum	0.04 RPM	131.31 RPM
SRP007412_heart	0.00 RPM	48.94 RPM
SRP007412_kidney	0.03 RPM	106.59 RPM
SRP007412_liver	0.00 RPM	54.31 RPM
SRP007412_testis	0.00 RPM	23.29 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2361 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2361 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2361 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3488
Gorilla gorilla	retro_ggor_2353
Pongo abelii	retro_pabe_2881

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 48 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000016575	1 retrocopy	retro_cjac_370,
Cavia porcellus	ENSCPOG00000006844	4 retrocopies	retro_cpor_158, retro_cpor_539, retro_cpor_605, retro_cpor_660,
Echinops telfairi	ENSETEG00000002467	1 retrocopy	retro_etel_1595,
Gorilla gorilla	ENSGGOG00000028602	13 retrocopies	retro_ggor_1220, retro_ggor_1500, retro_ggor_1667, retro_ggor_1824, retro_ggor_2061, retro_ggor_2118, retro_ggor_2353, retro_ggor_2849, retro_ggor_3005, retro_ggor_3034, retro_ggor_716, retro_ggor_738, retro_ggor_827,
Loxodonta africana	ENSLAFG00000015979	1 retrocopy	retro_lafr_886,
Macaca mulatta	ENSMMUG00000020027	1 retrocopy	retro_mmul_119,
Monodelphis domestica	ENSMODG00000004242	4 retrocopies	retro_mdom_1342, retro_mdom_1893, retro_mdom_610, retro_mdom_668,
Mustela putorius furo	ENSMPUG00000017045	1 retrocopy	retro_mputfur_1409,
Pan troglodytes	ENSPTRG00000002807	12 retrocopies	retro_ptro_1082, retro_ptro_1580, retro_ptro_1645, retro_ptro_1755, retro_ptro_2080, retro_ptro_2361 , retro_ptro_2889, retro_ptro_2890, retro_ptro_3114, retro_ptro_3238, retro_ptro_634, retro_ptro_714,
Rattus norvegicus	ENSRNOG00000050585	7 retrocopies	retro_rnor_1669, retro_rnor_2241, retro_rnor_2275, retro_rnor_2361, retro_rnor_2568, retro_rnor_691, retro_rnor_703,
Sus scrofa	ENSSSCG00000010517	1 retrocopy	retro_sscr_373,
Ictidomys tridecemlineatus	ENSSTOG00000025955	1 retrocopy	retro_itri_1187,
Drosophila melanogaster	FBgn0014869	1 retrocopy	retro_dmel_57,