RetrogeneDB ID: retro_mmul_2323

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 8:20834879..20835386(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.2685
• Ensembl ID: ENSMMUG00000019142
• Aliases: None
• Description: transmembrane protein 97 [Source:RefSeq peptide;Acc:NP_001244680]

Sequence

>retro_mmul_2323
CCGACCGACAGACAATGCCACGGCATGGAGTCACTGCTGGGCCTCTTCTTCCTCACCCGTGTCCCCATCACCCTGTTCAT
GGCCCTGCAGGTGGTGCTGCTGCAAGAGCTCTACCCAGTAGAGTTTAGAAACGTCCTGAAGTGGTATGCTAAGGAGTTCA
AAGACACGCTGCTGTGGGAGCCATCAGCCTGGTTTAAGTCCTTTCTATTTTACAAGCTTGTGTTTCAGCTACCTTTCTTT
CCCATTGCAACCTATGCCTTCCTCAAAGGAAGCTGCAAGTGGATTTGAACCCCTGCAAATCATCTACTCAGTTCCCACCA
TGACGACTTTAATTCCAATACTCTCCACATTTCTGTTTGAGGATTTTCCAAAGCCAGTGGTTTCAAAGGACAAAGACCTG
AGACTCTGCATGAACGGTTAAGCCCTGTATCTGTCTATGCACTCTACTTACTCATACCATTCGTCCTTTTAATGTTCATG
TTGCAGAGCCCCTACAAGTATGAGGAG

Alignment

ORF - retro_mmul_2323 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.65 %
• Parental protein coverage: 95.45 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  PATRRC--VEWLLGIYFLSHIPITLFMDLQAVLPRELYPVEFRNLLKWYAKEFKDPLLQEPPAWFKSFLF
          P..R.C...E.LLG..FL...PITLFM.LQ.VL..ELYPVEFRN.LKWYAKEFKD.LL.EP.AWFKSFLF
Retrocopy PTDRQCHGMESLLGLFFLTRVPITLFMALQVVLLQELYPVEFRNVLKWYAKEFKDTLLWEPSAWFKSFLF

Parental  CELVFQLPFFPIATYAFLKGCCKWIRTPA-IIYSVHTMTTLIPILSTFLFED-FSKASGFKGQRPETLHE
          ..LVFQLPFFPIATYAFLKG.CKWI.TPA.IIYSV.TMTTLIPILSTFLFED.FSKASGFKGQRPETLHE
Retrocopy YKLVFQLPFFPIATYAFLKGSCKWI*TPA>IIYSVPTMTTLIPILSTFLFED<FSKASGFKGQRPETLHE

Parental  RLTLISVYAPYLLIPFILLIFMLRSPYYKYEE
          RL...SVYA.YLLIPF.LL.FML.SP.YKYEE
Retrocopy RLSPVSVYALYLLIPFVLLMFMLQSP-YKYEE

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	4.26 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	4.68 RPM
SRP007412_cerebellum	0.00 RPM	4.71 RPM
SRP007412_heart	0.00 RPM	2.59 RPM
SRP007412_kidney	0.23 RPM	9.51 RPM
SRP007412_liver	0.12 RPM	27.91 RPM
SRP007412_testis	0.00 RPM	18.24 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2323 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2323 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2323 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4027
Pan troglodytes	retro_ptro_2731
Gorilla gorilla	retro_ggor_2703
Pongo abelii	retro_pabe_3307

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000011105	1 retrocopy	retro_chof_566,
Homo sapiens	ENSG00000109084	1 retrocopy	retro_hsap_4027,
Gorilla gorilla	ENSGGOG00000004565	1 retrocopy	retro_ggor_2703,
Macaca mulatta	ENSMMUG00000019142	1 retrocopy	retro_mmul_2323 ,
Mus musculus	ENSMUSG00000037278	1 retrocopy	retro_mmus_1451,
Nomascus leucogenys	ENSNLEG00000001868	1 retrocopy	retro_nleu_1574,
Otolemur garnettii	ENSOGAG00000003329	1 retrocopy	retro_ogar_1913,
Pongo abelii	ENSPPYG00000008086	1 retrocopy	retro_pabe_3307,
Pan troglodytes	ENSPTRG00000008909	1 retrocopy	retro_ptro_2731,
Ictidomys tridecemlineatus	ENSSTOG00000007542	2 retrocopies	retro_itri_341, retro_itri_758,
Tupaia belangeri	ENSTBEG00000005125	2 retrocopies	retro_tbel_2160, retro_tbel_2221,