RetrogeneDB ID: retro_mmul_1829

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 4:39054005..39054718(-)
• Located in intron of: ENSMMUG00000008993

Retrocopy information

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

Parental gene information

• Parental gene symbol: TPM3
• Ensembl ID: ENSMMUG00000010805
• Aliases: None
• Description: tropomyosin alpha-3 chain [Source:RefSeq peptide;Acc:NP_001244772]

Sequence

>retro_mmul_1829
ATGGCTGGGATCACCACCATTGAGGCAGTTAAGGGCAATATCCAGGTTCCGCAGCAGCAGGCAGATGATGCAGAGGGCCT
CCAGTGAGAAGTTGAGGGGGAAAGGTGGGCCCGGGAACAGGCTGAGGTTGAGGTGGCTTCCTTGAACTGCAGGATCCAGC
TGGTTGATGAGAAGCTGGACCATGCTCAGGAGCGCCTGGCCACTGCCCTGCAAAAGCTGGAAGAAGCGGAAAAAGCTGCT
GCTAAGAGTGAGAGAGGTATGAAAGTTATTGAAAACCGGCCTTAAAAAATGAAGAAAAGATGGAACTCCAGGAAATCCAA
CTCAAAGAAGCTAAGCACATTGCAAAAGAGGCAGATAGGAAGTATAAAAAGGTGGCTCATAAGTTGGTGATCATTGAAAG
AGACTTGAAACACGCAGAGGAACAAGCTGAGCTGGCAGAGTCCCGCTGCCGAGAGATAGATGAGCATATCAGACGGAGGG
ACCAGAACCTGAAGTGTCTGAGTGCTGCTGAAGAAAAGTACTCTCAAAAAGAAGACAAATATGAGAAAGAGATCAAGATT
CTTACTGATAAACTCAAGGAGGCAGAGACCTGTGCTGGGTTTGCTGAGAGATCCGTAGCCAAGCTGGAAAAGACAATTGA
TGACTTGGAAGATAAACTGAAATGCACCAAAGAAGAGCACCTCTGTACACAAAGGATGCTGGACCAGACTCTG

Alignment

ORF - retro_mmul_1829 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.19 %
• Parental protein coverage: 97.58 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAGITTIEAVKRKIQVLQQQADDAEERAERLQREVEGERRAREQAEAEVASLNRRIQLVEEELDRAQERL
          MAGITTIEAVK..IQV.QQQADD....AE.LQ.EVEGER.AREQAE.EVASLN.RIQLV.E.LD.AQERL
Retrocopy MAGITTIEAVKGNIQVPQQQADD----AEGLQ*EVEGERWAREQAEVEVASLNCRIQLVDEKLDHAQERL

Parental  ATALQKLEEAEKAADESERCMKVIENR-ALKDEEKMELQEIQLKEAKHIAEEADRKYEEVARKLVIIEGD
          ATALQKLEEAEKAA..SER.MKVIENR.ALK.EEKMELQEIQLKEAKHIA.EADRKY..VA.KLVIIE.D
Retrocopy ATALQKLEEAEKAAAKSERGMKVIENR<ALKNEEKMELQEIQLKEAKHIAKEADRKYKKVAHKLVIIERD

Parental  LERTEERAELAESRCREMDEQIRLMDQNLKCLSAAEEKYSQKEDKYEEEIKILTDKLKEAETRAEFAERS
          L...EE.AELAESRCRE.DE.IR..DQNLKCLSAAEEKYSQKEDKYE.EIKILTDKLKEAET.A.FAERS
Retrocopy LKHAEEQAELAESRCREIDEHIRRRDQNLKCLSAAEEKYSQKEDKYEKEIKILTDKLKEAETCAGFAERS

Parental  VAKLEKTIDDLEDKLKCTKEEHLCTQRMLDQTL
          VAKLEKTIDDLEDKLKCTKEEHLCTQRMLDQTL
Retrocopy VAKLEKTIDDLEDKLKCTKEEHLCTQRMLDQTL

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	140.51 RPM
SRP007412_brain_prefrontal_cortex	0.08 RPM	177.78 RPM
SRP007412_cerebellum	0.06 RPM	57.08 RPM
SRP007412_heart	0.00 RPM	39.28 RPM
SRP007412_kidney	0.12 RPM	86.03 RPM
SRP007412_liver	0.00 RPM	36.89 RPM
SRP007412_testis	0.00 RPM	60.35 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1829 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1829 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1829 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 43 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011877	2 retrocopies	retro_amel_1017, retro_amel_1212,
Bos taurus	ENSBTAG00000033217	3 retrocopies	retro_btau_1166, retro_btau_210, retro_btau_933,
Canis familiaris	ENSCAFG00000017311	4 retrocopies	retro_cfam_1278, retro_cfam_1678, retro_cfam_2089, retro_cfam_983,
Cavia porcellus	ENSCPOG00000007279	1 retrocopy	retro_cpor_150,
Dasypus novemcinctus	ENSDNOG00000019156	7 retrocopies	retro_dnov_1322, retro_dnov_1767, retro_dnov_329, retro_dnov_451, retro_dnov_848, retro_dnov_878, retro_dnov_944,
Equus caballus	ENSECAG00000010942	1 retrocopy	retro_ecab_390,
Felis catus	ENSFCAG00000012596	1 retrocopy	retro_fcat_1441,
Homo sapiens	ENSG00000143549	9 retrocopies	retro_hsap_1482, retro_hsap_1639, retro_hsap_2001, retro_hsap_2011, retro_hsap_2012, retro_hsap_2237, retro_hsap_2395, retro_hsap_3711, retro_hsap_3893,
Myotis lucifugus	ENSMLUG00000013331	1 retrocopy	retro_mluc_1038,
Macaca mulatta	ENSMMUG00000010805	10 retrocopies	retro_mmul_1019, retro_mmul_1240, retro_mmul_1384, retro_mmul_1385, retro_mmul_1703, retro_mmul_1829 , retro_mmul_2128, retro_mmul_2354, retro_mmul_314, retro_mmul_880,
Mustela putorius furo	ENSMPUG00000007875	1 retrocopy	retro_mputfur_604,
Mus musculus	ENSMUSG00000027940	1 retrocopy	retro_mmus_21,
Oryctolagus cuniculus	ENSOCUG00000011821	2 retrocopies	retro_ocun_699, retro_ocun_8,