RetrogeneDB ID: retro_ggor_848

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 12:4758542..4758971(-)
• Located in intron of: ENSGGOG00000014277

Retrocopy information

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

Parental gene information

• Parental gene symbol: RAB5A
• Ensembl ID: ENSGGOG00000015981
• Aliases: None
• Description: None

Sequence

>retro_ggor_848
ACAGATTCAGCTGATTTTCTAACCCAAAATGTGTGTCTTGATGACACTACAGTATAGTTTGAAATACGGGATACAGCTGG
TCAAGAATGATACTGTAGCCTAGCACCAATGTACTACAGAGGAGCACAAGCAGCCATAGCTGTATATGATACCACAAATG
AGGAGTCCTTTGCAAGAGCAAAAAATTGGGTTAAAGAACTTCAGAGGCAAGCATGTCCTGACATTGTAATAGCTTTATCA
GGAAACAAGACTGACCTAGCAAATAAAAGAGCAGTAGATTTCCAGGAAGCACAGTCCTATGCAGATGACAATAGTTTATT
ATTCATGAAGACATCAGCTAAAACATCAGTGAATGTAAATGAAATGTTCATGGCAATAGCTAAAAAATTGCCAAAGAATG
AACCACAAAATCCAGAAGCAAATTCTGCC

Alignment

ORF - retro_ggor_848 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.11 %
• Parental protein coverage: 66.51 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TIGAAFLTQTVCLDDTTVKFEIWDTAGQERYHSLAPMYYRGAQAAIVVYDITNEESFARAKNWVKELQRQ
          T..A.FLTQ.VCLDDTTV.FEI.DTAGQE.Y.SLAPMYYRGAQAAI.VYD.TNEESFARAKNWVKELQRQ
Retrocopy TDSADFLTQNVCLDDTTV*FEIRDTAGQE*YCSLAPMYYRGAQAAIAVYDTTNEESFARAKNWVKELQRQ

Parental  ASPNIVIALSGNKADLANKRAVDFQEAQSYADDNSLLFMETSAKTSMNVNEIFMAIAKKLPKNEPQNPGA
          A.P.IVIALSGNK.DLANKRAVDFQEAQSYADDNSLLFM.TSAKTS.NVNE.FMAIAKKLPKNEPQNP.A
Retrocopy ACPDIVIALSGNKTDLANKRAVDFQEAQSYADDNSLLFMKTSAKTSVNVNEMFMAIAKKLPKNEPQNPEA

Parental  NSA
          NSA
Retrocopy NSA

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	32.08 RPM
SRP007412_cerebellum	0.00 RPM	25.41 RPM
SRP007412_heart	0.00 RPM	3.81 RPM
SRP007412_kidney	0.04 RPM	28.46 RPM
SRP007412_liver	0.03 RPM	19.81 RPM
SRP007412_testis	0.00 RPM	35.22 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_848 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_848 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1074
Pongo abelii	retro_pabe_894
Macaca mulatta	retro_mmul_839
Callithrix jacchus	retro_cjac_3268

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Parental genes homology:

Parental genes homology involve 20 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000954	1 retrocopy	retro_amel_958,
Bos taurus	ENSBTAG00000046385	1 retrocopy	retro_btau_300,
Callithrix jacchus	ENSCJAG00000003731	1 retrocopy	retro_cjac_3268,
Cavia porcellus	ENSCPOG00000005322	2 retrocopies	retro_cpor_1213, retro_cpor_219,
Dipodomys ordii	ENSDORG00000012429	1 retrocopy	retro_dord_288,
Felis catus	ENSFCAG00000004455	2 retrocopies	retro_fcat_1349, retro_fcat_984,
Homo sapiens	ENSG00000144566	1 retrocopy	retro_hsap_1074,
Gorilla gorilla	ENSGGOG00000005472	1 retrocopy	retro_ggor_2182,
Gorilla gorilla	ENSGGOG00000015981	1 retrocopy	retro_ggor_848 ,
Loxodonta africana	ENSLAFG00000008321	1 retrocopy	retro_lafr_267,
Macaca mulatta	ENSMMUG00000006992	2 retrocopies	retro_mmul_227, retro_mmul_839,
Monodelphis domestica	ENSMODG00000014793	2 retrocopies	retro_mdom_1219, retro_mdom_1993,
Mus musculus	ENSMUSG00000017831	1 retrocopy	retro_mmus_1645,
Nomascus leucogenys	ENSNLEG00000003434	1 retrocopy	retro_nleu_2466,
Oryctolagus cuniculus	ENSOCUG00000012200	1 retrocopy	retro_ocun_1034,
Pongo abelii	ENSPPYG00000014074	2 retrocopies	retro_pabe_3094, retro_pabe_894,
Pan troglodytes	ENSPTRG00000014682	1 retrocopy	retro_ptro_731,
Ictidomys tridecemlineatus	ENSSTOG00000026229	1 retrocopy	retro_itri_398,
Tarsius syrichta	ENSTSYG00000007642	3 retrocopies	retro_tsyr_1544, retro_tsyr_315, retro_tsyr_946,
Tursiops truncatus	ENSTTRG00000001374	1 retrocopy	retro_ttru_949,