RetrogeneDB ID: retro_mmul_1729

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 3:146412309..146413126(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.1219
• Ensembl ID: ENSMMUG00000003092
• Aliases: None
• Description: mitotic checkpoint protein BUB3 [Source:RefSeq peptide;Acc:NP_001253182]

Sequence

>retro_mmul_1729
CTCAGATACCAACACACTGGTGCCGTCCTGGACTGAGCCTTCTACAATCCAGCGCAGGCCTGGAGAGGAGGACTAGATCA
TCAATTGAAAATGCATTATTTGAACACTGATCAAGAAAATCTTGTTGGGACCCATGATGTCCCCATCAGATGTGTCGAAT
ACTGTCCAGAAGTGAATGTGGTGGTTACTGGAAGTTGGGATCAGACAGTTAAATTGTGGGATCCCAGAAATCGTGGTAAC
GCCAGGACCTTCTCTCAGCCTAAAAAGGCATATACCTTCTCAGTGTCTGGAGACCGGCTGACTGTGAGAACACTGGGCCT
CAGAGTGTTGGTGTGGGGCTTATGGAACATGGGTTATGTGCAGCAGAGCAGGGAGTCCAGCCTGAAATACCAGACTTGCT
GCATACAAGCATCTCCAAACAAGCAGGGTTATGTATTAAGCTCTATTGAAGGCAGAGTGGCAGTTGAATACTTGGCCCAA
GCCCTGAGGTACAGAGGAAATATGCCTTCAAATGTCACAGACTAAAAGAAAATAATATTGAGCAGGTTTACCCAGTTAAT
GCCATTTCTTTCCAGAATATCCGTAATACATTTGCCATAGGTGGTTCTGATGGCTTTGTAAATACTTGGAATCCATTTAA
CAAAAAGCAACTGTGCCAGTTGCATCGGTACGCCATGAGCATCACATCACTTGCCTTCAGTAATGATAGGACTATGCTTG
CAATAGCATCATCATATATTATAAAATGGATGACACGGAACATCCTGAAGATGGTATCTTCATTCACCCAGTGACAGATG
CAGAAACGAAACCCAAG

Alignment

ORF - retro_mmul_1729 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.61 %
• Parental protein coverage: 83.54 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LKYQHTGAVLDCAFYDPTHAWSGGLDHQLKMHDLNTDQENLVGTHDAPIRCVEYCPEVNVMVTGSWDQTV
          L.YQHTGAVLD.AFY.P..AW.GGLDHQLKMH.LNTDQENLVGTHD.PIRCVEYCPEVNV.VTGSWDQTV
Retrocopy LRYQHTGAVLD*AFYNPAQAWRGGLDHQLKMHYLNTDQENLVGTHDVPIRCVEYCPEVNVVVTGSWDQTV

Parental  KLWDPRTPCNAGTFSQPEKVYTLSVSGDRLIVGTAGRRVLVWDLRNMGYVQQRRESSLKYQTRCIRAFPN
          KLWDPR...NA.TFSQP.K.YT.SVSGDRL.V.T.G.RVLVW.L.NMGYVQQ.RESSLKYQT.CI.A.PN
Retrocopy KLWDPRNRGNARTFSQPKKAYTFSVSGDRLTVRTLGLRVLVWGLWNMGYVQQSRESSLKYQTCCIQASPN

Parental  KQGYVLSSIEGRVAVEYL-DPSPEVQKKKYAFKCHRLKENNIEQIYPVNAISFHNIHNTFATGGSDGFVN
          KQGYVLSSIEGRVAVEYL..PSPEVQ..KYAFKCHRLKENNIEQ.YPVNAISF.NI.NTFA.GGSDGFVN
Retrocopy KQGYVLSSIEGRVAVEYL<GPSPEVQ-RKYAFKCHRLKENNIEQVYPVNAISFQNIRNTFAIGGSDGFVN

Parental  IWDPFNKKRLCQFHRYPTSIASLAFSNDGTTLAIASSYM-YEMDDTEHPEDGIFIRQVTDAETKPK
          .W.PFNKK.LCQ.HRY..SI.SLAFSND.T.LAIASSY..Y.MDDTEHPEDGIFI..VTDAETKPK
Retrocopy TWNPFNKKQLCQLHRYAMSITSLAFSNDRTMLAIASSYI<YKMDDTEHPEDGIFIHPVTDAETKPK

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	16.02 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	17.53 RPM
SRP007412_cerebellum	0.00 RPM	22.79 RPM
SRP007412_heart	0.00 RPM	14.37 RPM
SRP007412_kidney	0.00 RPM	17.84 RPM
SRP007412_liver	0.00 RPM	12.98 RPM
SRP007412_testis	0.00 RPM	65.10 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1729 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1729 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1729 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 15 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000012700	1 retrocopy	retro_cfam_399,
Choloepus hoffmanni	ENSCHOG00000010213	1 retrocopy	retro_chof_1339,
Callithrix jacchus	ENSCJAG00000001066	1 retrocopy	retro_cjac_3085,
Cavia porcellus	ENSCPOG00000011957	1 retrocopy	retro_cpor_997,
Homo sapiens	ENSG00000154473	1 retrocopy	retro_hsap_3887,
Gorilla gorilla	ENSGGOG00000023971	1 retrocopy	retro_ggor_2614,
Myotis lucifugus	ENSMLUG00000017732	1 retrocopy	retro_mluc_627,
Macaca mulatta	ENSMMUG00000003092	1 retrocopy	retro_mmul_1729 ,
Nomascus leucogenys	ENSNLEG00000027075	1 retrocopy	retro_nleu_1887,
Procavia capensis	ENSPCAG00000007736	1 retrocopy	retro_pcap_412,
Pongo abelii	ENSPPYG00000002731	1 retrocopy	retro_pabe_3168,
Sarcophilus harrisii	ENSSHAG00000010372	1 retrocopy	retro_shar_358,
Ictidomys tridecemlineatus	ENSSTOG00000021785	1 retrocopy	retro_itri_1095,
Tarsius syrichta	ENSTSYG00000013444	2 retrocopies	retro_tsyr_1652, retro_tsyr_732,
Tursiops truncatus	ENSTTRG00000016194	1 retrocopy	retro_ttru_1136,