RetrogeneDB ID: retro_mmul_1669

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 3:21733208..21733949(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMMUG00000013861
• Aliases: None
• Description: None

Sequence

>retro_mmul_1669
GAATTTAGGCAGGTGATGAATGGTTTTCAATACCAGAAGCACAGGAAGGGGAAGGAGTTCCAGGAACAACATCTTCTTGA
GATCCCCACATCTGTGGACTGGAGAGAGAAAGGCTACGTGACTCCTGTGAAGAATCAGGGTATGTGTGGCTCTTGTTGGG
CTTTTAGTGCAACTGGTGCTCTGGAAGGGCAGATGTTCTGGAAAACAGGCAAACTTATTTCACTGAGTGAGCAGAATCTG
GTAGACTGCTCTTGGCCTCAAGGCAATGAGGGCTACAACGGTGGTTTCATGGATAATTCCTTCCGGTATGTTCAGGAGAA
CGGAGGCCTGGACTCTGAGGCATCCTATCCATATGAAGGAAAGGTTAAAACCTGTAGGTACAATCCCAAGTACTCTGTTG
CTAATGACACTGGCTTTGTGGACATCCCTTCACGGGAGAAGGACCTGGCGAAGGCAGTGGCAACTGTGGGGCCCATCTCT
GTTGCTGTTGATGCAAGCCATTTCTCCTTCCAGTTCTACAAAAAAGGAATTTATTTTGAGCCACGTTGTGACCCTGAAGG
CCTAGATCATGCTATGCTGACGGTTGGCTATGGCTATGAAGGAGCAGACTCGGATAACAATAAATATTGGCTGGTGAAGA
ACAGCTGGGGTAAAAACTGGGGCATGGATGGCTACATAAAGATGGCCAAAGACCGGAGGAACAACTGTGGAATCGCCACA
GCAGCCAGCTACCCCACTGTG

Alignment

ORF - retro_mmul_1669 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.33 %
• Parental protein coverage: 74.1 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EFRQVMNGFQYQKHRKGKEFQERLLLEIPTSVDWREKGYMTPVKNQGMCGSCWAFSATGALEG-MFWKTG
          EFRQVMNGFQYQKHRKGKEFQE..LLEIPTSVDWREKGY.TPVKNQGMCGSCWAFSATGALEG.MFWKTG
Retrocopy EFRQVMNGFQYQKHRKGKEFQEQHLLEIPTSVDWREKGYVTPVKNQGMCGSCWAFSATGALEGQMFWKTG

Parental  KLISLSEQNLVDCSWPQGNEGCNGGFMDNSFWYVQENGGLDSEASYLYEGKVKTCRYNPKYSVANDTGFV
          KLISLSEQNLVDCSWPQGNEG.NGGFMDNSF.YVQENGGLDSEASY.YEGKVKTCRYNPKYSVANDTGFV
Retrocopy KLISLSEQNLVDCSWPQGNEGYNGGFMDNSFRYVQENGGLDSEASYPYEGKVKTCRYNPKYSVANDTGFV

Parental  DIPSREKDLAKAVATVGPVSVAVDASHFSFQFYKKGIYFEPRCDPEGLDHAMLAVGYGYEEADSDNNKYW
          DIPSREKDLAKAVATVGP.SVAVDASHFSFQFYKKGIYFEPRCDPEGLDHAML.VGYGYE.ADSDNNKYW
Retrocopy DIPSREKDLAKAVATVGPISVAVDASHFSFQFYKKGIYFEPRCDPEGLDHAMLTVGYGYEGADSDNNKYW

Parental  LVKNRTGKNWGMDGYVKMAKDRGNNCGIATAASYPTV
          LVKN..GKNWGMDGY.KMAKDR.NNCGIATAASYPTV
Retrocopy LVKNSWGKNWGMDGYIKMAKDRRNNCGIATAASYPTV

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	0.22 RPM	0.11 RPM
SRP007412_brain_prefrontal_cortex	0.08 RPM	0.00 RPM
SRP007412_cerebellum	0.19 RPM	0.06 RPM
SRP007412_heart	0.06 RPM	0.06 RPM
SRP007412_kidney	0.00 RPM	0.00 RPM
SRP007412_liver	0.00 RPM	0.00 RPM
SRP007412_testis	0.15 RPM	0.26 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1669 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1669 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1669 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000019810	1 retrocopy	retro_dord_197,
Macropus eugenii	ENSMEUG00000002168	2 retrocopies	retro_meug_1349, retro_meug_1567,
Macropus eugenii	ENSMEUG00000014293	1 retrocopy	retro_meug_1873,
Macropus eugenii	ENSMEUG00000016209	2 retrocopies	retro_meug_159, retro_meug_1727,
Myotis lucifugus	ENSMLUG00000003975	1 retrocopy	retro_mluc_2231,
Myotis lucifugus	ENSMLUG00000025440	1 retrocopy	retro_mluc_2399,
Macaca mulatta	ENSMMUG00000013861	1 retrocopy	retro_mmul_1669 ,
Monodelphis domestica	ENSMODG00000002844	1 retrocopy	retro_mdom_1101,
Petromyzon marinus	ENSPMAG00000003453	1 retrocopy	retro_pmar_7,
Tarsius syrichta	ENSTSYG00000002858	2 retrocopies	retro_tsyr_150, retro_tsyr_603,