RetrogeneDB ID: retro_mmul_934

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 12:1860088..1861202(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RNF14
• Ensembl ID: ENSMMUG00000009768
• Aliases: None
• Description: E3 ubiquitin-protein ligase RNF14 [Source:RefSeq peptide;Acc:NP_001247742]

Sequence

>retro_mmul_934
CTATCTGCTCTATGCAAGCACTTAGACTTCCTATGGGAAGAACACCATGCCAGCATGGTCCTTTTTGCCTGGATGCAGTT
TCTTAAGGAAGAGATCCTAGTGTACTTGAATATTGTCTCTCCTTTCGAGCTCACGGTGGGTTCTCAGAAAAAAGTATAGA
GAATGACAGCTCAAGCCTCTCCTAACACAGAGCTAGATATTGGAGGAGCTGCTGGATCTAATGTAGACCAAGAGGAAATT
GTGGATGAGAGAGCTGTGTGGATGTGGAATCACTGTCAAGTCTAATCCAGAAAATCTTGGACTTTGATCAAGCTCAGCAC
ATAAAATGCTTTAATAGTAAATTTTTCCTTTGCCATATCTGTTTCTGTGAGAAGCTGGGCAGTGAATGCATGTACTTCTT
GGAGGGCAGGTATGTATACTGCAAAGCTTGTCTGAAGGACTACTTTGAACTCCAGATCAGAGATGGTCAGGTCCAATGCC
TCAACTACCCAGAACCAAAGTGCCCTTCGATGGCCACTCCTGATCAGGTCAAAGAGCTAGTGGGACCAGAGTTATTTGCC
TGTTATCATTGCCTTCTCCTCTAGTCTACTTTGGACCTGATGGCACTTGTGGTATACTGCCCCCGCTCATGCTGCCAGCT
GCCTGTCATGCAGAATCCTGGCTGCACCATGGGCATCTGCTCCAGCTGCAATTTTGCCTTCTGTACCTTGGGCAAATTGA
CCTACCCTGGGGTCTCTCTATGTAAGGTGACTGCAGATAAATTAATAGACTTATGAAACAAATCCCTGAATGCAGATGAG
GCCAATAAAAGATTTTTGTAACAAAGGTATCATAAGAGGGTGATTCAGAAGGCACTGGAAGAGATGGAAAGTAAGGAGGG
GTTAGAAAAGAACTCAAAGAGCTGCCACATTGTGGAACTCCCATAGAGAAATTAGATGAATGTAATAAGATGACATGTAC
TGACTGTATGCAATATTTCTGTTGGATTTGCATGGGTTCTTTCTCTAGAGCAGACTCTTACAAACATTTCATTGATCCTA
CCTCACCATGTTTTAATGGGCTGTTTCACGCTATGGATGTTAATGGAGACATTTGGGAAGATGGGATTGAAGAC

Alignment

ORF - retro_mmul_934 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.62 %
• Parental protein coverage: 78.48 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LSALCKHLDNLWEEHRGSVVLFAWMQFLKEETLAYLNIVSPFELKIGSQKKVQRRTAQASPNTELDFGGA
          LSALCKHLD.LWEEH..S.VLFAWMQFLKEE.L.YLNIVSPFEL..GSQKKV.R.TAQASPNTELD.GGA
Retrocopy LSALCKHLDFLWEEHHASMVLFAWMQFLKEEILVYLNIVSPFELTVGSQKKV*RMTAQASPNTELDIGGA

Parental  AGSDVDQEEIVDERAVQ-DVESLSNLIQEILDFDQAQQIKCFNSKLFLCNICFCEKLGSECMYFLECRHV
          AGS.VDQEEIVDERAV..DVESLS.LIQ.ILDFDQAQ.IKCFNSK.FLC.ICFCEKLGSECMYFLE.R.V
Retrocopy AGSNVDQEEIVDERAVW<DVESLSSLIQKILDFDQAQHIKCFNSKFFLCHICFCEKLGSECMYFLEGRYV

Parental  YCKACLKDYFEIQIRDGQVQCLNCPEPKCPSVATPGQVKELVEAELFARYDRLLLQSTLDLMADVVYCPR
          YCKACLKDYFE.QIRDGQVQCLN.PEPKCPS.ATP.QVKELV..ELFA.Y..LLL.STLDLMA.VVYCPR
Retrocopy YCKACLKDYFELQIRDGQVQCLNYPEPKCPSMATPDQVKELVGPELFACYHCLLL*STLDLMALVVYCPR

Parental  PCCQLPVMQEPGCTMGICSSCNFAFCTLCRLTYHGVSPCKVTAEKLMDLRNEYLQADEANKRLLDQRYGK
          .CCQLPVMQ.PGCTMGICSSCNFAFCTL..LTY.GVS.CKVTA.KL.DL.N..L.ADEANKR.L.QRY.K
Retrocopy SCCQLPVMQNPGCTMGICSSCNFAFCTLGKLTYPGVSLCKVTADKLIDL*NKSLNADEANKRFL*QRYHK

Parental  RVIQKALEEMESKEWLEKNSKSC-PCCGTPIEKLDGCNKMTCTGCKQYFCWICMGSLSRANPYKHFNDPA
          RVIQKALEEMESKE.LEKNSKSC.P.CGTPIEKLD.CNKMTCT.C.QYFCWICMGS.SRA..YKHF.DP.
Retrocopy RVIQKALEEMESKEGLEKNSKSC<PHCGTPIEKLDECNKMTCTDCMQYFCWICMGSFSRADSYKHFIDPT

Parental  SPCFNRLFYAVDVDDDIWEDEVED
          SPCFN.LF.A.DV..DIWED..ED
Retrocopy SPCFNGLFHAMDVNGDIWEDGIED

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	39.67 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	36.89 RPM
SRP007412_cerebellum	0.00 RPM	43.59 RPM
SRP007412_heart	0.00 RPM	34.68 RPM
SRP007412_kidney	0.00 RPM	27.82 RPM
SRP007412_liver	0.00 RPM	24.98 RPM
SRP007412_testis	0.00 RPM	36.49 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_934 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_934 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_934 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000007803	1 retrocopy	retro_dnov_332,
Dasypus novemcinctus	ENSDNOG00000024423	1 retrocopy	retro_dnov_1704,
Homo sapiens	ENSG00000013561	2 retrocopies	retro_hsap_3790, retro_hsap_3881,
Gorilla gorilla	ENSGGOG00000008542	1 retrocopy	retro_ggor_2612,
Macaca mulatta	ENSMMUG00000009768	2 retrocopies	retro_mmul_1647, retro_mmul_934 ,
Pongo abelii	ENSPPYG00000015894	2 retrocopies	retro_pabe_3095, retro_pabe_3115,
Pan troglodytes	ENSPTRG00000017356	2 retrocopies	retro_ptro_2571, retro_ptro_2643,