RetrogeneDB ID: retro_mmul_2041

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 6:135040884..135041500(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPL10A
• Ensembl ID: ENSMMUG00000015907
• Aliases: None
• Description: 60S ribosomal protein L10a [Source:RefSeq peptide;Acc:NP_001253155]

Sequence

>retro_mmul_2041
GAGACCTTGTAGGAGGCAGTGCGGGAAGTCCTGGACAGGAACCAGTGCAAGTGCCAGAAACTTTTGGGAACACTGGAGCT
ACAGATCCGCTTGAAGAACTGTGACCCTCAGAAAGATGAACGCTTCTTGGGCACTGTCATCTGAAGTCCACTCCCCGCCC
CACGTTCTCCACATGTGTCCTGGGGGACCAGCAGCACTGGGATGAGGCCAAGGCTGTGGGTGTCTCCCATGTGGACATCG
AGGTGCTGAAGAAACTTGACAAGAACAAGAAGCTGCTTAACAAGTATGATGCCTTTTTGGCCTCAGGGTCTGTGATCAGG
CAGATCCCACAAATCCTGGGCCTAGGCCTAAATAAGGAAGGCAGGTTCCCTTCCCTGCTGACGTACAGTGAAGACATGGT
GGCCAAAGTTGATGAGGGGAAGTCCACAATCAAGTTCCAGAGGAAGAAAGGGCTCTGTCTGGCATGGCTCTTGGCCATGT
CCGGATGACAGACGACGAGCTTGTGTACAATGTCCATCTGGCTCTCAGCTTCCAGGTATCATTGCTCTGGAAGAACTGGC
AGAACATCTGGGCTTTATATGTCAGGAACACCATAGGCAAAAGCCCCAGTGCCTAT

Alignment

ORF - retro_mmul_2041 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.28 %
• Parental protein coverage: 96.77 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  DTLYEAVREVLHGNQRKRRKFLETVELQISLKNYDPQKDKRFSGTV-RLKSTPRPKFSVCVLGDQQHCDE
          .TL.EAVREVL..NQ.K..K.L.T.ELQI.LKN.DPQKD.RF.GTV..LKSTPRP.FS.CVLGDQQH.DE
Retrocopy ETL*EAVREVLDRNQCKCQKLLGTLELQIRLKNCDPQKDERFLGTV<HLKSTPRPTFSTCVLGDQQHWDE

Parental  AKAVDIPHMDIEALKKLNKNKKLVKKLAKKYDAFLASESLIKQIPRILGPGLNKAGKFPSLLTHNENMVA
          AKAV...H.DIE.LKKL.KN....KKL..KYDAFLAS.S.I.QIP.ILG.GLNK.G.FPSLLT..E.MVA
Retrocopy AKAVGVSHVDIEVLKKLDKN----KKLLNKYDAFLASGSVIRQIPQILGLGLNKEGRFPSLLTYSEDMVA

Parental  KVDEVKSTIKFQMKKVLCLA-VAVGHVKMTDDELVYNIHLAVNFLVSLLKKNWQNVRALYIKSTMGKPQR
          KVDE.KSTIKFQ.KK.LCLA..A.GHV.MTDDELVYN.HLA..F.VSLL.KNWQN..ALY...T.GK...
Retrocopy KVDEGKSTIKFQRKKGLCLA<MALGHVRMTDDELVYNVHLALSFQVSLLWKNWQNIWALYVRNTIGKSPS

Parental  LY
          .Y
Retrocopy AY

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	0.00 RPM	102.41 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	157.15 RPM
SRP007412_cerebellum	0.19 RPM	96.41 RPM
SRP007412_heart	0.00 RPM	174.01 RPM
SRP007412_kidney	0.00 RPM	159.15 RPM
SRP007412_liver	0.00 RPM	165.86 RPM
SRP007412_testis	0.08 RPM	49.11 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2041 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2041 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2041 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3245
Pan troglodytes	retro_ptro_2193

---

Parental genes homology:

Parental genes homology involve 14 parental genes, and 86 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000670	13 retrocopies	retro_amel_1144, retro_amel_1223, retro_amel_1262, retro_amel_1591, retro_amel_1813, retro_amel_198, retro_amel_318, retro_amel_320, retro_amel_417, retro_amel_520, retro_amel_609, retro_amel_710, retro_amel_970,
Echinops telfairi	ENSETEG00000013325	2 retrocopies	retro_etel_1974, retro_etel_326,
Felis catus	ENSFCAG00000012904	7 retrocopies	retro_fcat_1144, retro_fcat_1488, retro_fcat_1561, retro_fcat_1971, retro_fcat_210, retro_fcat_262, retro_fcat_560,
Homo sapiens	ENSG00000198755	13 retrocopies	retro_hsap_142, retro_hsap_1462, retro_hsap_1710, retro_hsap_177, retro_hsap_1935, retro_hsap_2795, retro_hsap_3025, retro_hsap_3245, retro_hsap_3353, retro_hsap_337, retro_hsap_3949, retro_hsap_4025, retro_hsap_4040,
Gorilla gorilla	ENSGGOG00000028140	10 retrocopies	retro_ggor_1, retro_ggor_1124, retro_ggor_1282, retro_ggor_1407, retro_ggor_2088, retro_ggor_2273, retro_ggor_234, retro_ggor_2702, retro_ggor_358, retro_ggor_57,
Macropus eugenii	ENSMEUG00000005760	6 retrocopies	retro_meug_1337, retro_meug_1578, retro_meug_2066, retro_meug_407, retro_meug_541, retro_meug_705,
Macaca mulatta	ENSMMUG00000015907	6 retrocopies	retro_mmul_1931, retro_mmul_2041 , retro_mmul_2321, retro_mmul_2330, retro_mmul_306, retro_mmul_583,
Monodelphis domestica	ENSMODG00000013766	2 retrocopies	retro_mdom_276, retro_mdom_499,
Nomascus leucogenys	ENSNLEG00000008650	13 retrocopies	retro_nleu_1174, retro_nleu_1210, retro_nleu_1697, retro_nleu_1778, retro_nleu_1980, retro_nleu_2055, retro_nleu_2342, retro_nleu_2436, retro_nleu_2879, retro_nleu_662, retro_nleu_838, retro_nleu_986, retro_nleu_989,
Ornithorhynchus anatinus	ENSOANG00000014574	1 retrocopy	retro_oana_86,
Oryctolagus cuniculus	ENSOCUG00000004065	2 retrocopies	retro_ocun_130, retro_ocun_4,
Rattus norvegicus	ENSRNOG00000000505	4 retrocopies	retro_rnor_2302, retro_rnor_37, retro_rnor_400, retro_rnor_43,
Sarcophilus harrisii	ENSSHAG00000002047	1 retrocopy	retro_shar_438,
Tursiops truncatus	ENSTTRG00000009431	6 retrocopies	retro_ttru_100, retro_ttru_1137, retro_ttru_1325, retro_ttru_1477, retro_ttru_205, retro_ttru_494,