RetrogeneDB ID: retro_ggor_2824

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 9:107120258..107120454(+)
• Located in intron of: ENSGGOG00000016611

Retrocopy information

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

Parental gene information

• Parental gene symbol: LSM5
• Ensembl ID: ENSGGOG00000010325
• Aliases: None
• Description: None

Sequence

>retro_ggor_2824
ATGGCGGCTAAGGCTACCACCTACTTGCCCAGCTGTTGCTGCTAGAGCTTGTAGACAAATGCATAGGCTCAAGAATTCAC
ATTGTGGTGAAGAGTAATTAAGAAATTGTGGGTACTCTTCTAGGAGTTGATGACTTTGTCAATATGGACTAGAAGAGGTC
ACTGAGTTTGAAATCACACCAGAAGGAAGAAGTATT

Alignment

ORF - retro_ggor_2824 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.41 %
• Parental protein coverage: 72.53 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAANATTNP-SQLLPLELVDKCIGSRIHIVMKSDKEIVGTLLGFDDFVNM-VLEDVTEFEITPEGRRI
          MAA.ATT....QLL.LELVDKCIGSRIHIV.KS..EIVGTLLG.DDFVNM..LE.VTEFEITPEGR.I
Retrocopy MAAKATTYL<AQLLLLELVDKCIGSRIHIVVKSN*EIVGTLLGVDDFVNM<GLEEVTEFEITPEGRSI

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	2.83 RPM
SRP007412_cerebellum	0.00 RPM	3.62 RPM
SRP007412_heart	0.00 RPM	0.84 RPM
SRP007412_kidney	0.00 RPM	9.36 RPM
SRP007412_liver	0.00 RPM	5.35 RPM
SRP007412_testis	0.00 RPM	5.80 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_2824 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_2824 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4216
Pan troglodytes	retro_ptro_2862
Pongo abelii	retro_pabe_3449

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 32 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000009185	3 retrocopies	retro_cjac_1883, retro_cjac_2760, retro_cjac_3068,
Echinops telfairi	ENSETEG00000018068	8 retrocopies	retro_etel_1305, retro_etel_1502, retro_etel_1907, retro_etel_198, retro_etel_2054, retro_etel_2193, retro_etel_454, retro_etel_964,
Homo sapiens	ENSG00000106355	2 retrocopies	retro_hsap_3703, retro_hsap_4216,
Gorilla gorilla	ENSGGOG00000010325	2 retrocopies	retro_ggor_2504, retro_ggor_2824 ,
Microcebus murinus	ENSMICG00000005353	3 retrocopies	retro_mmur_1345, retro_mmur_69, retro_mmur_950,
Myotis lucifugus	ENSMLUG00000017028	1 retrocopy	retro_mluc_2439,
Oryctolagus cuniculus	ENSOCUG00000029043	5 retrocopies	retro_ocun_1284, retro_ocun_1452, retro_ocun_1513, retro_ocun_1556, retro_ocun_903,
Ochotona princeps	ENSOPRG00000002443	3 retrocopies	retro_opri_26, retro_opri_562, retro_opri_701,
Pongo abelii	ENSPPYG00000017661	1 retrocopy	retro_pabe_3449,
Rattus norvegicus	ENSRNOG00000042126	3 retrocopies	retro_rnor_1171, retro_rnor_567, retro_rnor_694,
Sus scrofa	ENSSSCG00000026064	1 retrocopy	retro_sscr_385,