RetrogeneDB ID: retro_mmul_2180

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 7:120066856..120068050(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ZCCHC7
• Ensembl ID: ENSMMUG00000007421
• Aliases: None
• Description: zinc finger CCHC domain-containing protein 7 [Source:RefSeq peptide;Acc:NP_001248112]

Sequence

>retro_mmul_2180
GAAGAGAGATCAGGTGTAATCTGAGAGCTCATGATTAGAGCTGTCAGTTCAAGTGAAGAGGAAGAAAGCACCATTTCAGA
AGGCAATAATGTGAAAAGCTGGATGCTACTGGGATGTGAAGTAGATGATAGAGATGATGATATCCTTCTCAACGTTGCGG
GATGTGAAAACTCTGTTATTGAAGAAGATGATATAAACTGGTTCATCAGTGACAAAGACATTGAGGCCGAGATAGCTAAT
AACAAATCACCTGGAAGACACACCCAGAGATATTATTCAGCCAACAAAAACATTATCTGTAGAAATTGTGACAAATGTGG
CCATTTAACAAAAAACTGCCCCTTACCAGGAAAAGTTCGTCGCTGCTTCCTGTGCTCCGGGAGAGGACATCTCCTGTGTT
CCTGGCCAGCCCCCCTTTGCGAATACTGTCCTGTGCCTAAGATGTTGGACCACTCATGTCTTTTCAGACATTCCTGGGAT
AAACAGTGTGACTGATGTCATATGCTAGGTCACTATACAGATACTTGCACAGAAATCTGGGGGCAGTATCACCTAACGAC
CAAACCTGGACCATCCAAAAAGCCAAAGACCCCTTCAAGACCATCAGCCTTAGCATATTACTGTCACTGCATGCAAAAGG
CAATTCTGGGCACAAGTGTCCAGAATGAGAAGTGTATGACCCGTCTCCAATATCTCCATTCATCTGCTACTACGATGACA
AATATGAAATTCAGGAGAGAGAAAAGAGACTAAAACAAAAAATAAAAGTACTGAAGAAAAATGGAGATATCCCAGAGCCA
TCTAAGCTACCTTAGATAAAAACAGCAAATGAGAACTCCCATCATTATATAAGGAAGGGCCATGCCTTGTGGAAAAGCAA
CAGGTGGCCTCAATAAAATAAGGAAACACAAAAAGAAATGAAGAACAAGAACAGAAACTGGGAGAAGCACAGGAAGGCTG
ACAGACATGTGAAGTGGGTGAGGATTTTCCTAGGGGCCCCAAAACCTACTCTTCTCCTGGCAGTTTTAAAACCCAGAAGC
CTTCCAAGCCCTTTCACCATTCATCACATTACTTCACATCAAGAGGAGACAAGTCTCCCAAGGAGGTTAAGAGGGGCAAG
AGAAGAAAAAGGAGAGGTGCTTGGAAGATGATGACAATGATAACTTATTTCTTATTAAGCAGAGGGAAAAAAAG

Alignment

ORF - retro_mmul_2180 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.62 %
• Parental protein coverage: 73.8 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  EERSDVIREVMIIEVSSSEEEESTISEGDNVESWMLLGCEVDDKDDDILLNLVGCENSVTEGEDGINWFI
          EERS.VI.E.MI..VSSSEEEESTISEG.NV.SWMLLGCEVDD.DDDILLN..GCENSV.E.ED.INWFI
Retrocopy EERSGVI*ELMIRAVSSSEEEESTISEGNNVKSWMLLGCEVDDRDDDILLNVAGCENSVIE-EDDINWFI

Parental  SDKDIEAQIANNRTPGRWTQRYYSANKNIICRNCDKRGHLSKNCPLPRKVRRCFLCSRSGHLLYSCPAPL
          SDKDIEA.IANN..PGR.TQRYYSANKNIICRNCDK.GHL.KNCPLP.KVRRCFLCS..GHLL.S.PAPL
Retrocopy SDKDIEAEIANNKSPGRHTQRYYSANKNIICRNCDKCGHLTKNCPLPGKVRRCFLCSGRGHLLCSWPAPL

Parental  CEYCPVPKMLDHSCLFRHSWDKQCDRCHMLGHYTDACTEIWRQYHLTTKPGPPKKPKTPSRPSALAYCYH
          CEYCPVPKMLDHSCLFRHSWDKQCD.CHMLGHYTD.CTEIW.QYHLTTKPGP.KKPKTPSRPSALAY..H
Retrocopy CEYCPVPKMLDHSCLFRHSWDKQCD*CHMLGHYTDTCTEIWGQYHLTTKPGPSKKPKTPSRPSALAYYCH

Parental  CAQ-KGHYGHECPEREVYDPSPVSPFICYYDDKYEIQEREKRLKQKIKVLKKNGVIPEPSKLPYLKAANE
          C.Q.KG..GH.CPE.EVYDPSP.SPFICYYDDKYEIQEREKRLKQKIKVLKKNG.IPEPSKLP..K.ANE
Retrocopy CMQ<KGNSGHKCPE*EVYDPSPISPFICYYDDKYEIQEREKRLKQKIKVLKKNGDIPEPSKLP*IKTANE

Parental  NPHHDIRKGRASWKSNRWPQENKETQKEMKNKNRNWEKHRRADRH-REVDEDFPRGPKPYSPTGSFKTQK
          N.HH.IRKG.A.WKSNRWPQ.NKETQKEMKNKNRNWEKHR.ADRH..EV.EDFPRGPK.YS..GSFKTQK
Retrocopy NSHHYIRKGHALWKSNRWPQ*NKETQKEMKNKNRNWEKHRKADRH<CEVGEDFPRGPKTYSSPGSFKTQK

Parental  PSKFFHRSSHYHMSREDKSPKEGKRGK-QKKKERCLEDDDNDNLFLIKQRKKK
          PSK.FH.SSHY..SR.DKSPKE.KRGK..KKKERCLEDDDNDNLFLIKQR.KK
Retrocopy PSKPFHHSSHYFTSRGDKSPKEVKRGK<EKKKERCLEDDDNDNLFLIKQREKK

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	13.11 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	4.92 RPM
SRP007412_cerebellum	0.00 RPM	13.69 RPM
SRP007412_heart	0.00 RPM	7.01 RPM
SRP007412_kidney	0.00 RPM	9.39 RPM
SRP007412_liver	0.00 RPM	4.67 RPM
SRP007412_testis	0.11 RPM	17.83 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2180 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2180 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2180 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1342
Pan troglodytes	retro_ptro_917

---

Parental genes homology:

Parental genes homology involve 5 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000147905	1 retrocopy	retro_hsap_1342,
Macaca mulatta	ENSMMUG00000007421	1 retrocopy	retro_mmul_2180 ,
Pongo abelii	ENSPPYG00000029763	1 retrocopy	retro_pabe_1114,
Pan troglodytes	ENSPTRG00000020939	2 retrocopies	retro_ptro_2962, retro_ptro_917,
Tursiops truncatus	ENSTTRG00000006054	2 retrocopies	retro_ttru_1606, retro_ttru_505,