RetrogeneDB ID: retro_mmul_2114

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 6:154472138..154472789(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LXN
• Ensembl ID: ENSMMUG00000004963
• Aliases: None
• Description: latexin [Source:RefSeq peptide;Acc:NP_001253917]

Sequence

>retro_mmul_2114
ATAGAAATCTCATGGACCCATGACCCAGCCTCCAAGGCGGCCTCAGTGGCAGTGAACTGCCTCAACTACCAGTGGGGGAC
ACCCCACAAGGTATTTCTGAGGCAGAGAGTTAAACAAGCCAGCACAGAGAATATTCCAGGAAGAGGACATAAGTATCACC
TCAAATGCTCTGTGGAATGAGTTATTCTAAAACAAGTTACAGTGAACTGCATAGCTGAATTCCCTTATCTTACAGTGGGA
CAAGATACTGCACCAGAAATCAACGTCACATGTGAAGGAGAAATGGAAAGAGCCCAGATGGAGAAAACAACACATCTGAT
CAAAAACTCAAGTCCATGAAGGAATCACTAGAAGCACAAAATGTTCCAGACATTTTGAGAAATGTATCTCCAAAAATGAA
GCCAGGTCAACATTTAGCCTGGGTTACCTGTTGTTATATAACATGGAAAATTCTACTGAAAACACCTGGTATAAAAGTGG
TAAAATTAAACTGTCAAGAAAATGCAAAAAAATGACTTTATTGAATAGACTATAACATTCTACTTCATGACATTGCATCC
CGGGACATTGATTCCTTGGCAAATGCAAGTTCTTTGGCACTGACAAGATGGTGCTAAAGTAAAATGTAATCTCTCTCTGC
CAAGGGAAGTC

Alignment

ORF - retro_mmul_2114 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.29 %
• Parental protein coverage: 98.65 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  MEIPPTNYPASRAALVAQNYINYQQGTPHRVFEVQKVKQASMEDIPGRGHKYRLKFAVEEIIQKQVKVNC
          .EI..T..PAS.AA.VA.N..NYQ.GTPH.VF..Q.VKQAS.E.IPGRGHKY.LK..VE..I.KQV.VNC
Retrocopy IEISWTHDPASKAASVAVNCLNYQWGTPHKVFLRQRVKQASTENIPGRGHKYHLKCSVE*VILKQVTVNC

Parental  TAEVLYPLMGQETAPEVNFTFEGE-TGKNPDEEDNTFYQRLKSMKEPLEAQNIPDNFGNVSPEMTLLLHL
          .AE..Y...GQ.TAPE.N.T.EGE..GK.PD.E.NT..Q.LKSMKE.LEAQN.PD...NVSP.M....HL
Retrocopy IAEFPYLTVGQDTAPEINVTCEGE<NGKSPDGENNTSDQKLKSMKESLEAQNVPDILRNVSPKMKPGQHL

Parental  AWVACGYIIW-QNSTEDTWYKMVKIQ-TVKQVQRNDDFIE-LDYTILLHDIGSQEI-IPWQMQVLWHPQY
          AWV.C.YI.W..NSTE.TWYK..KI..TVK..Q.N.DFIE..DY.ILLHDI.S..I.IPWQMQVLWH.Q.
Retrocopy AWVTCCYITW<ENSTENTWYKSGKIK<TVKKMQKN-DFIE<IDYNILLHDIASRDI>IPWQMQVLWH*QD

Parental  GTKVKHNSRLPKEV
          G.KVK.N..LP.EV
Retrocopy GAKVKCNLSLPREV

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	2.13 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	1.75 RPM
SRP007412_cerebellum	0.00 RPM	1.81 RPM
SRP007412_heart	0.00 RPM	5.42 RPM
SRP007412_kidney	0.00 RPM	19.01 RPM
SRP007412_liver	0.00 RPM	2.26 RPM
SRP007412_testis	0.00 RPM	0.60 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2114 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2114 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2114 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3397
Pan troglodytes	retro_ptro_2308
Gorilla gorilla	retro_ggor_2300
Pongo abelii	retro_pabe_2791

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000009336	2 retrocopies	retro_btau_569, retro_btau_860,
Canis familiaris	ENSCAFG00000009096	1 retrocopy	retro_cfam_1863,
Callithrix jacchus	ENSCJAG00000000386	1 retrocopy	retro_cjac_1890,
Homo sapiens	ENSG00000079257	1 retrocopy	retro_hsap_3397,
Gorilla gorilla	ENSGGOG00000003092	1 retrocopy	retro_ggor_2300,
Macaca mulatta	ENSMMUG00000004963	1 retrocopy	retro_mmul_2114 ,
Nomascus leucogenys	ENSNLEG00000004229	1 retrocopy	retro_nleu_1949,
Pongo abelii	ENSPPYG00000014245	1 retrocopy	retro_pabe_2791,
Pan troglodytes	ENSPTRG00000015571	1 retrocopy	retro_ptro_2308,
Pteropus vampyrus	ENSPVAG00000013608	2 retrocopies	retro_pvam_94, retro_pvam_962,
Tupaia belangeri	ENSTBEG00000017673	3 retrocopies	retro_tbel_2746, retro_tbel_3329, retro_tbel_4516,