RetrogeneDB ID: retro_mmul_2093

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 6:89135346..89136617(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.1980
• Ensembl ID: ENSMMUG00000012448
• Aliases: None
• Description: T-complex protein 1 subunit eta [Source:RefSeq peptide;Acc:NP_001252680]

Sequence

>retro_mmul_2093
CTGAAGCTTCTTGAAGTTGTCCGTCCTGCAACAAAGACTTCAATGGGCATTGCCAAATATCAAGATGCTGAGGTGAGTGA
TGGCACCACCTCAGTGACCTTGCTGGTTGCAGAGTTTCTGAAGCAGGTGAAACCTTATGTGGAAGAAGGTTTGTACCTGA
AGATCATCATTCAAGCTTTCTGAACAGCCATCCAATGGGCAGTTAATGATAGCAAAGAGATCACTGTGACCATGAAGAAG
ACAGAAAAAGAGGAGCAGAAGAAGCTGTTTGGAGAAATGTGCCATCCTGCTCTGAGCTCCAAGCTCATCTCCCAGCAGAA
AGCCTTCTTTGCAAAGATGGTGGTTGAGCTTAAAATGCTCAATCATTTTAAGCTACAGCTTAAAATGATTGGAATCAAGA
AGATACAGGGTGGAACCCTAGAGGATTCCCATCTGGTAGCTGGTGTTGCATTCAATAATTTCTTTTATGCTGGGTTGGAA
ATGCAACCACAAAAGTGCCATAATCCCAAGATTGCACTTTTAAATGTTAAGCTTGAGTTGAAAGTTGAGAAAGATAATGC
TGAGATCAGAGTCCTCACAATGGGGAATTACCAGGCAATTGTTGGTGCTGAGTGGAACATTCTCTATGACAAGTTAGTGA
GGATCCATCATTCTGGAGCCAAAGTTGTCTTGTCCAAACTCTCCAGTGGGGATGTGGTCACTCAGTACTTTGTTCACAGG
GGCAGGTTCTGTGCTGGCCAAGTACCTGAGAAGGATCTGAAGAGGACAATGATGGCCTACAGAGGGTCAATCCAGACCAT
TGTGAACGCTCTGTCAGCAGACATGCTGGGCAACTGCCAGGTGTTTGAGGAGACCCTGACTGGAGGTGAGAGGTATAATT
TCTTTACTGGCCTCCTAAGGCCAAGACATACACATTTATCCTCCACAGTGATGCCACAGCTTATGGCGGAGACAGAACAG
TTCATGCCTAATGCCATCATGATTGTCAGGAGGGCCATCGAAAATGATTTGGTGGTGGCTGGTGGTGGGGCCATTGAGAT
AAAGCTCTCCAAGTACCTGTAGGATTAGTAAGGACTATTCCAGGAATGCAGCAGCTGGATTGGGGTGTATGCTAAGGCCT
TGGAGATATCCTACGGCAGCTATGTGACAATACTGGTTTTGATACCACAAGCATTCTTAACAAGCTGAGGGCATAGCATG
CCCAGAGAGGCACATGGTATGGCATGGACATCAACAATGAGGATATTGCTGACAACTCTGAGACCTTCGTA

Alignment

ORF - retro_mmul_2093 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.09 %
• Parental protein coverage: 78.64 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  LKLLDVVHPAAKTLVDIAKSQDAEVGDGTTSVTLLAAEFLKQVKPYVEEGLHPQIIIRAFRTATQLAVNK
          LKLL.VV.PA.KT...IAK.QDAEV.DGTTSVTLL.AEFLKQVKPYVEEGL...III.AF.TA.Q.AVN.
Retrocopy LKLLEVVRPATKTSMGIAKYQDAEVSDGTTSVTLLVAEFLKQVKPYVEEGLYLKIIIQAF*TAIQWAVND

Parental  IKEIAVTVKKADKVEQRKL-LEKCAMT-ALSSKLISQQKAFFAKMVVDAVMMLDDLLQLKMIGIKKVQGG
          .KEI.VT.KK..K.EQ.KL.LEKCA...ALSSKLISQQKAFFAKMVV...M.....LQLKMIGIKK.QGG
Retrocopy SKEITVTMKKTEKEEQKKL>LEKCAIL<ALSSKLISQQKAFFAKMVVELKMLNHFKLQLKMIGIKKIQGG

Parental  ALEDSQLVAGVAFKKTFSYAGFEMQPKKYHNPKIALLNVELELKAEKDNAEIRVHTVEDYQAIVDAEWNI
          .LEDS.LVAGVAF...F.YAG.EMQP.K.HNPKIALLNV.LELK.EKDNAEIRV.T...YQAIV.AEWNI
Retrocopy TLEDSHLVAGVAFNNFF-YAGLEMQPQKCHNPKIALLNVKLELKVEKDNAEIRVLTMGNYQAIVGAEWNI

Parental  LYDKLEKIHHSGAKVVLSKLPIGDVATQYFADRDMFCAGRVPEEDLKRTMMACGGSIQTSVNALSADVLG
          LYDKL..IHHSGAKVVLSKL..GDV.TQYF..R..FCAG.VPE.DLKRTMMA..GSIQT.VNALSAD.LG
Retrocopy LYDKLVRIHHSGAKVVLSKLSSGDVVTQYFVHRGRFCAGQVPEKDLKRTMMAYRGSIQTIVNALSADMLG

Parental  RCQVFEETQIGGERYNFFTGCPKAKTCTFILRGGAEQFMEETERSLHDAIMIVRRAIKNDSVVAGGGAIE
          .CQVFEET..GGERYNFFTG.......T........Q.M.ETE.....AIMIVRRAI.ND.VVAGGGAIE
Retrocopy NCQVFEETLTGGERYNFFTGLLRPRH-THLSSTVMPQLMAETEQFMPNAIMIVRRAIENDLVVAGGGAIE

Parental  MELSKYLRD-YSRTIPGKQQLLIGAYAKALEIIPRQLCDNAGFDATNILNKLRARHAQGGTWYGVDINNE
          ..LSKYL.D...RTIPG.QQL..G.....L..I.RQLCDN.GFD.T.ILNKLRA.HAQ.GTWYG.DINNE
Retrocopy IKLSKYL*D<LVRTIPGMQQLDWGV-C*GLGDILRQLCDNTGFDTTSILNKLRA*HAQRGTWYGMDINNE

Parental  DIADNFEAFV
          DIADN.E.FV
Retrocopy DIADNSETFV

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	81.91 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	113.84 RPM
SRP007412_cerebellum	0.06 RPM	107.39 RPM
SRP007412_heart	0.00 RPM	94.51 RPM
SRP007412_kidney	0.00 RPM	84.74 RPM
SRP007412_liver	0.00 RPM	93.54 RPM
SRP007412_testis	0.00 RPM	220.02 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2093 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2093 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2093 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3354
Pan troglodytes	retro_ptro_2133
Gorilla gorilla	retro_ggor_2274
Pongo abelii	retro_pabe_2760

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000008879	1 retrocopy	retro_cfam_151,
Choloepus hoffmanni	ENSCHOG00000007937	1 retrocopy	retro_chof_2313,
Cavia porcellus	ENSCPOG00000019869	1 retrocopy	retro_cpor_1458,
Echinops telfairi	ENSETEG00000009409	2 retrocopies	retro_etel_1478, retro_etel_607,
Homo sapiens	ENSG00000135624	1 retrocopy	retro_hsap_3354,
Gorilla gorilla	ENSGGOG00000007766	1 retrocopy	retro_ggor_2274,
Macropus eugenii	ENSMEUG00000000416	1 retrocopy	retro_meug_1995,
Macaca mulatta	ENSMMUG00000012448	1 retrocopy	retro_mmul_2093 ,
Nomascus leucogenys	ENSNLEG00000010414	1 retrocopy	retro_nleu_1175,
Otolemur garnettii	ENSOGAG00000009162	2 retrocopies	retro_ogar_2001, retro_ogar_2698,
Pongo abelii	ENSPPYG00000012297	1 retrocopy	retro_pabe_2760,
Pan troglodytes	ENSPTRG00000012060	1 retrocopy	retro_ptro_2133,
Rattus norvegicus	ENSRNOG00000015630	2 retrocopies	retro_rnor_2179, retro_rnor_535,
Sorex araneus	ENSSARG00000011475	1 retrocopy	retro_sara_539,
Tupaia belangeri	ENSTBEG00000002066	2 retrocopies	retro_tbel_3708, retro_tbel_3751,