RetrogeneDB ID: retro_ptro_2172

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 5:98483546..98484263(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPTRG00000038674
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PSME2
• Ensembl ID: ENSPTRG00000006196
• Aliases: None
• Description: None

Sequence

>retro_ptro_2172
ATGGCCAAGCCGTGTGGGGCGCGCCTGAGCGGAGAAGCCCTTAAACAGGTGGAGGTCTTCAGGCAGAATCTTTTCCAGGA
GGCTGAAGAATTCCTCTGCAGATTCTTGCTACAGAAAATCATATATGTGAATCAGCTCTTGCAAGAGGACTCCCTCAATG
TGGCTGACCTGACTTCCCTCCGGGCCCCACTGGACGTCCCCATCCCAGACCCTCCACCCAAGGATGATGAGATGGAAACA
GATAAGCAGGAGAAGAAAGAAGTCCCTAAGTGTGGACTTCTCCCTGGGGATGAGAAAGTCCTGTCCCTCTTTGCCCTGGT
TAAGCCAGAAGTCTGGACTCTCAAAGAGAAATGCATTCTGCTGATTACGTGGATCCAACACCTGATCCCCAAGATTGACG
ATGGAAATGAGTTTGGGGTAGCAATCCAGGAGAAGGTGCTGGAGAGGGTGAATGCCGTCAAGACCAAAGTGGAAGCTTTC
CAGACAACCATTTCCAAGTACTTCTCAGAACGTGGGGATGCTGTGGCCAAGGCCTCCAAGGAGACTCATGTAATGGATTA
CTGGGCCTTGGTGCATGAACGAGATGAGGCAGCCTATGGGGAGCTCAGGGCCATGGTGCTGGACCTGAGGGCCTTCTATG
CTGAGCTTTATCATATCATCAGCAGCAACTTGTAGAAAATTGTCAACCCAAAGGTTGAAGAGAAGCCATCTATGTAC

Alignment

ORF - retro_ptro_2172 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.72 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAKPCGVRLSGEARKQVEVFRQNLFQEAEEFLYRFLPQKIIYLNQLLQEDSLNVADLTSLRAPLDIPIPD
          MAKPCG.RLSGEA.KQVEVFRQNLFQEAEEFL.RFL.QKIIY.NQLLQEDSLNVADLTSLRAPLD.PIPD
Retrocopy MAKPCGARLSGEALKQVEVFRQNLFQEAEEFLCRFLLQKIIYVNQLLQEDSLNVADLTSLRAPLDVPIPD

Parental  PPPKDDEMETDKQEKKEVPKCGFLPGNEKVLSLLALVKPEVWTLKEKCILVITWIQHLIPKIEDGNDFGV
          PPPKDDEMETDKQEKKEVPKCG.LPG.EKVLSL.ALVKPEVWTLKEKCIL.ITWIQHLIPKI.DGN.FGV
Retrocopy PPPKDDEMETDKQEKKEVPKCGLLPGDEKVLSLFALVKPEVWTLKEKCILLITWIQHLIPKIDDGNEFGV

Parental  AIQEKVLERVNAVKTKVEAFQTTISKYFSERGDAVAKASKETHVMDYRALVHERDEAAYGELRAMVLDLR
          AIQEKVLERVNAVKTKVEAFQTTISKYFSERGDAVAKASKETHVMDY.ALVHERDEAAYGELRAMVLDLR
Retrocopy AIQEKVLERVNAVKTKVEAFQTTISKYFSERGDAVAKASKETHVMDYWALVHERDEAAYGELRAMVLDLR

Parental  AFYAELYHIISSNLEKIVNPKGEEKPSMY
          AFYAELYHIISSNL.KIVNPK.EEKPSMY
Retrocopy AFYAELYHIISSNL*KIVNPKVEEKPSMY

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	0.05 RPM	40.79 RPM
SRP007412_cerebellum	0.04 RPM	45.28 RPM
SRP007412_heart	0.06 RPM	39.96 RPM
SRP007412_kidney	0.16 RPM	104.35 RPM
SRP007412_liver	0.36 RPM	202.36 RPM
SRP007412_testis	0.00 RPM	19.50 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2172 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2172 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2172 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3222
Gorilla gorilla	retro_ggor_2188
Pongo abelii	retro_pabe_2669

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 30 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000007167	3 retrocopies	retro_cjac_233, retro_cjac_322, retro_cjac_71,
Homo sapiens	ENSG00000100911	4 retrocopies	retro_hsap_1200, retro_hsap_2999, retro_hsap_3033, retro_hsap_3222,
Gorilla gorilla	ENSGGOG00000016025	4 retrocopies	retro_ggor_2078, retro_ggor_2093, retro_ggor_2188, retro_ggor_935,
Macaca mulatta	ENSMMUG00000012473	4 retrocopies	retro_mmul_1229, retro_mmul_1919, retro_mmul_1940, retro_mmul_2281,
Mus musculus	ENSMUSG00000079197	1 retrocopy	retro_mmus_145,
Nomascus leucogenys	ENSNLEG00000015260	4 retrocopies	retro_nleu_2086, retro_nleu_2726, retro_nleu_3086, retro_nleu_844,
Otolemur garnettii	ENSOGAG00000016584	1 retrocopy	retro_ogar_61,
Pongo abelii	ENSPPYG00000005684	4 retrocopies	retro_pabe_1000, retro_pabe_2486, retro_pabe_2512, retro_pabe_2669,
Pan troglodytes	ENSPTRG00000006196	4 retrocopies	retro_ptro_2028, retro_ptro_2046, retro_ptro_2172 , retro_ptro_820,
Pan troglodytes	ENSPTRG00000009225	1 retrocopy	retro_ptro_212,