RetrogeneDB ID: retro_mmul_2021

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 6:79376675..79377212(+)
• Located in intron of: ENSMMUG00000021609

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.4043
• Ensembl ID: ENSMMUG00000017928
• Aliases: None
• Description: 60S ribosomal protein L13 [Source:UniProtKB/TrEMBL;Acc:F6XL94]

Sequence

>retro_mmul_2021
ATGGTGCCCAGCAGGAATGGCATAATCCTGAAGCTCCACTTTTATAAGAACTGGCAGTGGCCCATAGCGACATGGTTCAC
CCAGCCTGCAAGGAAGAGCCACAGACATGAGACCAGAGAAGTCAAAGCCCACTGCATTGCCCGGTGCCTTGTATCTGGAC
CCATTGGCCCCTAGTAAAATGTCCCACATGAGGTTTCACACCAAGTACAAGCTGGCAGGGGCTTCAGCTTGGAAGAATTA
AGGGTGGCCAGCATCCACAAGAAGATGGCCTGGACCATTGATTTCTCTATTGATCCAAGAAGGTGAAACAAGTCCATTGA
GTCCTTGCAGGCCAATGTATAACAGCTTTAGGAGTACTGCTGGAAGCTTATCCTCCTTCTCTAGGAACCTCAGCCTCCAA
GAAGGGAGACGGCTACACTGAAGAACTCAAATTGGCCATCACACTGACAGGACCAGTAATGTTCATATGGAATACCTATA
AGAAGGAGAAGCCAGAGTCATCACCAAGAGGAAGAGAACTTCAAGACTGCCACATCA

Alignment

ORF - retro_mmul_2021 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.71 %
• Parental protein coverage: 85.78 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  MAPSRNGMILKPHFHKDWQRRVATWFNQPARKIRRRKARQAKARRIAPRPASGPIRP-IVRCPT-VRYHT
          M.PSRNG.ILK.HF.K.WQ...ATWF.QPARK..R...R..KA..IA....SGPI.P..V.CPT..R.HT
Retrocopy MVPSRNGIILKLHFYKNWQWPIATWFTQPARKSHRHETREVKAHCIARCLVSGPIGP<LVKCPT<MRFHT

Parental  K-VRAGRGFSLEELRVAGVHKKVARTIGISVDPRRRNKSTESLQANVQRLKEYRSKLILFPRKP-SAPKK
          K.V.AGRGFSLEELRVA..HKK.A.TI..S.DPRR.NKS.ESLQANV..L.EY..KLIL....P.SA.KK
Retrocopy K<VQAGRGFSLEELRVASIHKKMAWTIDFSIDPRR*NKSIESLQANV*QL*EYCWKLILLL*EP<SASKK

Parental  GDSSAEELKLATQLTGPVMPIRNVYKKEK-ARVIT-EEEKNFKAFAS
          GD...EELKLA..LTGPVM.I.N.YKKEK.ARVIT..EE.NFK...S
Retrocopy GDGYTEELKLAITLTGPVMFIWNTYKKEK<ARVIT<QEEENFKTATS

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	55.35 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	178.57 RPM
SRP007412_cerebellum	0.06 RPM	56.18 RPM
SRP007412_heart	0.00 RPM	132.96 RPM
SRP007412_kidney	0.00 RPM	111.85 RPM
SRP007412_liver	0.00 RPM	241.58 RPM
SRP007412_testis	0.00 RPM	98.68 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2021 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2021 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2021 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3207
Pan troglodytes	retro_ptro_2242

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 75 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000017072	1 retrocopy	retro_acar_70,
Canis familiaris	ENSCAFG00000019840	5 retrocopies	retro_cfam_1135, retro_cfam_1919, retro_cfam_2122, retro_cfam_565, retro_cfam_897,
Callithrix jacchus	ENSCJAG00000009672	5 retrocopies	retro_cjac_2607, retro_cjac_2961, retro_cjac_4054, retro_cjac_663, retro_cjac_747,
Echinops telfairi	ENSETEG00000015057	4 retrocopies	retro_etel_1240, retro_etel_1382, retro_etel_1606, retro_etel_703,
Gorilla gorilla	ENSGGOG00000025427	6 retrocopies	retro_ggor_1548, retro_ggor_1963, retro_ggor_2231, retro_ggor_2732, retro_ggor_562, retro_ggor_767,
Loxodonta africana	ENSLAFG00000004054	5 retrocopies	retro_lafr_659, retro_lafr_766, retro_lafr_827, retro_lafr_828, retro_lafr_829,
Macaca mulatta	ENSMMUG00000017928	7 retrocopies	retro_mmul_2021 , retro_mmul_2150, retro_mmul_2350, retro_mmul_579, retro_mmul_593, retro_mmul_737, retro_mmul_781,
Monodelphis domestica	ENSMODG00000003663	4 retrocopies	retro_mdom_1001, retro_mdom_416, retro_mdom_439, retro_mdom_674,
Mus musculus	ENSMUSG00000000740	23 retrocopies	retro_mmus_1091, retro_mmus_1522, retro_mmus_1533, retro_mmus_1854, retro_mmus_2074, retro_mmus_2163, retro_mmus_2186, retro_mmus_2321, retro_mmus_2333, retro_mmus_2351, retro_mmus_25, retro_mmus_2668, retro_mmus_2718, retro_mmus_3097, retro_mmus_3274, retro_mmus_3453, retro_mmus_3489, retro_mmus_3500, retro_mmus_355, retro_mmus_3711, retro_mmus_692, retro_mmus_732, retro_mmus_863,
Ornithorhynchus anatinus	ENSOANG00000006729	1 retrocopy	retro_oana_78,
Rattus norvegicus	ENSRNOG00000015335	14 retrocopies	retro_rnor_1054, retro_rnor_1260, retro_rnor_158, retro_rnor_160, retro_rnor_1719, retro_rnor_1720, retro_rnor_1834, retro_rnor_1848, retro_rnor_2471, retro_rnor_2574, retro_rnor_2608, retro_rnor_2787, retro_rnor_2854, retro_rnor_682,