RetrogeneDB ID: retro_ptro_1732

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 2B:200714767..200715421(-)
• Located in intron of: ENSPTRG00000012761

Retrocopy information

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

Parental gene information

• Parental gene symbol: GSTA5
• Ensembl ID: ENSPTRG00000032453
• Aliases: GSTA5, GSTA1
• Description: glutathione S-transferase alpha 5 [Source:HGNC Symbol;Acc:19662]

Sequence

>retro_ptro_1732
ATGGCAGCCAAACCCAAGCTCTACTACTTTCATGTCAGGGGCAGGGTGGAGTCAGTCCCCTGGCTGCTGGCTGCAGCTGG
AATAGAGTTTGAAGAAGAATTTATTGAAACAAGATAATAATATGAAAAGTTGCAGAAGGATAGACGCCTGCATTTTGGCC
AAGTGCCTTTGGTTGAAATTGATGGAATGATGCTGACACTGACTACAGCCATCCTCAGCTATCTTGCTGCTAAGTACAAT
GTCTGTGGAAAGGACCTGAAGGAGAGAGTCGGGATCAACATGTGTGCTGAGGGCACCCTGGACCTGATGATGATGATGGC
GCTGGCCCACTGAGGAAAAAGAGGAGAACCTTGCTCAGTTGTGAAGAAAGCTAAAACCCAGTACTTGGCCATCTTTGAAA
AGATTTTGAAAGACCATGGAGAGGATCTTCTTGTTGGCAACAAATTCAGTTGGGCAGACATACAACTGTTAGAAGCTGTT
CTAATGGTAGAAGAACTCAATGCTTCTGTTCTTTCTGACTTCCCTCTGTTGAAGGCGTTTTAAACAGGAATCAGCAACAT
CCCCAGAATTAAGAAATTCCTGCAACCTGGGAGTCAGAGGAAGCCACTCCCTGATACCCAATATGTTGAACTAGTTAGAA
ACATTCTGCAGTTC

Alignment

ORF - retro_ptro_1732 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.6 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAEKPKLHYSNARGRMESIRWLLAAAGVEFEEKFLESAEDLDKLRNDGSLLFQQVPMVEIDGMKLVQTRA
          MA.KPKL.Y...RGR.ES..WLLAAAG.EFEE.F.E......KL..D..L.F.QVP.VEIDGM.L..T.A
Retrocopy MAAKPKLYYFHVRGRVESVPWLLAAAGIEFEEEFIETR**YEKLQKDRRLHFGQVPLVEIDGMMLTLTTA

Parental  ILNYIASKYNLYGKDMKERALIDMYTEGIVDLTEMIVLLLVCQPEERDAKTALVKEKIKNRYFPAFEKVL
          IL.Y.A.KYN..GKD.KER..I.M..EG..DL..............R......VK.K.K..Y...FEK.L
Retrocopy ILSYLAAKYNVCGKDLKERVGINMCAEGTLDL---MMMMALAH*GKRGEPCSVVK-KAKTQYLAIFEKIL

Parental  KSQGQDYLVGNKLSRADIHLVELLYYVEELDSSLISSFPLLKALKTRISNLPTVKKFLQPGSQRKPPMDE
          K..G.D.LVGNK.S.ADI.L.E....VEEL..S..S.FPLLKA..T.ISN.P..KKFLQPGSQRKP..D.
Retrocopy KDHGEDLLVGNKFSWADIQLLEAVLMVEELNASVLSDFPLLKAF*TGISNIPRIKKFLQPGSQRKPLPDT

Parental  KSLEEARKIFRF
          ...E..R.I..F
Retrocopy QYVELVRNILQF

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	0.09 RPM	0.00 RPM
SRP007412_cerebellum	0.00 RPM	0.00 RPM
SRP007412_heart	0.00 RPM	0.00 RPM
SRP007412_kidney	0.00 RPM	0.05 RPM
SRP007412_liver	0.00 RPM	0.29 RPM
SRP007412_testis	0.00 RPM	0.84 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1732 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1732 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1732 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2366
Gorilla gorilla	retro_ggor_1797
Callithrix jacchus	retro_cjac_2841

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000009819	1 retrocopy	retro_dnov_2390,
Homo sapiens	ENSG00000182793	1 retrocopy	retro_hsap_2366,
Gorilla gorilla	ENSGGOG00000027587	1 retrocopy	retro_ggor_1797,
Microcebus murinus	ENSMICG00000002208	1 retrocopy	retro_mmur_350,
Otolemur garnettii	ENSOGAG00000003726	1 retrocopy	retro_ogar_345,
Pan troglodytes	ENSPTRG00000032453	1 retrocopy	retro_ptro_1732 ,
Tupaia belangeri	ENSTBEG00000001413	1 retrocopy	retro_tbel_2120,