RetrogeneDB ID: retro_mmul_1571

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 20:75295606..75295976(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TPRKB
• Ensembl ID: ENSMMUG00000030805
• Aliases: None
• Description: None

Sequence

>retro_mmul_1571
ATGCCGTTAACACATCAGCTAGATGTATTTCCCAAATGCGGGGTGATCATTCTCTTATTTGAAGACATAAAGAGTGCTGA
AGACTTGAGATAAAAGGTCACAGAAGTCATCTTCAATGGTTCATTAATAAATGCTATGGTGACTATTGATCTATTTCAAA
TACTTGTGGCATAAACAAAGCAGTTCACCTCTACAAAGTGGGAAAAATAAAGACCAGAATTCTATGTATGGAAATCATTC
CCAATGTTTCCCCAAATAATATTATTTTAGAGGCTTTGAAAAAAATTATGTCTCAATAAATGGCACTTTAATTTTAATTT
TTTTACAGTAAAAAGAGAGAAGAAATCAAGAACTTTATATGTTAAGTAGA

Alignment

ORF - retro_mmul_1571 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.69 %
• Parental protein coverage: 71.43 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MQLTHQLDLFPECRVTLLLFKDVKNAGDLRRKAMEGTIDGSLINPTVIVDPFQILVA-ANKAVHLYKLGK
          M.LTHQLD.FP.C.V..LLF.D.K.A.DLR.K..E....GSLIN..V..D.FQILVA..NKAVHLYK.GK
Retrocopy MPLTHQLDVFPKCGVIILLFEDIKSAEDLR*KVTEVIFNGSLINAMVTIDLFQILVA<INKAVHLYKVGK

Parental  MKTRTLSTEIIFNLSPNNNISEALKKF-GISANDTSILIVYIEEGEKQINQEYLISQ
          .KTR.L..EII.N.SPNN.I.EALKK....S.N.T.ILI......E......Y..S.
Retrocopy IKTRILCMEIIPNVSPNNIILEALKKI<YVSINGTLILI-FLQ*KERRNQELYMLSR

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	5.27 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	2.62 RPM
SRP007412_cerebellum	0.00 RPM	6.52 RPM
SRP007412_heart	0.00 RPM	4.12 RPM
SRP007412_kidney	0.00 RPM	4.23 RPM
SRP007412_liver	0.00 RPM	1.39 RPM
SRP007412_testis	0.00 RPM	9.16 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1571 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1571 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1571 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 25 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000012021	1 retrocopy	retro_chof_35,
Callithrix jacchus	ENSCJAG00000004162	3 retrocopies	retro_cjac_1999, retro_cjac_2867, retro_cjac_3065,
Homo sapiens	ENSG00000144034	1 retrocopy	retro_hsap_552,
Gorilla gorilla	ENSGGOG00000009062	1 retrocopy	retro_ggor_501,
Macaca mulatta	ENSMMUG00000030805	1 retrocopy	retro_mmul_1571 ,
Monodelphis domestica	ENSMODG00000016950	2 retrocopies	retro_mdom_1264, retro_mdom_465,
Nomascus leucogenys	ENSNLEG00000000300	2 retrocopies	retro_nleu_2021, retro_nleu_957,
Oryctolagus cuniculus	ENSOCUG00000016251	2 retrocopies	retro_ocun_519, retro_ocun_769,
Otolemur garnettii	ENSOGAG00000032893	2 retrocopies	retro_ogar_523, retro_ogar_849,
Pongo abelii	ENSPPYG00000012292	1 retrocopy	retro_pabe_509,
Pteropus vampyrus	ENSPVAG00000012419	1 retrocopy	retro_pvam_75,
Ictidomys tridecemlineatus	ENSSTOG00000016406	4 retrocopies	retro_itri_1613, retro_itri_453, retro_itri_918, retro_itri_919,
Tupaia belangeri	ENSTBEG00000014584	2 retrocopies	retro_tbel_33, retro_tbel_3630,
Vicugna pacos	ENSVPAG00000007934	2 retrocopies	retro_vpac_149, retro_vpac_192,