RetrogeneDB ID: retro_ptro_2286

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 5:110312572..110313004(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PGAM5
• Ensembl ID: ENSPTRG00000005657
• Aliases: None
• Description: Phosphoglycerate mutase family member 5 [Source:UniProtKB/TrEMBL;Acc:K7DH40]

Sequence

>retro_ptro_2286
GCTGGCACAGTGGGGAAGCCGCGCGCAGCCGAGCCGCGGGCCTGGGCGTGGGGCACGCGGCCGAGCCTCAGCGTCTGGGA
CCCCGACCGGGACAGGCAAGAACCACTGTCTCTGAACAACCTAAGGAAGAGGAACGTGGAATCTGGAGAAGAGCTGGCTT
CCAGGCTGGACCACTGCAGAGTCAAGGCCACAGGGCACACCCTCCTCGTCATGCGTTCCCAATACCATGTGGACGGCTCC
CTGGAAAAGGACTGCAGTCTGAACCCACCGGGTCGTGAACAGGTCGAACTAACTGGACTCCGACTTGCAAGCTTGGGGTT
GAGGTTTAATAAAATCGTGCATTCCTCCATGACCCACCCCACAGAAACCACTGGCTTCAGCAACAGGCACCCGCCAAGGG
TCTTCAAAGGCCGCACAGACCTGGGGCGGGAA

Alignment

ORF - retro_ptro_2286 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.28 %
• Parental protein coverage: 51.6 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AGGDAEPRPAEPPAWAGGARPGPGVWDPNWDRREPLSLINVRKRNVESGEEELASKLDHYKAKATRHIFL
          AG....PR.AEP.AWA.G.RP...VWDP..DR.EPLSL.N.RKRNVESGEE.LAS.LDH...KAT.H..L
Retrocopy AGTVGKPRAAEPRAWAWGTRPSLSVWDPDRDRQEPLSLNNLRKRNVESGEE-LASRLDHCRVKATGHTLL

Parental  IRHSQYHVDGSLEKDRTLTPLGREQAELTGLRLASLGLKFNKIVHSSMTRAIETTDIISRHLPGVCKVST
          ...SQYHVDGSLEKD..L.P.GREQ.ELTGLRLASLGL.FNKIVHSSMT...ETT....RH.P.V.K..T
Retrocopy VMRSQYHVDGSLEKDCSLNPPGREQVELTGLRLASLGLRFNKIVHSSMTHPTETTGFSNRHPPRVFKGRT

Parental  DLLRE
          DL.RE
Retrocopy DLGRE

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	12.91 RPM
SRP007412_cerebellum	0.00 RPM	13.87 RPM
SRP007412_heart	0.00 RPM	7.17 RPM
SRP007412_kidney	0.00 RPM	12.92 RPM
SRP007412_liver	0.03 RPM	17.19 RPM
SRP007412_testis	2.85 RPM	12.22 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2286 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2286 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2286 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3363
Macaca mulatta	retro_mmul_2101

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000013437	2 retrocopies	retro_amel_1052, retro_amel_173,
Choloepus hoffmanni	ENSCHOG00000011867	2 retrocopies	retro_chof_1762, retro_chof_2590,
Felis catus	ENSFCAG00000002503	2 retrocopies	retro_fcat_800, retro_fcat_960,
Homo sapiens	ENSG00000247077	1 retrocopy	retro_hsap_3363,
Myotis lucifugus	ENSMLUG00000013646	1 retrocopy	retro_mluc_1270,
Macaca mulatta	ENSMMUG00000015466	1 retrocopy	retro_mmul_2101,
Mustela putorius furo	ENSMPUG00000002639	1 retrocopy	retro_mputfur_684,
Pan troglodytes	ENSPTRG00000005657	1 retrocopy	retro_ptro_2286 ,
Rattus norvegicus	ENSRNOG00000037443	1 retrocopy	retro_rnor_1597,
Sus scrofa	ENSSSCG00000026764	1 retrocopy	retro_sscr_821,
Tursiops truncatus	ENSTTRG00000010653	1 retrocopy	retro_ttru_208,