RetrogeneDB ID: retro_pabe_2990

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 6:113232805..113233456(-)
• 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_2990
ATGCCCGTGACACTGGGGTACTGGGACATCTGAGGGCTGGCCCACGCCGTCTGCCTGCTCCTGCAATACACAGACTTAAG
CTATGAGGAAAAGAAGTACATGATGGGGGAAGCTCCTGACTATGACAGAAGCCAGTGGCTGAATGAAAAATTCGAGCTGG
GCCTGGACCTTCCCAATCTGCCCTACTTGATTGATGGGGCTCACAAGATCACCCAGAGCAAGGCCATCCTGGGCTGCATT
GCCTACAAGCACAACCTATGTGGGGAGACAGAAGGAGAGAAGATTTGGGAAGACATTTTGGAGAACCAGCTTGTGGACAA
CCACGTGCAGCTGGCCAGACTCTGCTACAACCCAGATTTTGAGAAACTGAAGCCAGACTACCTGGATGCACTCCCTGCAA
TGCTGAAGCTCTACTCACAGTTTCTGGGGAAGCAGCCATGGTTGCTTGGGGACAAGATCACACTTGCGGATTTCATCGCT
TATGGTGTCCTTGAGAGAAACCAAGTATTTGAGCCCAAGTGGTTGGACGCCTTCCCAAACCTGAAGGACTTCATCTCCCG
ATTTGAGGGCTTGGAGATCTCTGCCTACATGAAATCCAGCTGCTTCCTCCCAAGACCTGTGTTCACAAAGATGGCTGTCT
GGGGCAACAAG

Alignment

ORF - retro_pabe_2990 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.9 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MPMTLGYWDIRGLAHAIRLLLEYTDSSYEEKKYTMGDAPDYDRSQWLNEKFKLGLDFPNLPYLIDGTHKI
          MP.TLGYWDI.GLAHA..LLL.YTD.SYEEKKY.MG.APDYDRSQWLNEKF.LGLD.PNLPYLIDG.HKI
Retrocopy MPVTLGYWDI*GLAHAVCLLLQYTDLSYEEKKYMMGEAPDYDRSQWLNEKFELGLDLPNLPYLIDGAHKI

Parental  TQSNAILCYIARKHNLCGETEEEKIRVDILENQTMDNHMQLGMICYNPEFEKLKPKYLEELPEKLKLYSE
          TQS.AIL..IA.KHNLCGETE.EKI..DILENQ..DNH.QL...CYNP.FEKLKP.YL..LP..LKLYS.
Retrocopy TQSKAILGCIAYKHNLCGETEGEKIWEDILENQLVDNHVQLARLCYNPDFEKLKPDYLDALPAMLKLYSQ

Parental  FLGKQPWFAGNKITFADFLVYDVLDLHRIFEPKCLDAFPNLKDFISRFEGLEKISAYMKSSRFLPRPVFT
          FLGKQPW..G.KIT.ADF..Y.VL.....FEPK.LDAFPNLKDFISRFEGLE.ISAYMKSS.FLPRPVFT
Retrocopy FLGKQPWLLGDKITLADFIAYGVLERNQVFEPKWLDAFPNLKDFISRFEGLE-ISAYMKSSCFLPRPVFT

Parental  KMAVWGNK
          KMAVWGNK
Retrocopy KMAVWGNK

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	8.63 RPM
SRP007412_cerebellum	0.49 RPM	16.90 RPM
SRP007412_heart	0.03 RPM	5.96 RPM
SRP007412_kidney	0.13 RPM	10.51 RPM
SRP007412_liver	0.24 RPM	23.99 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2990 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2990 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2990 has 5 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3643
Pan troglodytes	retro_ptro_2468
Gorilla gorilla	retro_ggor_2459
Macaca mulatta	retro_mmul_1806
Callithrix jacchus	retro_cjac_2463

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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,