RetrogeneDB ID: retro_ptro_1825

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 3:134293946..134294639(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GSTO1
• Ensembl ID: ENSPTRG00000002925
• Aliases: None
• Description: glutathione S-transferase omega-1 [Source:RefSeq peptide;Acc:NP_001233486]

Sequence

>retro_ptro_1825
ATGTTAGAGGACTCAGCCAGGAGCCTGGGGAAGGGAAGCACGCCCCTGGGGCTGGTCCCAGAGGGGCTGATCTGCATCTG
CAGCATGAGGTTCTGCCCGTTTGCTGAGAAGACGCGTCTGGTTCTGAAGGCCGAGGGAATCAGGTATGAAGTCATCTATA
TCAACCTGAAAGATAAGCCTGAGTGGTTCTTTAAGAAAAATCCCTTTAGTTTGGTGCCAGTTCTGGAAAACAGTCAGGGT
CAGCTGATCTACGAGCCTGCCATCACCTGTGAGTACCTGGATGAAGCATACTCAGGGAAGAAGCTGTTGCCGGATGACCC
CTATGAGAAAGCTTGCCAGAAGATGGTCTTTGAGTTGTTTTCTAAGGTGCCATCTTTGGTAGGAAGCTTCCTTAGAACCC
AAAATAAGGAAGACGGTGCTGGCCTGAAAGAAGCATTGTGTAAAGAATTTAGCAAGCTAGAGGAGGTTCTGATTAATAAG
AAGACAACCTTCTTTGGTGGCAATTCCGTCTCTATGATTGACTATGTCATCTGGCCCTCGTTTGAACGGCTGGAAGCAAT
GAAGTTAAATGAGTGTGTAGACCACACTCCAGAACTTAAACTGTGGATGGCAGCCATGAGGGAAGATCCCACAGTCTCAG
CCCTGCTCACTGGTGTGAAGGACTGGCAAGGTTTCACAGAGCTCTACTTACAG

Alignment

ORF - retro_ptro_1825 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.98 %
• Parental protein coverage: 95.85 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSGESARSLGKGSAPPGPVPEGSIRVYSMRFCPFAERTRLVLKAKGIRHEVININLKNKPEWFFKKNPFG
          M...SARSLGKGS.P.G.VPEG.I...SMRFCPFAE.TRLVLKA.GIR.EVI.INLK.KPEWFFKKNPF.
Retrocopy MLEDSARSLGKGSTPLGLVPEGLICICSMRFCPFAEKTRLVLKAEGIRYEVIYINLKDKPEWFFKKNPFS

Parental  LVPVLENSQGQLIYESAITCEYLDEAYPGKKLLPDDPYEKACQKMILELFSKVPSLVGSFIRSQNKEDYA
          LVPVLENSQGQLIYE.AITCEYLDEAY.GKKLLPDDPYEKACQKM..ELFSKVPSLVGSF.R.QNKED.A
Retrocopy LVPVLENSQGQLIYEPAITCEYLDEAYSGKKLLPDDPYEKACQKMVFELFSKVPSLVGSFLRTQNKEDGA

Parental  GLKEEFRKEFTKLEEVLTNKTTTFFGGNSISMIDYLIWPWFERLEAMKLNECVDHTPKLKLWMAAMKEDP
          GLKE...KEF.KLEEVL.NK.TTFFGGNS.SMIDY.IWP.FERLEAMKLNECVDHTP.LKLWMAAM.EDP
Retrocopy GLKEALCKEFSKLEEVLINKKTTFFGGNSVSMIDYVIWPSFERLEAMKLNECVDHTPELKLWMAAMREDP

Parental  TVSALLTSEKDWQGFLELYLQ
          TVSALLT..KDWQGF.ELYLQ
Retrocopy TVSALLTGVKDWQGFTELYLQ

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	0.04 RPM	50.58 RPM
SRP007412_cerebellum	0.00 RPM	19.14 RPM
SRP007412_heart	0.00 RPM	38.21 RPM
SRP007412_kidney	0.03 RPM	65.61 RPM
SRP007412_liver	0.07 RPM	113.10 RPM
SRP007412_testis	0.21 RPM	2.85 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1825 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1825 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1825 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2704
Pongo abelii	retro_pabe_2256

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000018474	1 retrocopy	retro_cjac_295,
Echinops telfairi	ENSETEG00000017967	1 retrocopy	retro_etel_1413,
Homo sapiens	ENSG00000148834	1 retrocopy	retro_hsap_2704,
Gorilla gorilla	ENSGGOG00000005064	1 retrocopy	retro_ggor_24,
Macaca mulatta	ENSMMUG00000015334	1 retrocopy	retro_mmul_142,
Nomascus leucogenys	ENSNLEG00000015358	1 retrocopy	retro_nleu_1577,
Pongo abelii	ENSPPYG00000002633	1 retrocopy	retro_pabe_2256,
Pan troglodytes	ENSPTRG00000002925	1 retrocopy	retro_ptro_1825 ,