RetrogeneDB ID: retro_mmul_839

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 11:4733560..4734051(-)
• Located in intron of: ENSMMUG00000020812

Retrocopy information

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

Parental gene information

• Parental gene symbol: RAB5A
• Ensembl ID: ENSMMUG00000006992
• Aliases: None
• Description: ras-related protein Rab-5A [Source:RefSeq peptide;Acc:NP_001248077]

Sequence

>retro_mmul_839
ACAGATTCAGCTGATTTTCTAACCCAAACTGTGTGTCTTGATGACACTACGGTATAGTTTGAAATATGGGATACAGCTGG
TCAAGAACAATACCGCAGCCTAGCACCAATGTACTGCAGAGGAGCACAAACAGCCATCGTTGTATACGATATCACAAATG
AGGAGTCCTTTGCAAGTGCGAAAAATTGGGCTGAAGAACTTCAGAGGCAAGCATGTCCTGACATTGTAATAGCTTTATCA
GGAAACAAGGCTGACCTAGCAAATAAAAGAGCAGTAGATTTCCAGGAAGCACAGCCCTATGCAGATGACAATAGTTTATT
ATTCATGAAGACATCAGCTAAAACATCAATGAATGTAAATGAAATGTTCATGGCAATAGCTAAAAAATTGCCAAAGAATG
AACCACGAAATGCAGGAGCAAACTCTGCCAGGGGAAGAGGAGTAGCCCTTACTGAACCCACACAACCAACCAGGAGTCAG
TGTGTAGTAAT

Alignment

ORF - retro_mmul_839 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.88 %
• Parental protein coverage: 76.28 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  TIGAAFLTQTVCLDDTTVKFEIWDTAGQERYHSLAPMYYRGAQAAIVVYDITNEESFARAKNWVKELQRQ
          T..A.FLTQTVCLDDTTV.FEIWDTAGQE.Y.SLAPMY.RGAQ.AIVVYDITNEESFA.AKNW..ELQRQ
Retrocopy TDSADFLTQTVCLDDTTV*FEIWDTAGQEQYRSLAPMYCRGAQTAIVVYDITNEESFASAKNWAEELQRQ

Parental  ASPNIVIALSGNKADLANKRAVDFQEAQSYADDNSLLFMETSAKTSMNVNEIFMAIAKKLPKNEPQNPGA
          A.P.IVIALSGNKADLANKRAVDFQEAQ.YADDNSLLFM.TSAKTSMNVNE.FMAIAKKLPKNEP.N.GA
Retrocopy ACPDIVIALSGNKADLANKRAVDFQEAQPYADDNSLLFMKTSAKTSMNVNEMFMAIAKKLPKNEPRNAGA

Parental  NSARGRGVDLTEPTQPTRSQC-CSN
          NSARGRGV.LTEPTQPTRSQC.CSN
Retrocopy NSARGRGVALTEPTQPTRSQC<CSN

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	0.11 RPM	61.63 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	31.65 RPM
SRP007412_cerebellum	0.00 RPM	45.65 RPM
SRP007412_heart	0.00 RPM	21.14 RPM
SRP007412_kidney	0.00 RPM	26.64 RPM
SRP007412_liver	0.12 RPM	11.36 RPM
SRP007412_testis	0.11 RPM	22.65 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_839 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_839 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_839 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1074
Gorilla gorilla	retro_ggor_848
Pongo abelii	retro_pabe_894
Callithrix jacchus	retro_cjac_3268

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Parental genes homology:

Parental genes homology involve 21 parental genes, and 28 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	ENSGGOG00000015981	1 retrocopy	retro_ggor_848,
Loxodonta africana	ENSLAFG00000008321	1 retrocopy	retro_lafr_267,
Macaca mulatta	ENSMMUG00000005692	1 retrocopy	retro_mmul_1557,
Macaca mulatta	ENSMMUG00000006992	2 retrocopies	retro_mmul_227, retro_mmul_839 ,
Macaca mulatta	ENSMMUG00000014761	1 retrocopy	retro_mmul_2022,
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,