RetrogeneDB ID: retro_ptro_1859

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 3:12472433..12473087(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPTRG00000041464
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: GSTM1
• Ensembl ID: ENSPTRG00000001061
• Aliases: None
• Description: glutathione S-transferase mu 1 [Source:HGNC Symbol;Acc:4632]

Sequence

>retro_ptro_1859
ATGCCCATGACACTGGGGTACGGGGACATCCACGGGCTGGCACATGCCATCCACCTGCTCCTTGAATACACAGACTCAAG
CTACGAGGAAAAGAAGTACACAAAGGGGGACTCTACTGACTATGACAGAAGCTAGTAGCTGAATTAAAAATTCAAGCTGG
GCCTGGACTTTCCCAATCTGCCCTACTTGTTTGATGGGGCTCACAAGATCACCCAGAGCAACGCCATCCTGTGCCACATT
TCCTGCAAGCACAGCCTGTGTGAGGAGACAGAAGAGGAGAAGATTCGTGTGGACATTTCGGAGAACCAGACCATGGACAA
CCTGATGCAGCTGGCCATGATCTGCTACATCCCAGAATTTGAGAAACTGAAGCCAAAGTACCTGGAGGAACTCCCTGAAA
AGCTAAAGCTCTACTCACAGTTTCTGGGGAAGTGGCCATGGTTTGCATGAGACAAGATCACCTATGTGGATTTCCTTGCC
TATGACATCCTTGACCTGAACTGTATATTTGACCCCAGCTGCCTGGACGCCTTCCCAAACCTGAAGGACTTCATGTCCTG
AATTGAGGGTTTGAAGAAGATCTCTGCCTACATGAAGTCCAGCCAATGCCTCCAAGGTCCTTTGTTTGGGAAGTCAGCTA
CGTGGAACAGTAAA

Alignment

ORF - retro_ptro_1859 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.44 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 5
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MPMTLGYWDIRGLAHAIRLLLEYTDSSYEEKKYSMGDAPDYDRSQWLNEKFKLGLDFPNLPYLIDGAHKI
          MPMTLGY.DI.GLAHAI.LLLEYTDSSYEEKKY..GD..DYDRS..LN.KFKLGLDFPNLPYL.DGAHKI
Retrocopy MPMTLGYGDIHGLAHAIHLLLEYTDSSYEEKKYTKGDSTDYDRS**LN*KFKLGLDFPNLPYLFDGAHKI

Parental  TQSNAILCYIARKHNLCGETEEEKICVDILENQTMDNHMQLGMICYNPEFEKLKPKYLEELPEKLKLYSE
          TQSNAILC.I..KH.LC.ETEEEKI.VDI.ENQTMDN.MQL.MICY.PEFEKLKPKYLEELPEKLKLYS.
Retrocopy TQSNAILCHISCKHSLCEETEEEKIRVDISENQTMDNLMQLAMICYIPEFEKLKPKYLEELPEKLKLYSQ

Parental  FLGKRPWFAGNKITFVDFLVYDVLDLHRIFEPKCLDAFPNLKDFISRFEDLEKISAYMKSSRFLPRPVFT
          FLGK.PWFA..KIT.VDFL.YD.LDL..IF.P.CLDAFPNLKDF.S..E.L.KISAYMKSS..L..P.F.
Retrocopy FLGKWPWFA*DKITYVDFLAYDILDLNCIFDPSCLDAFPNLKDFMS*IEGLKKISAYMKSSQCLQGPLFG

Parental  KMAVWGNK
          K.A.W..K
Retrocopy KSATWNSK

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	0.11 RPM	18.46 RPM
SRP007412_cerebellum	0.14 RPM	5.92 RPM
SRP007412_heart	0.00 RPM	1.87 RPM
SRP007412_kidney	0.00 RPM	9.89 RPM
SRP007412_liver	0.07 RPM	42.26 RPM
SRP007412_testis	0.00 RPM	12.54 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1859 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1859 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1859 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2751
Gorilla gorilla	retro_ggor_1913
Pongo abelii	retro_pabe_2218
Macaca mulatta	retro_mmul_1432

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000003123	7 retrocopies	retro_cjac_1299, retro_cjac_2226, retro_cjac_2463, retro_cjac_2498, retro_cjac_3004, retro_cjac_3084, retro_cjac_811,
Gorilla gorilla	ENSGGOG00000005148	2 retrocopies	retro_ggor_1913, retro_ggor_2459,
Nomascus leucogenys	ENSNLEG00000003194	2 retrocopies	retro_nleu_1546, retro_nleu_504,
Pongo abelii	ENSPPYG00000001064	2 retrocopies	retro_pabe_2218, retro_pabe_2990,
Pan troglodytes	ENSPTRG00000001061	2 retrocopies	retro_ptro_1859 , retro_ptro_2468,
Pan troglodytes	ENSPTRG00000001063	2 retrocopies	retro_ptro_1393, retro_ptro_1709,