RetrogeneDB ID: retro_mmul_394

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 1:95714463..95714909(+)
• Located in intron of: ENSMMUG00000005070

Retrocopy information

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

Parental gene information

• Parental gene symbol: ZFAND1
• Ensembl ID: ENSMMUG00000002626
• Aliases: None
• Description: None

Sequence

>retro_mmul_394
AGACATAAATTTTACCCATGCTCATTCAAGGGCCGTGTTGAAAGAGAACTTGTGGCAGTTATACATCCTTACTGTGAGAA
TAATTTTTTCCTGAGACACCATCATCAGTCAGATCACAAGTGTGAAAAACTGGAAATCCCAAAGCCTTACACAGCTGCCA
CTCAGAAACTTGTTAAAGACATTGATTCCAAAACAGGAGAGACAGCAAGTAAACAAGGGAAAGGTGACAAAAAATAGTGA
AACAGCTGCAAAGGAATTGCACTGATGAAATTAAGGATATACAACGATGGGGATAAATCACTGCCACAGGCATAAAGTAT
TTGCTTTCAAGTTTTCTTACCTAAGGGGAGCAAAGAAAAAGGTAAACCAATGTTCTTTTCCATGGATGAAGCATCAAAAA
GGTCACAGACTTTGCTGCTTCTCTGGCCAGTCTTAAAGATGACAAT

Alignment

ORF - retro_mmul_394 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.52 %
• Parental protein coverage: 55.6 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  QHTSYPCSFKDCAERELVAVICPHCEKNFCLRHRHQSDHECEKLEIPKPRMAATQKLVKDIIDSKTGETA
          .H..YPCSFK...ERELVAVI.P.CE.NF.LRH.HQSDH.CEKLEIPKP..AATQKLVKDI.DSKTGETA
Retrocopy RHKFYPCSFKGRVERELVAVIHPYCENNFFLRHHHQSDHKCEKLEIPKPYTAATQKLVKDI-DSKTGETA

Parental  SKRRKGAKNSETAAK-VALMKLKMHADGDKSLPQTERIYFQVFLPKGSKEKSKPMFFC-HRWSIGKAIDF
          SK..KG.K......K..ALMKL....DGDKSLPQ...I.FQVFLPKGSKEK.KPMFF..H..SI.K..DF
Retrocopy SKQGKGDKK**NSCKGIALMKLRIYNDGDKSLPQA*SICFQVFLPKGSKEKGKPMFFS<HG*SIKKVTDF

Parental  AASLASLKNDN
          AASLASLK.DN
Retrocopy AASLASLKDDN

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	20.62 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	11.98 RPM
SRP007412_cerebellum	0.26 RPM	24.67 RPM
SRP007412_heart	0.18 RPM	6.42 RPM
SRP007412_kidney	0.00 RPM	15.38 RPM
SRP007412_liver	0.08 RPM	6.21 RPM
SRP007412_testis	0.19 RPM	3.24 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_394 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_394 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_394 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_187
Gorilla gorilla	retro_ggor_268

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000014075	1 retrocopy	retro_cpor_312,
Homo sapiens	ENSG00000104231	1 retrocopy	retro_hsap_187,
Gorilla gorilla	ENSGGOG00000023665	1 retrocopy	retro_ggor_268,
Microcebus murinus	ENSMICG00000016889	1 retrocopy	retro_mmur_1073,
Macaca mulatta	ENSMMUG00000002626	1 retrocopy	retro_mmul_394 ,
Mus musculus	ENSMUSG00000039795	1 retrocopy	retro_mmus_2093,
Nomascus leucogenys	ENSNLEG00000002584	1 retrocopy	retro_nleu_997,
Otolemur garnettii	ENSOGAG00000009813	2 retrocopies	retro_ogar_2608, retro_ogar_514,
Tupaia belangeri	ENSTBEG00000015393	1 retrocopy	retro_tbel_3648,