RetrogeneDB ID: retro_mmul_1647

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 3:172608669..172609793(+)
• 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_1647
ACAGAATTTCAAGATATTTGTGAGCGCTATCTGCTCTATGGGAAGAACACCGTGGCAGCATGATCCTGTTTGCCTGCATG
CAATTTCTTAAGGAAGAGACCCTACTATACCTGAATATTGTCTCTCCTTTTGAGCTCAAGATTGGTTCTCACAAAAATGT
GCAGAGAAGGACAGCTCAAGCCTCTCCCAACACAGACCTAGTTTTTGGAGGAACTTCTGGATCTGATACAGACCAAGAGG
AAATTGTGGACGAGACAGCTGTGCAGGATGTGGAATCATTGTTAAATATGATCCGGGAAATGTTGGACTTTGATCAAGCT
CAGCAGATAAAATGCTTTAGTAGTAATTTGTTCCTATGCAATATCTGTTTCTGTAACAAGCTGGAGAGTGAATGCATGTA
CTTCTTGGAGTGCAGGCATGTGTACTGCAAAGCCTGTCTGAAGGACTACTTTGAAACCCAGATCAGAGATGGCCAGGTTC
AATGCCTCAACTGCCCAGAACCAAAGTGCCCTTCGGTGGCCACTCCTGGTCAGGTCAAAGAGGAGCTAGTGGAAGCAGAG
TTATTTGCCTCTTATGACCGCCTTCTTCTCCAGTTCACCTTGGACCTGATGGCAGATGTGGTGTACTGCCCCTACCCATG
CTGCCAGCTACCTGTCATGCAGGAGCCTGGCTGCACCATGGGTATCTGCTCCAGCTGCAATTTTGCCTTCTGTACCTTAT
GCAGGTTGACCTACCATGGGGTCTCTCCATGTAAGGTGACTGCAGAGAAATTAATAGACTTACGAAATGAATACCTGCAA
GCAGATGAGGCCAATAAAGGACTTTTGGAACAAAGGTGTGGTAAGAGGGTGATTCAGAAGGCACTGGAAAAGATGGAAAG
TAAGGAATGGCCAGAGAAAAACTTCAAGAACTGACCATGTTGTGGAACTCCCATAGAGAAATTAGATGGATATAACAAGA
TGACATGTACTGGCTGTATGCAATACTTCTGTTGGATTTGCATGAGTTCTCTCTCTAGAGCAAACCCTTACAAACATTTC
ACTGATCCTGCTTCACCACGTTTTAACCAGCTGTTTTATGCTGTGGATGTTGATGAAGATATTTTGGAAGATGAGATTGA
AGAC

Alignment

ORF - retro_mmul_1647 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.9 %
• Parental protein coverage: 78.9 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  TQLSALCKH-LDNLWEEHRGSVVLFAWMQFLKEETLAYLNIVSPFELKIGSQKKVQRRTAQASPNTELDF
          T.....C...L..LWEEHRGS..LFA.MQFLKEETL.YLNIVSPFELKIGS.K.VQRRTAQASPNT.L.F
Retrocopy TEFQDICER<LSALWEEHRGSMILFACMQFLKEETLLYLNIVSPFELKIGSHKNVQRRTAQASPNTDLVF

Parental  GGAAGSDVDQEEIVDERAVQDVESLSNLIQEILDFDQAQQIKCFNSKLFLCNICFCEKLGSECMYFLECR
          GG..GSD.DQEEIVDE.AVQDVESL.N.I.E.LDFDQAQQIKCF.S.LFLCNICFC.KL.SECMYFLECR
Retrocopy GGTSGSDTDQEEIVDETAVQDVESLLNMIREMLDFDQAQQIKCFSSNLFLCNICFCNKLESECMYFLECR

Parental  HVYCKACLKDYFEIQIRDGQVQCLNCPEPKCPSVATPGQVKE-LVEAELFARYDRLLLQSTLDLMADVVY
          HVYCKACLKDYFE.QIRDGQVQCLNCPEPKCPSVATPGQVKE.LVEAELFA.YDRLLLQ.TLDLMADVVY
Retrocopy HVYCKACLKDYFETQIRDGQVQCLNCPEPKCPSVATPGQVKEELVEAELFASYDRLLLQFTLDLMADVVY

Parental  CPRPCCQLPVMQEPGCTMGICSSCNFAFCTLCRLTYHGVSPCKVTAEKLMDLRNEYLQADEANKRLLDQR
          CP.PCCQLPVMQEPGCTMGICSSCNFAFCTLCRLTYHGVSPCKVTAEKL.DLRNEYLQADEANK.LL.QR
Retrocopy CPYPCCQLPVMQEPGCTMGICSSCNFAFCTLCRLTYHGVSPCKVTAEKLIDLRNEYLQADEANKGLLEQR

Parental  YGKRVIQKALEEMESKEWLEKNSKSCPCCGTPIEKLDGCNKMTCTGCKQYFCWICMGSLSRANPYKHFND
          .GKRVIQKALE.MESKEW.EKN.K..PCCGTPIEKLDG.NKMTCTGC.QYFCWICM.SLSRANPYKHF.D
Retrocopy CGKRVIQKALEKMESKEWPEKNFKN*PCCGTPIEKLDGYNKMTCTGCMQYFCWICMSSLSRANPYKHFTD

Parental  PASPCFNRLFYAVDVDDDIWEDEVED
          PASP.FN.LFYAVDVD.DI.EDE.ED
Retrocopy PASPRFNQLFYAVDVDEDILEDEIED

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	0.23 RPM	27.82 RPM
SRP007412_liver	0.04 RPM	24.98 RPM
SRP007412_testis	0.34 RPM	36.49 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1647 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1647 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1647 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3790
Pan troglodytes	retro_ptro_2571
Pongo abelii	retro_pabe_3095

---

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,