RetrogeneDB ID: retro_mmul_1607

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 3:60593443..60594318(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.18258
• Ensembl ID: ENSMMUG00000021233
• Aliases: None
• Description: selenide, water dikinase 1 [Source:RefSeq peptide;Acc:NP_001177347]

Sequence

>retro_mmul_1607
GGCTGCAAAATGCCCCAAGATATCCTGCAAAAATTGCTGGAATCTTTACAGGCGAACCACTTCCAAGAAGATGAGCAATT
TTTGGAAGCCATTATGCCAAGGCTTGGCATTGGAATGGATACTTGTGTCATTCCTTTGAGACACAGTGGGCTTTCCTTGG
TTCAAATCACAGATTACATTTACCTGATCGTAGACGACTCCTATATGATGGGCAGGATAGCATGTGCCAATGTCCTCAGT
GACCTCTATGCAATGGGGGTCACGGAATGTGGCAATATGCTGATGCTCCTTAGAGTCAATAATAAAATGATCGACAGGGA
AAGAGATAAAGTGATGCTTCTGATTATCCAAGGTTTTAAAGATGCAGCTGAATAAACAGGAACATCTGTAACAGGCAGCC
AAACAGTACTAAACCCCTGGATTGTCCTGGGAGGAGTCGCTACCACTGTCTGCCAGCCCAGTGAATTTATCATGCCAGAC
AATGCAGTGCCAGGGGACGTGCTGGTGTTGACAAAACCCCTGGGGACACAGGTGGCAGTGACTGTGCACCAGTGGCTGGA
TATTCCTGAGAAATGGAATAAGATTAAACTAGTGGTCACCCAAGAAGATGTAGAGCTGGCCTACCAGAAGGTGATGATGA
ACATGGGGAGGCTCAACAGGACAGGCGGCCTTCTGATCTGTTTACCACGTGAGCAAGCAGCTCGGTTCTGTGCAGAGATA
AAGTCCTCCAGATGTGGTGAAGGCAACCAAGCATGATTATTGGGATTGTAGAGAAGGGCAACCACACAGCCAGAATCATA
GACAAACCCTGGATCATCAAGATTGCACCACAAGTGGCCACTCAAAATGTGAATCCCACACCTGGGGCCACCTCT

Alignment

ORF - retro_mmul_1607 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.08 %
• Parental protein coverage: 90.97 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GCKVPQDVLQKLLESLQENHFQEDEQFLGAVMPRLGIGMDTCVIPLRHGGLSLVQTTDYIYPIVDDPYMM
          GCK.PQD.LQKLLESLQ.NHFQEDEQFL.A.MPRLGIGMDTCVIPLRH.GLSLVQ.TDYIY.IVDD.YMM
Retrocopy GCKMPQDILQKLLESLQANHFQEDEQFLEAIMPRLGIGMDTCVIPLRHSGLSLVQITDYIYLIVDDSYMM

Parental  GRIACANVLSDLYAMGVTECDNMLMLLGVSNKMTDRERDKVMPLIIQGFKDAAEEAGTSVTGGQTVLNPW
          GRIACANVLSDLYAMGVTEC.NMLMLL.V.NKM.DRERDKVM.LIIQGFKDAAE..GTSVTG.QTVLNPW
Retrocopy GRIACANVLSDLYAMGVTECGNMLMLLRVNNKMIDRERDKVMLLIIQGFKDAAE*TGTSVTGSQTVLNPW

Parental  IVLGGVATTVCQPNEFIMPDNAVPGDVLVLTKPLGTQVAVAVHQWLDIPEKWNKIKLVVTQEDVELAYQE
          IVLGGVATTVCQP.EFIMPDNAVPGDVLVLTKPLGTQVAV.VHQWLDIPEKWNKIKLVVTQEDVELAYQ.
Retrocopy IVLGGVATTVCQPSEFIMPDNAVPGDVLVLTKPLGTQVAVTVHQWLDIPEKWNKIKLVVTQEDVELAYQK

Parental  AMMNMARLNRTGGLLICLPREQAARFCAEIKSPKYGEGHQA-WIIGIVEKGNRTARIIDKPRIIEVAPQV
          .MMNM.RLNRTGGLLICLPREQAARFCAEIKS...GEG.QA..IIGIVEKGN.TARIIDKP.II..APQV
Retrocopy VMMNMGRLNRTGGLLICLPREQAARFCAEIKSSRCGEGNQA<MIIGIVEKGNHTARIIDKPWIIKIAPQV

Parental  ATQNVNPTPGATS
          ATQNVNPTPGATS
Retrocopy ATQNVNPTPGATS

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	0.56 RPM	10.76 RPM
SRP007412_brain_prefrontal_cortex	0.87 RPM	19.12 RPM
SRP007412_cerebellum	0.32 RPM	17.18 RPM
SRP007412_heart	0.12 RPM	8.72 RPM
SRP007412_kidney	0.12 RPM	20.30 RPM
SRP007412_liver	0.00 RPM	30.40 RPM
SRP007412_testis	0.34 RPM	8.33 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1607 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1607 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1607 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 23 parental genes, and 46 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000013555	1 retrocopy	retro_amel_21,
Canis familiaris	ENSCAFG00000004743	2 retrocopies	retro_cfam_1787, retro_cfam_250,
Callithrix jacchus	ENSCJAG00000009494	2 retrocopies	retro_cjac_166, retro_cjac_2219,
Dipodomys ordii	ENSDORG00000014119	1 retrocopy	retro_dord_792,
Equus caballus	ENSECAG00000014281	1 retrocopy	retro_ecab_77,
Felis catus	ENSFCAG00000003921	1 retrocopy	retro_fcat_96,
Homo sapiens	ENSG00000086475	3 retrocopies	retro_hsap_2196, retro_hsap_3860, retro_hsap_4705,
Gorilla gorilla	ENSGGOG00000003806	2 retrocopies	retro_ggor_147, retro_ggor_2924,
Loxodonta africana	ENSLAFG00000004670	1 retrocopy	retro_lafr_125,
Macropus eugenii	ENSMEUG00000012188	1 retrocopy	retro_meug_245,
Myotis lucifugus	ENSMLUG00000001971	2 retrocopies	retro_mluc_2350, retro_mluc_728,
Macaca mulatta	ENSMMUG00000021233	4 retrocopies	retro_mmul_1607 , retro_mmul_2495, retro_mmul_2647, retro_mmul_922,
Monodelphis domestica	ENSMODG00000016864	1 retrocopy	retro_mdom_86,
Mustela putorius furo	ENSMPUG00000000948	1 retrocopy	retro_mputfur_20,
Mus musculus	ENSMUSG00000026662	1 retrocopy	retro_mmus_248,
Nomascus leucogenys	ENSNLEG00000012205	7 retrocopies	retro_nleu_1868, retro_nleu_2211, retro_nleu_234, retro_nleu_2668, retro_nleu_2873, retro_nleu_3004, retro_nleu_327,
Otolemur garnettii	ENSOGAG00000007807	1 retrocopy	retro_ogar_3026,
Procavia capensis	ENSPCAG00000015617	1 retrocopy	retro_pcap_341,
Pongo abelii	ENSPPYG00000002099	6 retrocopies	retro_pabe_1324, retro_pabe_1378, retro_pabe_2074, retro_pabe_2620, retro_pabe_3047, retro_pabe_3652,
Pan troglodytes	ENSPTRG00000002303	3 retrocopies	retro_ptro_1135, retro_ptro_1669, retro_ptro_3126,
Pteropus vampyrus	ENSPVAG00000002945	2 retrocopies	retro_pvam_115, retro_pvam_566,
Rattus norvegicus	ENSRNOG00000018125	1 retrocopy	retro_rnor_59,
Tursiops truncatus	ENSTTRG00000011114	1 retrocopy	retro_ttru_649,