RetrogeneDB ID: retro_mmul_431

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 1:150095023..150096058(+)
• Located in intron of: ENSMMUG00000007784

Retrocopy information

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

Parental gene information

• Parental gene symbol: AURKA
• Ensembl ID: ENSMMUG00000000070
• Aliases: None
• Description: None

Sequence

>retro_mmul_431
ATGGACCAATCTAAAGAAAACTACATTTCAGGGCCTGTTAAGGCTACATCTCCAGTTGGAGGTCCAAAACATGTTCTCGT
GACTCAGCAATTTCCTTGTCAGAATCCATTACCTGCAAATAGTGGCCAGGCTCAGTGGGTCTTGTGTCCTTCAAATTCTT
CCCAGCGTGTTCCTTTGCAAGCACAAAAGCTTGGCTCCAGTCACAAGCCAGTTCAGAATCAGAAACAGAAGCAATTGCAG
GCAACCAGTGTACCTCATCCTGTCTCCAGGCCACTGAATAACACCCAAAAGAGCAAGCAGCCCCCGCTGTCGGCACCTGA
AAATAATCCTGAGGAGGAACTGGCATCAAAACAGAAAAATGAAGAATCAAAAAAGAGGGAATGGGCTTTGGAAGACTTTG
AAATTGGTCACCTTCTGGGTAAAGGAAAGTTTGGTAATGTTTATTTGGCAAGAGAAAAACAAAGCAAGTTTATTCTGGCT
CTTAAAGTGTTATTTAAAGTTCAGCTGGAGAAAGCAGGATTGGAGCATCAACTCAGAAGAGAAGTAGAAATACAGTCCTA
CCTTCAACATCCTGATATAATCAGACTGTGTGGTTATTTCCATGATGCCACCAGAGTCTACCTAATTCTGGAATATACAC
CACTTGAAACAGTCAATAGAGAACTTCAGAAACTTTCGAAGTTTGATGAGCAGAGAACTGCTACTTATATCACAGAATTG
GCCAATGCCCTGTCTTACTGTCATTCAAAGACAGTTATTCATAGAGACATTAAGCCAGAGAACTTACTTCTTGGATCAGC
TGGATAGCTTAACATTGCAAATTTTGGGTGGTCAGTACATGCTCCATCTTCCGGGAGGACCACTCTCTGTGGCACCCTGG
ACGACCTGCCCCCCGAAATGATTGAGGGTCAGATGCATGATGAGAAGGTGGATCTCTGGAGCCTTGGAGTTCTTTGCTAT
GAATTTTTAGTTGGGAAGCCTCCTTTTAAGGCAGACACATACCAAGAGACCTACAAAAGAATATCATCAGTTGAG

Alignment

ORF - retro_mmul_431 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.99 %
• Parental protein coverage: 86.68 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MDRSKENCISGPVKPAAPVGGPKRVLVTQQFPCQNPLPANSGQAQRVLCPSNSSQRVPLQAQKLVSSHKL
          MD.SKEN.ISGPVK...PVGGPK.VLVTQQFPCQNPLPANSGQAQ.VLCPSNSSQRVPLQAQKL.SSHK.
Retrocopy MDQSKENYISGPVKATSPVGGPKHVLVTQQFPCQNPLPANSGQAQWVLCPSNSSQRVPLQAQKLGSSHKP

Parental  VQNQKQKQLQATSVPHPVSRPPSHTPKSKQPLPSAPENNPEEELASKQKNEESKKRQWALEDFEIGRPLG
          VQNQKQKQLQATSVPHPVSRP...T.KSKQP..SAPENNPEEELASKQKNEESKKR.WALEDFEIG..LG
Retrocopy VQNQKQKQLQATSVPHPVSRPLNNTQKSKQPPLSAPENNPEEELASKQKNEESKKREWALEDFEIGHLLG

Parental  KGKFGNVYLAREKQSKFILALKVLFKAQLEKAGVEHQLRREVEIQSHLRHPNILRLYGYFHDATRVYLIL
          KGKFGNVYLAREKQSKFILALKVLFK.QLEKAG.EHQLRREVEIQS.L.HP.I.RL.GYFHDATRVYLIL
Retrocopy KGKFGNVYLAREKQSKFILALKVLFKVQLEKAGLEHQLRREVEIQSYLQHPDIIRLCGYFHDATRVYLIL

Parental  EYAPLGTVYRELQKLSKFDEQRTATYITELANALSYCHSKRVIHRDIKPENLLLGSAGELKIADFGWSVH
          EY.PL.TV.RELQKLSKFDEQRTATYITELANALSYCHSK.VIHRDIKPENLLLGSAG.L.IA.FGWSVH
Retrocopy EYTPLETVNRELQKLSKFDEQRTATYITELANALSYCHSKTVIHRDIKPENLLLGSAG*LNIANFGWSVH

Parental  APSSRRTTLCGTLDYLPPEMIEGRMHDEKVDLWSLGVLCYEFLVGKPPFEANTYQETYKRISRVE
          APSS.RTTLCGTLD.LPPEMIEG.MHDEKVDLWSLGVLCYEFLVGKPPF.A.TYQETYKRIS.VE
Retrocopy APSSGRTTLCGTLDDLPPEMIEGQMHDEKVDLWSLGVLCYEFLVGKPPFKADTYQETYKRISSVE

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	0.22 RPM	0.90 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	1.75 RPM
SRP007412_cerebellum	0.06 RPM	1.74 RPM
SRP007412_heart	0.18 RPM	2.77 RPM
SRP007412_kidney	0.12 RPM	2.00 RPM
SRP007412_liver	0.08 RPM	0.67 RPM
SRP007412_testis	0.11 RPM	114.81 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_431 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_431 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_431 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_510
Pan troglodytes	retro_ptro_381
Gorilla gorilla	retro_ggor_470
Pongo abelii	retro_pabe_231

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 33 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000029331	3 retrocopies	retro_cfam_1027, retro_cfam_257, retro_cfam_764,
Choloepus hoffmanni	ENSCHOG00000005976	8 retrocopies	retro_chof_1302, retro_chof_1575, retro_chof_1709, retro_chof_2213, retro_chof_2389, retro_chof_259, retro_chof_565, retro_chof_764,
Cavia porcellus	ENSCPOG00000006633	1 retrocopy	retro_cpor_106,
Felis catus	ENSFCAG00000024493	1 retrocopy	retro_fcat_495,
Homo sapiens	ENSG00000087586	1 retrocopy	retro_hsap_510,
Gorilla gorilla	ENSGGOG00000007197	1 retrocopy	retro_ggor_470,
Myotis lucifugus	ENSMLUG00000007925	1 retrocopy	retro_mluc_1931,
Macaca mulatta	ENSMMUG00000000070	1 retrocopy	retro_mmul_431 ,
Macaca mulatta	ENSMMUG00000002997	1 retrocopy	retro_mmul_2367,
Mus musculus	ENSMUSG00000027496	1 retrocopy	retro_mmus_2825,
Nomascus leucogenys	ENSNLEG00000007029	1 retrocopy	retro_nleu_1553,
Otolemur garnettii	ENSOGAG00000004441	3 retrocopies	retro_ogar_2805, retro_ogar_3440, retro_ogar_980,
Pongo abelii	ENSPPYG00000011148	1 retrocopy	retro_pabe_231,
Pan troglodytes	ENSPTRG00000013646	1 retrocopy	retro_ptro_381,
Rattus norvegicus	ENSRNOG00000004479	2 retrocopies	retro_rnor_664, retro_rnor_670,
Sus scrofa	ENSSSCG00000007493	1 retrocopy	retro_sscr_936,
Ictidomys tridecemlineatus	ENSSTOG00000011958	2 retrocopies	retro_itri_366, retro_itri_772,
Tupaia belangeri	ENSTBEG00000013284	2 retrocopies	retro_tbel_1137, retro_tbel_2604,
Tarsius syrichta	ENSTSYG00000009221	1 retrocopy	retro_tsyr_378,