RetrogeneDB ID: retro_pabe_2218

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 3:57692502..57693156(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GSTM1
• Ensembl ID: ENSPPYG00000001064
• Aliases: None
• Description: glutathione S-transferase mu 1 [Source:HGNC Symbol;Acc:4632]

Sequence

>retro_pabe_2218
ATGCCCATGACACTGGGGTACGGGGACATCCACAGGCTGGCACATGCCATCCGTCTGCTCCTTGAATACACAGACTCAAG
CTACGAGGAAAAGAAGTACACAATGGGGGACCTTCCTGACTATGACAGAAGCCAGTAGCTGAATTAAAAATTCAAGGTGG
GCCTGGACTTTCCCAATCTGCCCTACTTGTTTGATGGGGCTCACAAGATCATCCAGAGCAACACCATCCTGTGCCACATC
GCCCGCAAGCACAACCTGTGTGAGGAGACAGAAGAGGAGAAGATTCGTGTGGACATTTCGGAGAACCAGACCATGGACAA
CCTGATGCAGCTGGCCATGATCTGCTACATCCCAGAATTTGAGAAACTGAAGCCAAAGTACCTGGAGGAACTCCCCGAAA
AGCTAAAGCTCTACTCACAGTTTCTGGGGAAGTGGCCATGGTTTGCATGAGACAAGATCACCTATGTGGATTTCCTCGCC
TATGACATCCTTGACCTGAACTGTATATTTGACCCCAGCTGCCTGGACGCCTTCCCAAACCTGAAGGACTTCATCTCCCG
AATTGAGGGTTTGAAGAAGATCTCTGCCTACGTGAAGTCCAGCCAATGCCTCCAAGGTCCTTTGTTTGGGAAGTCAGCTA
TGTGGAACAGTAAA

Alignment

ORF - retro_pabe_2218 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.73 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MPMTLGYWDIRGLAHAIRLLLEYTDSSYEEKKYTMGDAPDYDRSQWLNEKFKLGLDFPNLPYLIDGTHKI
          MPMTLGY.DI..LAHAIRLLLEYTDSSYEEKKYTMGD.PDYDRSQ.LN.KFK.GLDFPNLPYL.DG.HKI
Retrocopy MPMTLGYGDIHRLAHAIRLLLEYTDSSYEEKKYTMGDLPDYDRSQ*LN*KFKVGLDFPNLPYLFDGAHKI

Parental  TQSNAILCYIARKHNLCGETEEEKIRVDILENQTMDNHMQLGMICYNPEFEKLKPKYLEELPEKLKLYSE
          .QSN.ILC.IARKHNLC.ETEEEKIRVDI.ENQTMDN.MQL.MICY.PEFEKLKPKYLEELPEKLKLYS.
Retrocopy IQSNTILCHIARKHNLCEETEEEKIRVDISENQTMDNLMQLAMICYIPEFEKLKPKYLEELPEKLKLYSQ

Parental  FLGKQPWFAGNKITFADFLVYDVLDLHRIFEPKCLDAFPNLKDFISRFEGLEKISAYMKSSRFLPRPVFT
          FLGK.PWFA..KIT..DFL.YD.LDL..IF.P.CLDAFPNLKDFISR.EGL.KISAY.KSS..L..P.F.
Retrocopy FLGKWPWFA*DKITYVDFLAYDILDLNCIFDPSCLDAFPNLKDFISRIEGLKKISAYVKSSQCLQGPLFG

Parental  KMAVWGNK
          K.A.W..K
Retrocopy KSAMWNSK

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	0.06 RPM	8.63 RPM
SRP007412_cerebellum	0.73 RPM	16.90 RPM
SRP007412_heart	0.00 RPM	5.96 RPM
SRP007412_kidney	0.00 RPM	10.51 RPM
SRP007412_liver	0.00 RPM	23.99 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2218 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2218 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2218 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2751
Pan troglodytes	retro_ptro_1859
Gorilla gorilla	retro_ggor_1913
Macaca mulatta	retro_mmul_1432

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 15 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,