RetrogeneDB ID: retro_ptro_2028

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 4:162106396..162106798(+)
• Located in intron of: ENSPTRG00000016556

Retrocopy information

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

Parental gene information

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

Sequence

>retro_ptro_2028
ATGGCCAAGCCGTGTGGGGTGCGCCTGAGACGGGAGGCCTGTAAACAGGTGGAGATCTTCAGGCAGAATCTTTTCCAGGA
GGCTGAGGAATTCCTCTACAGATTCTTGCCACAGAAAATCATATACCTGAATCAGCTCTTGCAAGGTACTGCCTCAATGT
GGCTGACCTGACTTCCCTCCGGGCCCCACTGGACATCTCATCCCAGGCCCTCCACCCAAGGATGATGAGATGGAAACAGA
TAAGCAGGAGATGAAAGAAGTCCCTAAGAGTGGATTTCTCCCTAGGAATGAGAAGGTCCTGTTCCTGCTTGCCCTGGTTA
AGCCAGGAGTCTGGAGTCTCAAAGAGAAATGCATTCTAGTGATCACGGGATCCAGCACCTGATCCTCAAGATTGAAGATG
GA

Alignment

ORF - retro_ptro_2028 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.51 %
• Parental protein coverage: 56.49 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MAKPCGVRLSGEARKQVEVFRQNLFQEAEEFLYRFLPQKIIYLNQLLQEDS-LNVADLTSLRAPLDIP-I
          MAKPCGVRL..EA.KQVE.FRQNLFQEAEEFLYRFLPQKIIYLNQLLQ....LNVADLTSLRAPLDI..I
Retrocopy MAKPCGVRLRREACKQVEIFRQNLFQEAEEFLYRFLPQKIIYLNQLLQGTA<LNVADLTSLRAPLDIS<I

Parental  PDPPPKDDEMETDKQEKKEVPKCGFLPGNEKVLSLLALVKPEVWTLKEKCILVIT-WIQHLIPKIEDG
          P.PPPKDDEMETDKQE.KEVPK.GFLP.NEKVL.LLALVKP.VW.LKEKCILVIT..IQHLI.KIEDG
Retrocopy PGPPPKDDEMETDKQEMKEVPKSGFLPRNEKVLFLLALVKPGVWSLKEKCILVIT<GIQHLILKIEDG

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	40.79 RPM
SRP007412_cerebellum	0.00 RPM	45.28 RPM
SRP007412_heart	0.00 RPM	39.96 RPM
SRP007412_kidney	0.03 RPM	104.35 RPM
SRP007412_liver	0.16 RPM	202.36 RPM
SRP007412_testis	0.11 RPM	19.50 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2028 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2028 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2028 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2999
Pongo abelii	retro_pabe_2486
Macaca mulatta	retro_mmul_1919

---

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,