RetrogeneDB ID: retro_mmul_999

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 13:90119620..90120717(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.4625
• Ensembl ID: ENSMMUG00000019099
• Aliases: None
• Description: developmentally-regulated GTP-binding protein 1 [Source:RefSeq peptide;Acc:NP_001253866]

Sequence

>retro_mmul_999
ATGGGCAGCACCTTAGCTAAGATCGTGGAGACAGAAGCCGAGATGACTCAGACTCAAAAGAACGAGGCCACAGCACACCA
CCTAGGGCTACTTAAAGCTCGTCTTGCTAAGCTTCGTCGAGAACTCATTACTCCAAAGGGTGCTGGTGGTGGAGGTCCAG
GAGAACGTTTTGATGTGGCCAAGACAGGTGATGCTAGAACTGGATTTGTTGGTTTTTCATCTGTGGCGAAGTCGACACTG
CTTAGTAACCTGGCAGGGATATATTCTGAGGTGGCAGCCTATGAATTCACTACTCTGACCACTGTGCCTGGTGTCATCAG
ACACAAAGGTGGCAAGATCCAGCTCCTGGCTCTCCCAGGTATCATTAAAGGTGCCAAGGATGGGAAAGGTAAAGGTCAAG
TCATTGCAGTGGCCCAAACCTGTAACTTGATCCTGATTGTTCTGGATGTCCTGAAACCTTTGGGACATAAGAAGATAAAT
GAAAATGAGCTGGAAGGCTTTGGCATTCGCTTGAACAGCAAACCCCCCAACATTGGCTTTAAGAAGAAAGAGAAGGGAGG
CATTAATCTCACAGTCACTTGCCCCCAGAGTGAGCTGGATGCTGAAACTGTGAAGAGCATTCTGGTCAAATACAAGATTC
ATAATGCCGATGTGACTCTACGTAGTGATGCTACAGCTGATGACCTCATTGATGTGTTGGAAGGAAACAGAGTTTATATC
GCCTGTATCTACGTGTTAAATAAGATAGACTGAATCTCTATTGAGGAATTGGATATCATCTATAAGGTTCCTCACTGTGT
ACCCATCTCTGCCCATCACCGCTGGAATTTTGATGACCTATTGGAAAAGATCTGGGACTATCTGAAACTAGTGAGAATTT
ACACCAAACTCAAAGGCCAATTACCAGATTACCCATCCCCACTGGTGCTTCCTTACTCCAGGACCACAGTGGAGGATTTC
TGCATGAAGAGTCACAAAAATCTTACAAAGAATTTAAATATGCTCTGGTCTGGGGTCTCTCTGTGAAACACAATCCTCAG
AAAGTGGGTAAAGACCATACGTTGGAGGACGAGGATGTCATTTAAATTGTGAAGAAG

Alignment

ORF - retro_mmul_999 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.76 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSSTLAKIAEIEAEMARTQKNKATAHHLGLLKARLAKLRRELITPKGGGGGGPGEGFDVAKTGDARIGFV
          M.STLAKI.E.EAEM..TQKN.ATAHHLGLLKARLAKLRRELITPKG.GGGGPGE.FDVAKTGDAR.GFV
Retrocopy MGSTLAKIVETEAEMTQTQKNEATAHHLGLLKARLAKLRRELITPKGAGGGGPGERFDVAKTGDARTGFV

Parental  GFPSVGKSTLLSNLAGVYSEVAAYEFTTLTTVPGVIRYKGAKIQLLDLPGIIEGAKDGKGRGRQVIAVAR
          GF.SV.KSTLLSNLAG.YSEVAAYEFTTLTTVPGVIR.KG.KIQLL.LPGII.GAKDGKG.G.QVIAVA.
Retrocopy GFSSVAKSTLLSNLAGIYSEVAAYEFTTLTTVPGVIRHKGGKIQLLALPGIIKGAKDGKGKG-QVIAVAQ

Parental  TCNLILIVLDVLKPLGHKKIIENELEGFGIRLNSKPPNIGFKKKDKGGINLTATCPQSELDAETVKSILA
          TCNLILIVLDVLKPLGHKKI.ENELEGFGIRLNSKPPNIGFKKK.KGGINLT.TCPQSELDAETVKSIL.
Retrocopy TCNLILIVLDVLKPLGHKKINENELEGFGIRLNSKPPNIGFKKKEKGGINLTVTCPQSELDAETVKSILV

Parental  EYKIHNADVTLRSDATADDLIDVVEGNRVYIPCIYVLNKIDQISIEELDIIYKVPHCVPISAHHRWNFDD
          .YKIHNADVTLRSDATADDLIDV.EGNRVYI.CIYVLNKID.ISIEELDIIYKVPHCVPISAHHRWNFDD
Retrocopy KYKIHNADVTLRSDATADDLIDVLEGNRVYIACIYVLNKID*ISIEELDIIYKVPHCVPISAHHRWNFDD

Parental  LLEKIWDYLKLVRIYTKPKGQLPDYTSPVVLPYSRTTVEDFCMKIHKNL-IKEFKYALVWGLSVKHNPQK
          LLEKIWDYLKLVRIYTK.KGQLPDY.SP.VLPYSRTTVEDFCMK.HKNL..KEFKYALVWGLSVKHNPQK
Retrocopy LLEKIWDYLKLVRIYTKLKGQLPDYPSPLVLPYSRTTVEDFCMKSHKNL<YKEFKYALVWGLSVKHNPQK

Parental  VGKDHTLEDEDVIQIVKK
          VGKDHTLEDEDVI.IVKK
Retrocopy VGKDHTLEDEDVI*IVKK

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	37.87 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	36.81 RPM
SRP007412_cerebellum	0.00 RPM	30.54 RPM
SRP007412_heart	0.00 RPM	26.03 RPM
SRP007412_kidney	0.12 RPM	24.53 RPM
SRP007412_liver	0.00 RPM	16.31 RPM
SRP007412_testis	0.08 RPM	109.95 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_999 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_999 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_999 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000007040	1 retrocopy	retro_amel_1448,
Canis familiaris	ENSCAFG00000032601	6 retrocopies	retro_cfam_1535, retro_cfam_1807, retro_cfam_382, retro_cfam_415, retro_cfam_453, retro_cfam_607,
Ciona intestinalis	ENSCING00000003305	1 retrocopy	retro_cint_1,
Callithrix jacchus	ENSCJAG00000011009	4 retrocopies	retro_cjac_1104, retro_cjac_2246, retro_cjac_2606, retro_cjac_855,
Cavia porcellus	ENSCPOG00000010791	1 retrocopy	retro_cpor_1401,
Ciona savignyi	ENSCSAVG00000006503	1 retrocopy	retro_csav_10,
Dasypus novemcinctus	ENSDNOG00000001312	1 retrocopy	retro_dnov_531,
Homo sapiens	ENSG00000185721	1 retrocopy	retro_hsap_2231,
Gorilla gorilla	ENSGGOG00000011185	1 retrocopy	retro_ggor_1665,
Myotis lucifugus	ENSMLUG00000007033	1 retrocopy	retro_mluc_1447,
Macaca mulatta	ENSMMUG00000019099	1 retrocopy	retro_mmul_999 ,
Mustela putorius furo	ENSMPUG00000012810	1 retrocopy	retro_mputfur_339,
Mus musculus	ENSMUSG00000020457	1 retrocopy	retro_mmus_2366,
Nomascus leucogenys	ENSNLEG00000027001	1 retrocopy	retro_nleu_2627,
Pan troglodytes	ENSPTRG00000014272	1 retrocopy	retro_ptro_1578,
Ictidomys tridecemlineatus	ENSSTOG00000014187	1 retrocopy	retro_itri_460,
Tarsius syrichta	ENSTSYG00000010160	3 retrocopies	retro_tsyr_1374, retro_tsyr_1918, retro_tsyr_405,