RetrogeneDB ID: retro_mmul_210

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 14:69717650..69718226(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMMUG00000003957
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: MMU.4064
• Ensembl ID: ENSMMUG00000018854
• Aliases: None
• Description: ras-related C3 botulinum toxin substrate 2 [Source:RefSeq peptide;Acc:NP_001248306]

Sequence

>retro_mmul_210
ATGCAGAGCATCAAGTGCGTGGTGGTGGGTGATGGGGCTGTGGGCAAGACGTGCCTGCTCATCTGCTACACAACTAACGC
TTTCCCCAAAGAGTACATCCCCACCGTGTTCGACAATTACAGCGCGCAGAGCGCAGTTGACGGGCGCACAGTGAACCTGA
ACCTGTGGGACACTGCGGGCCAGGAGGAGTATGACCGCCTCCGCACACTCTCCTACCCTCAGACCAACGTCTTTGTCATC
TGTTTCTCCATTGCCAGTCCACCTTCCTATGAGAACGTGCGACACAAGTGGCATCCAGAGGTGTGCCACCACTGCCCTGA
TGTGCCCATCCTGCTGGTGGGCACCAAGAAGGACCTGAGAGCCCAGCCTGACACTCTACGGCGCCTCAAGGAGCAGGGCC
AGGCGCCCATCACACCGCAGCAGGGCCAGGCACTGGCCAAGCAGATCCACGCTGTGCGCTACCTCGAATGCTCAGCCCTG
CAACAGGATGGTGTCAAGGAAGTGTTCGCCGAGGCTGTCCGGGCTGTGCTCAACCCCACTCCGATCAAGCGGGGACGGTC
CTGCGTCCTCTTGTGA

Alignment

ORF - retro_mmul_210 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.35 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MQAIKCVVVGDGAVGKTCLLISYTTNAFPGEYIPTVFDNYSANVMVDSKPVNLGLWDTAGQEDYDRLRPL
          MQ.IKCVVVGDGAVGKTCLLI.YTTNAFP.EYIPTVFDNYSA...VD...VNL.LWDTAGQE.YDRLR.L
Retrocopy MQSIKCVVVGDGAVGKTCLLICYTTNAFPKEYIPTVFDNYSAQSAVDGRTVNLNLWDTAGQEEYDRLRTL

Parental  SYPQTDVFLICFSLVSPASYENVRAKWFPEVRHHCPSTPIILVGTKLDLRDDKDTIEKLKEKKLAPITYP
          SYPQT.VF.ICFS..SP.SYENVR.KW.PEV.HHCP..PI.LVGTK.DLR...DT...LKE...APIT..
Retrocopy SYPQTNVFVICFSIASPPSYENVRHKWHPEVCHHCPDVPILLVGTKKDLRAQPDTLRRLKEQGQAPITPQ

Parental  QGLALAKEIDSVKYLECSALTQRGLKTVFDEAIRAVLCPQPTRQQKRACSLL
          QG.ALAK.I..V.YLECSAL.Q.G.K.VF.EA.RAVL.P.P.....R.C.LL
Retrocopy QGQALAKQIHAVRYLECSALQQDGVKEVFAEAVRAVLNPTPIK-RGRSCVLL

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	2.58 RPM	0.67 RPM
SRP007412_brain_prefrontal_cortex	9.76 RPM	0.24 RPM
SRP007412_cerebellum	3.81 RPM	0.45 RPM
SRP007412_heart	4.53 RPM	3.42 RPM
SRP007412_kidney	6.22 RPM	5.75 RPM
SRP007412_liver	19.48 RPM	11.68 RPM
SRP007412_testis	2.83 RPM	0.34 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_210 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_210 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_210 has 6 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_28
Gorilla gorilla	retro_ggor_188
Pongo abelii	retro_pabe_21
Mus musculus	retro_mmus_234
Rattus norvegicus	retro_rnor_230
Oryctolagus cuniculus	retro_ocun_43

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Parental genes homology:

Parental genes homology involve 23 parental genes, and 66 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009889	2 retrocopies	retro_amel_1691, retro_amel_647,
Callithrix jacchus	ENSCJAG00000002144	4 retrocopies	retro_cjac_1158, retro_cjac_1954, retro_cjac_2917, retro_cjac_847,
Equus caballus	ENSECAG00000022570	2 retrocopies	retro_ecab_619, retro_ecab_705,
Erinaceus europaeus	ENSEEUG00000009509	1 retrocopy	retro_eeur_20,
Felis catus	ENSFCAG00000025776	2 retrocopies	retro_fcat_1064, retro_fcat_826,
Gorilla gorilla	ENSGGOG00000010612	2 retrocopies	retro_ggor_1403, retro_ggor_188,
Loxodonta africana	ENSLAFG00000013012	1 retrocopy	retro_lafr_117,
Macropus eugenii	ENSMEUG00000012295	2 retrocopies	retro_meug_252, retro_meug_552,
Microcebus murinus	ENSMICG00000017775	4 retrocopies	retro_mmur_1104, retro_mmur_1557, retro_mmur_20, retro_mmur_600,
Myotis lucifugus	ENSMLUG00000012668	2 retrocopies	retro_mluc_326, retro_mluc_860,
Macaca mulatta	ENSMMUG00000018854	2 retrocopies	retro_mmul_1346, retro_mmul_210 ,
Macaca mulatta	ENSMMUG00000021075	4 retrocopies	retro_mmul_1310, retro_mmul_1964, retro_mmul_2642, retro_mmul_721,
Macaca mulatta	ENSMMUG00000022009	8 retrocopies	retro_mmul_1449, retro_mmul_1612, retro_mmul_1685, retro_mmul_1900, retro_mmul_1932, retro_mmul_24, retro_mmul_349, retro_mmul_598,
Mustela putorius furo	ENSMPUG00000012682	2 retrocopies	retro_mputfur_872, retro_mputfur_911,
Nomascus leucogenys	ENSNLEG00000014759	7 retrocopies	retro_nleu_1215, retro_nleu_1330, retro_nleu_2094, retro_nleu_2355, retro_nleu_689, retro_nleu_724, retro_nleu_87,
Oryctolagus cuniculus	ENSOCUG00000016115	1 retrocopy	retro_ocun_43,
Otolemur garnettii	ENSOGAG00000004138	1 retrocopy	retro_ogar_2977,
Pongo abelii	ENSPPYG00000011791	3 retrocopies	retro_pabe_1591, retro_pabe_21, retro_pabe_3818,
Pteropus vampyrus	ENSPVAG00000002281	2 retrocopies	retro_pvam_21, retro_pvam_609,
Sarcophilus harrisii	ENSSHAG00000014852	1 retrocopy	retro_shar_763,
Sus scrofa	ENSSSCG00000021944	4 retrocopies	retro_sscr_40, retro_sscr_565, retro_sscr_582, retro_sscr_882,
Ictidomys tridecemlineatus	ENSSTOG00000023766	1 retrocopy	retro_itri_510,
Tursiops truncatus	ENSTTRG00000001099	8 retrocopies	retro_ttru_1029, retro_ttru_1065, retro_ttru_1188, retro_ttru_1599, retro_ttru_1904, retro_ttru_318, retro_ttru_379, retro_ttru_825,