RetrogeneDB ID: retro_mmul_2118

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 6:168640635..168641151(-)
• Located in intron of: ENSMMUG00000003151

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.1544
• Ensembl ID: ENSMMUG00000003363
• Aliases: None
• Description: Krueppel-like factor 3 [Source:RefSeq peptide;Acc:NP_001248209]

Sequence

>retro_mmul_2118
TCTTCTATGGAGGAGACGGAAAATTCTAGTGGTAGCCTACCTGTAATTGAATCATAAGAAAATCCTGTATCACAGAAAAA
AATTAAAATAGAACCTGGGATCGAACCACAGAGAACAGATTATCCTGAAGAAATGTCACCCCCCCTTAATGAACTCAGTG
TCCCCCTGCAAGCATTGTTGCAAGAAAATCACCGTTTGGTCGTCGTGCAACCTGGGAAGAGACCTGTACCTGTGGAATTC
CCGGATACGCAAAGGAAGTGGAGGATACGCAGATGTGATTACAGTGGATGCAATAAAATGTACACTGAAAGCTCCCACTT
GAAAGCACACAGAAGACCACACACAGAAAAACCCTACAAATGTACATGGGAAGGATGCACATGGACATTTGCTCCGTCTG
ATGAACTAAAAAGACATTTAGGAAAACATATTGGAATAAAACCTTTACAGTGTCCAGACTGTAACCGCAGCTTTTCCTGA
TCTGACCATCTTGCCTTCCATAGGAAATGCCACCTG

Alignment

ORF - retro_mmul_2118 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.65 %
• Parental protein coverage: 51.01 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SLSEEMENSSSSMQVPVIESYEKPISQKKIKIEPGIEPQRTDYYPEEMSPPL-MNSVS-PPQALLQENHP
          S..EE.ENSS.S...PVIES.E.P.SQKKIKIEPGIEPQRTD.YPEEMSPPL.MNSVS.P.QALLQENH.
Retrocopy SSMEETENSSGSL--PVIES*ENPVSQKKIKIEPGIEPQRTD-YPEEMSPPL>MNSVS<PLQALLQENHR

Parental  SVIVQPGKRPLPVESPDTQRKRRIHRCDYDGCNKVYTKSSHLKAHRRTHTGEKPYKCTWEGCTWKFARSD
          .V.VQPGKRP.PVE.PDTQRK.RI.RCDY.GCNK.YT.SSHLKAHRR.HT.EKPYKCTWEGCTW.FA.SD
Retrocopy LVVVQPGKRPVPVEFPDTQRKWRIRRCDYSGCNKMYTESSHLKAHRRPHT-EKPYKCTWEGCTWTFAPSD

Parental  ELTRHFRKHTGIKPFQCPDCDRSFSRSDHLALHRKRHM
          EL.RH..KH.GIKP.QCPDC.RSFS.SDHLA.HRK.H.
Retrocopy ELKRHLGKHIGIKPLQCPDCNRSFS*SDHLAFHRKCHL

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	21.07 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	17.37 RPM
SRP007412_cerebellum	0.58 RPM	17.82 RPM
SRP007412_heart	0.24 RPM	16.61 RPM
SRP007412_kidney	0.00 RPM	24.88 RPM
SRP007412_liver	0.16 RPM	28.38 RPM
SRP007412_testis	0.79 RPM	7.54 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2118 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2118 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2118 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000017488	1 retrocopy	retro_btau_271,
Choloepus hoffmanni	ENSCHOG00000004256	1 retrocopy	retro_chof_181,
Macaca mulatta	ENSMMUG00000003363	1 retrocopy	retro_mmul_2118 ,
Macaca mulatta	ENSMMUG00000014678	1 retrocopy	retro_mmul_1561,
Nomascus leucogenys	ENSNLEG00000017046	1 retrocopy	retro_nleu_2431,
Otolemur garnettii	ENSOGAG00000006524	1 retrocopy	retro_ogar_1686,