RetrogeneDB ID: retro_mmul_422

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 1:142960128..142960539(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.2633
• Ensembl ID: ENSMMUG00000005645
• Aliases: None
• Description: nuclear ubiquitous casein and cyclin-dependent kinases substrate [Source:RefSeq peptide;Acc:NP_001253410]

Sequence

>retro_mmul_422
TTCAGAAATAGGAAGGTTTGTTGATTTCTCACAGTTTCAGGAATCTGATGATACAGATGAAGATTCGGGCCCTACCACTA
AGAAAATTTGATCATCTCCCCTAGAAGCTAAAAATAAGGCGATCTGGAAAGAATTCACAGGAAGATAGTGAGGACTCAGA
AGAAAAAGATCTGAAGACCAAGAAGGATGACTTTCACTCAGCAGAGGATAATGAAGATGAAAACGAAGATCATAAAAATG
TACACCAGCACAGCAGGCAGCATCTAAAGCAGCTTCTGAACAGAGGGAGACGCTCACGGAAGATGTGGGCGTGAGGAAGA
ACAAGAAGAGGATGAGGCACCCTTCCAGGAGAATTCCGGCAGCAATGAAGATTTCCTAATGGAAGATGATGACGATAGTG
ACTAAGGCAAT

Alignment

ORF - retro_mmul_422 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.97 %
• Parental protein coverage: 59.26 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  YRNRKV-VDYSQFQESDDADEDYGRDSGP-PTKKIRSSPREAKNKRRSGKNSQEDSEDSEDKDVKTKKDD
          .RNRKV.VD.SQFQESDD.DE....DSGP.P..K....P...K..RRSGKNSQEDSEDSE.KD.KTKKDD
Retrocopy FRNRKV>VDFSQFQESDDTDE----DSGP>PLRKFDHLP*KLKI-RRSGKNSQEDSEDSEEKDLKTKKDD

Parental  SHSAEDSEDEKEDHKNVRQQ-RQAASKAASKQREMLMEDV-GSEEEQEEEDEAPFQEKDSGSDEDFLMED
          .HSAED.EDE.EDHKNV.Q...QAASKAAS.QRE.L.EDV.G.EEEQ.EEDEAPFQE..SGS.EDFLMED
Retrocopy FHSAEDNEDENEDHKNVHQH<QQAASKAASEQRETLTEDV<GREEEQ-EEDEAPFQE-NSGSNEDFLMED

Parental  DDDSDYGS
          DDDSD.G.
Retrocopy DDDSD*GN

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	0.11 RPM	94.68 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	64.81 RPM
SRP007412_cerebellum	0.00 RPM	96.99 RPM
SRP007412_heart	0.00 RPM	64.07 RPM
SRP007412_kidney	0.00 RPM	61.74 RPM
SRP007412_liver	0.00 RPM	25.41 RPM
SRP007412_testis	0.00 RPM	40.97 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_422 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_422 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_422 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_521
Pan troglodytes	retro_ptro_389
Gorilla gorilla	retro_ggor_480

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012950	1 retrocopy	retro_amel_339,
Bos taurus	ENSBTAG00000008001	1 retrocopy	retro_btau_541,
Choloepus hoffmanni	ENSCHOG00000001855	1 retrocopy	retro_chof_437,
Dasypus novemcinctus	ENSDNOG00000017212	2 retrocopies	retro_dnov_348, retro_dnov_6,
Dipodomys ordii	ENSDORG00000003183	1 retrocopy	retro_dord_688,
Homo sapiens	ENSG00000069275	1 retrocopy	retro_hsap_521,
Gorilla gorilla	ENSGGOG00000026655	1 retrocopy	retro_ggor_480,
Macropus eugenii	ENSMEUG00000007829	2 retrocopies	retro_meug_2015, retro_meug_372,
Macaca mulatta	ENSMMUG00000005645	1 retrocopy	retro_mmul_422 ,
Monodelphis domestica	ENSMODG00000001832	1 retrocopy	retro_mdom_980,
Nomascus leucogenys	ENSNLEG00000014564	1 retrocopy	retro_nleu_2576,
Pan troglodytes	ENSPTRG00000001904	1 retrocopy	retro_ptro_389,
Rattus norvegicus	ENSRNOG00000047287	2 retrocopies	retro_rnor_2337, retro_rnor_2338,
Tupaia belangeri	ENSTBEG00000015641	1 retrocopy	retro_tbel_2591,
Tarsius syrichta	ENSTSYG00000000910	1 retrocopy	retro_tsyr_987,
Vicugna pacos	ENSVPAG00000003751	1 retrocopy	retro_vpac_313,