RetrogeneDB ID: retro_ptro_337

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 1:123974808..123975181(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PTS
• Ensembl ID: ENSPTRG00000004288
• Aliases: None
• Description: 6-pyruvoyl tetrahydrobiopterin synthase [Source:UniProtKB/TrEMBL;Acc:H2R4Y8]

Sequence

>retro_ptro_337
GGTGCTAGAAGCCATCAAGTGCTAGTGTACAGCCTCCACTCCTTCAGCACTAAGCCACTGGCTGGCACAGCAAATCTCTG
AGTATCAAAGAAAGCATCAAACAGTTTTAGAACTGCAACAATGCAAATGTCCATGAACATGATTATAAAGTTGTAGTTAT
AGCATATGGAGGGATTGATCCAGTTACAGGAATGGTTATGAATATGATCAACCTCATAAAGTAACGGAGGAGGCAATTAT
GAAGCCCCTTGATCATAAGAATCTGGACCTGGATGTACCATACTTTGCAGATGTTACAAGCATGAAAGAAAAGGTAGTTA
GATATATCTGGGGAAACATCCAGAAATTTCTTCCTGTAGAAGTTATTTATAAA

Alignment

ORF - retro_ptro_337 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.84 %
• Parental protein coverage: 85.52 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  GGRRCQAKVSRRISFSA-SHRL-YSKFLSDEENLKLFGKCNNPNGHGHNYKVVVTVHGEIDPATGMVMNL
          G.R..Q..V....SFS..SH.L..SK.LS..E..K.F..CNN.N.H.H.YKVVV...G.IDP.TGMVMN.
Retrocopy GARSHQVLVYSLHSFST>SHWL>HSKSLSIKESIKQF*NCNNANVHEHDYKVVVIAYGGIDPVTGMVMNM

Parental  ADL-KKYMEEAIMQPLDHKNLDMDVPYFADVVSTTENVAVYIWDNLQKVLPVGVLYK
          ..L..K..EEAIM.PLDHKNLD.DVPYFADV.S..E.V..YIW.N.QK.LPV.V.YK
Retrocopy INL<HKVTEEAIMKPLDHKNLDLDVPYFADVTSMKEKVVRYIWGNIQKFLPVEVIYK

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	10.30 RPM
SRP007412_cerebellum	0.00 RPM	3.30 RPM
SRP007412_heart	0.00 RPM	3.03 RPM
SRP007412_kidney	0.00 RPM	6.33 RPM
SRP007412_liver	0.00 RPM	7.89 RPM
SRP007412_testis	0.11 RPM	2.00 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_337 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_337 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_337 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pongo abelii	retro_pabe_432

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000013	2 retrocopies	retro_chof_1925, retro_chof_2556,
Callithrix jacchus	ENSCJAG00000012437	2 retrocopies	retro_cjac_2534, retro_cjac_2853,
Dasypus novemcinctus	ENSDNOG00000014823	1 retrocopy	retro_dnov_1747,
Echinops telfairi	ENSETEG00000008145	2 retrocopies	retro_etel_1924, retro_etel_2039,
Homo sapiens	ENSG00000150787	1 retrocopy	retro_hsap_3408,
Macaca mulatta	ENSMMUG00000015255	1 retrocopy	retro_mmul_995,
Nomascus leucogenys	ENSNLEG00000007299	1 retrocopy	retro_nleu_1856,
Otolemur garnettii	ENSOGAG00000017191	3 retrocopies	retro_ogar_1718, retro_ogar_2790, retro_ogar_609,
Pongo abelii	ENSPPYG00000003880	1 retrocopy	retro_pabe_432,
Pan troglodytes	ENSPTRG00000004288	3 retrocopies	retro_ptro_2315, retro_ptro_2979, retro_ptro_337 ,