RetrogeneDB ID: retro_ggor_394

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 1:55145825..55146493(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SLC25A3
• Ensembl ID: ENSGGOG00000015886
• Aliases: None
• Description: None

Sequence

>retro_ggor_394
CTCTGGGCGGCGGCTGTGGAGGCGGCCAGCGTGGAGTACGGCTCGGCCCGGTACCTGCTGCTGTGCGGCCTGGGCGGGAT
GCTGAGCTGCGGCTGACACACACGGCCATCGTGTCCCTGGACCTGGTCAAGTGCCGCATGCAGGTGGATCCCGGCTGGTA
CAAGGGCGTCCTTAGCGGCTTCGGCGTGACGGTGCGCAGCGACTGGCTGTGCGGCCTGGCTCGCGGCTGCGCCCAGACCT
TCTTCGGCCACTCCCTGCAGGGCTTCTTCAAGTTCGGCCTTTACGAGGTCTTCAAGATCCGCTACGCGGAGCTCCTGGGC
CCAGAGAAGGCCTACGGGTGGAGAGCCGGCCTGTACCTTTTCGCCTGGGCCAGCGCCGAGTTCTTCCCCGATGTCTCGCT
GGCGCCTATGGAGGAGGTCAAGGTCCACGTGCAGACGCGACCGGGCTACGCCAGCACCCTGCGAGCCGCGGCGCCCAGGA
TGTAGGGCGAGGAGGGCCTGTGGGCCTTCTACAAGGGCGTGACGCCGCTGTGGCTGAGGCAGATCCCCTACACCATGATG
AAGTTCGCCTGCTTCAAGCGCATGGTAGAGGAGCTCTACAGGTATGCCGTGCCCAAGCCCCAGAGCCAGTGCACCAAGGC
CAAGCAGCTGGGCATCACCTTCGTGGCG

Alignment

ORF - retro_ggor_394 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.62 %
• Parental protein coverage: 61.77 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LAAAAVEEYSCEFGSAKYYALCGFGGVLSCG-LTHTAVVPLDLVKCRMQVDPQKYKGIFNGFSVTLKEDG
          L.AAAVE..S.E.GSA.Y..LCG.GG.LSCG.LTHTA.V.LDLVKCRMQVDP..YKG...GF.VT...D.
Retrocopy LWAAAVEAASVEYGSARYLLLCGLGGMLSCG<LTHTAIVSLDLVKCRMQVDPGWYKGVLSGFGVTVRSDW

Parental  VRGLAKGWAPTFLGYSMQGLCKFGFYEVFKVLYSNMLGEENTYLWRTSLYLAASASAEFFADIALAPMEA
          ..GLA.G.A.TF.G.S.QG..KFG.YEVFK..Y...LG.E..Y.WR..LYL.A.ASAEFF.D..LAPME.
Retrocopy LCGLARGCAQTFFGHSLQGFFKFGLYEVFKIRYAELLGPEKAYGWRAGLYLFAWASAEFFPDVSLAPMEE

Parental  AKVRIQTQPGYANTLRDAAPKMYKEEGLKAFYKGVAPLWMRQIPYTMMKFACFERTVEALYKFVVPKPRS
          .KV..QT.PGYA.TLR.AAP.M..EEGL.AFYKGV.PLW.RQIPYTMMKFACF.R.VE.LY...VPKP.S
Retrocopy VKVHVQTRPGYASTLRAAAPRM*GEEGLWAFYKGVTPLWLRQIPYTMMKFACFKRMVEELYRYAVPKPQS

Parental  ECSKPEQLVVTFIA
          .C.K..QL..TF.A
Retrocopy QCTKAKQLGITFVA

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	120.46 RPM
SRP007412_cerebellum	0.00 RPM	83.09 RPM
SRP007412_heart	0.00 RPM	313.51 RPM
SRP007412_kidney	0.00 RPM	260.42 RPM
SRP007412_liver	0.00 RPM	96.25 RPM
SRP007412_testis	0.52 RPM	81.12 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_394 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_394 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_392
Pan troglodytes	retro_ptro_302
Equus caballus	retro_ecab_481

---

Parental genes homology:

Parental genes homology involve 27 parental genes, and 32 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000013232	1 retrocopy	retro_acar_35,
Bos taurus	ENSBTAG00000012890	1 retrocopy	retro_btau_172,
Canis familiaris	ENSCAFG00000006545	1 retrocopy	retro_cfam_880,
Callithrix jacchus	ENSCJAG00000002392	2 retrocopies	retro_cjac_3315, retro_cjac_812,
Dipodomys ordii	ENSDORG00000011431	1 retrocopy	retro_dord_321,
Equus caballus	ENSECAG00000015135	1 retrocopy	retro_ecab_481,
Echinops telfairi	ENSETEG00000012678	1 retrocopy	retro_etel_1748,
Homo sapiens	ENSG00000075415	1 retrocopy	retro_hsap_392,
Gorilla gorilla	ENSGGOG00000015886	1 retrocopy	retro_ggor_394 ,
Latimeria chalumnae	ENSLACG00000007024	1 retrocopy	retro_lcha_4,
Macropus eugenii	ENSMEUG00000016593	2 retrocopies	retro_meug_405, retro_meug_658,
Microcebus murinus	ENSMICG00000003520	1 retrocopy	retro_mmur_298,
Myotis lucifugus	ENSMLUG00000008330	1 retrocopy	retro_mluc_1184,
Macaca mulatta	ENSMMUG00000023036	1 retrocopy	retro_mmul_496,
Monodelphis domestica	ENSMODG00000007717	2 retrocopies	retro_mdom_2026, retro_mdom_293,
Mus musculus	ENSMUSG00000061904	1 retrocopy	retro_mmus_1959,
Nomascus leucogenys	ENSNLEG00000005973	1 retrocopy	retro_nleu_2402,
Oryctolagus cuniculus	ENSOCUG00000011847	1 retrocopy	retro_ocun_390,
Otolemur garnettii	ENSOGAG00000012222	2 retrocopies	retro_ogar_1816, retro_ogar_2052,
Pongo abelii	ENSPPYG00000004858	1 retrocopy	retro_pabe_1768,
Pan troglodytes	ENSPTRG00000005333	1 retrocopy	retro_ptro_302,
Pteropus vampyrus	ENSPVAG00000005890	1 retrocopy	retro_pvam_212,
Sorex araneus	ENSSARG00000001149	1 retrocopy	retro_sara_262,
Ictidomys tridecemlineatus	ENSSTOG00000027633	2 retrocopies	retro_itri_485, retro_itri_90,
Tupaia belangeri	ENSTBEG00000014548	1 retrocopy	retro_tbel_1792,
Tursiops truncatus	ENSTTRG00000004739	1 retrocopy	retro_ttru_692,
Vicugna pacos	ENSVPAG00000004704	1 retrocopy	retro_vpac_455,