RetrogeneDB ID: retro_ggor_2078

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 4:169423485..169423888(+)
• Located in intron of: ENSGGOG00000000301

Retrocopy information

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

Parental gene information

• Parental gene symbol: PSME2
• Ensembl ID: ENSGGOG00000016025
• Aliases: None
• Description: None

Sequence

>retro_ggor_2078
ATGGCCAAGCCGTGTGGGGTGCGCCTGAGACGGGAGGCCTGTAAACAGGTGGAGATCTTCAGGCAGAATCTTTTCCAGGA
GGCTGAGGAATTCCTCTACAGATTCTTGCCACAGAAAATCATATACCTGAATCAGCTCTTGCAAGGTACTGCCTCAATGT
GGCTGACCTGACTTCCCTCCGGGCCCCACTGGACATCTCATCCCAGGCCCTCCACCCAAGGATGATGAGATGGAAACAGA
TAAGCAGGAGATGAAAGAAGTCCCTAAGAGTGGATTTCTCCCTGGGAATGAGAAGGTCCTGTTCCTGCTTGCCCTAGTTA
AGCCAGGAGTCTGGAGTCTCAAAGAGAAATGCATTCTAGTGATCACAGGGATCCAGCACCTGATCCTCAAGGTTGAAGAT
GGA

Alignment

ORF - retro_ggor_2078 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.13 %
• Parental protein coverage: 56.25 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

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

Parental  PDPPPKDDEMETDKQEKKEVPKCGFLPGNEKVLSLLALVKPEVWTLKEKCILVITWIQHLIPKIEDG
          P.PPPKDDEMETDKQE.KEVPK.GFLPGNEKVL.LLALVKP.VW.LKEKCILVIT.IQHLI.K.EDG
Retrocopy PGPPPKDDEMETDKQEMKEVPKSGFLPGNEKVLFLLALVKPGVWSLKEKCILVITGIQHLILKVEDG

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	17.98 RPM
SRP007412_cerebellum	0.00 RPM	31.05 RPM
SRP007412_heart	0.03 RPM	18.07 RPM
SRP007412_kidney	0.04 RPM	66.20 RPM
SRP007412_liver	0.03 RPM	67.03 RPM
SRP007412_testis	0.10 RPM	28.08 RPM

ChIP-Seq

Gorilla gorilla was not studied using ChIP-Seq data.

EST

Gorilla gorilla was not studied using EST data.

TSS

Gorilla gorilla was not studied using FANTOM5 data.

Lab

retro_ggor_2078 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_2078 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 9 parental genes, and 29 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,