RetrogeneDB ID: retro_mmul_420

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 1:142798665..142799248(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.13916
• Ensembl ID: ENSMMUG00000019802
• Aliases: None
• Description: None

Sequence

>retro_mmul_420
TATATGAACCCAATAGCAATGGCGAGATCAAGGGGTCCAATCCAGTCTTCAGGGCCAACAATACCAGATTACTTGAATCA
ACCAAGGCCTATCTGGGAAGAAGTAAAAGAGCAACTAGAAGAGGAAAAGAAAGGCTCCAAGACTTTGGCTGAATTTGAAG
AAAAACATGAATGAGAACTGGAAGAAAGAACTAGAAAAACACAGGGAGAAATTGTTAGGTGGAAGTGAGAGCTCATCAAA
AAAAAAAGAAAGAAAGAAAAAAGAAAAGAATAAATCTGGCAGGTATTCATCTTCTTCATCAAGTTCTATTTCTTCTAGCA
GTTCTTCTGATTCTGAAGATGAGGATAAGAAACAAGGAAAATAGAGAAAGAAAAAGAACCGTTCATATAAATCTTCTGAA
AGCTCCACGTAATAAACTGAATCAGAGAGTAAGGATAGTTTAAAAAAGAAAAAGAAGTCAAAAGATGCAACTGAGAAAGA
AAAGGACATTAAAGGACTCAGCAAAAAGAGAAAGATAAATTCTTAAGATAAAACTTTATCATCCAAGTCCTTGTCAGAAT
CACAGTATATTAAGGAGGTACGA

Alignment

ORF - retro_mmul_420 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.1 %
• Parental protein coverage: 78.71 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  YMNPIAMARSRGPVQSSGPTIQDYLNRPRPTWEEVKEQLEKKKKGSKALAEFEEK-MNENWKKELEKHRE
          YMNPIAMARSRGP.QSSGPTI.DYLN.PRP.WEEVKEQLE..KKGSK.LAEFEEK.MNENWKKELEKHRE
Retrocopy YMNPIAMARSRGPIQSSGPTIPDYLNQPRPIWEEVKEQLEEEKKGSKTLAEFEEK>MNENWKKELEKHRE

Parental  KLLSGSESSSKKRQRKKKEKKKSGRYSSSSSSSSDSSSSSSDSEDEDKKQGKRRKKKKNRSHKSSESSMS
          KLL.GSESS.............SGRYSSSSSSS..SSSSSSDSEDEDKKQGK.R.KKKNRS.KSSESS..
Retrocopy KLLGGSESSXXXXXXXXXXXXXSGRYSSSSSSSI-SSSSSSDSEDEDKKQGK*R-KKKNRSYKSSESST*

Parental  ETESDSKDSLKKKKKSKDGTEKEKDIKGLSKKRKMYSEDKPLSSESLSESEYIEEVR
          .TES.SKDS...............DIKGLSKKRK..S.DK.LSS.SLSES.YI.EVR
Retrocopy *TESESKDSXXXXXXXXXXXXXXXDIKGLSKKRKINS*DKTLSSKSLSESQYIKEVR

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	5.83 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	5.08 RPM
SRP007412_cerebellum	0.06 RPM	10.53 RPM
SRP007412_heart	0.06 RPM	3.06 RPM
SRP007412_kidney	0.00 RPM	3.87 RPM
SRP007412_liver	0.00 RPM	1.15 RPM
SRP007412_testis	0.11 RPM	1.55 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_420 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_420 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_420 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pongo abelii	retro_pabe_225

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000007438	1 retrocopy	retro_amel_102,
Callithrix jacchus	ENSCJAG00000013910	3 retrocopies	retro_cjac_1084, retro_cjac_1163, retro_cjac_4095,
Equus caballus	ENSECAG00000026810	1 retrocopy	retro_ecab_95,
Homo sapiens	ENSG00000234545	4 retrocopies	retro_hsap_2336, retro_hsap_3179, retro_hsap_55, retro_hsap_577,
Loxodonta africana	ENSLAFG00000029755	1 retrocopy	retro_lafr_594,
Myotis lucifugus	ENSMLUG00000005933	1 retrocopy	retro_mluc_2301,
Macaca mulatta	ENSMMUG00000019802	4 retrocopies	retro_mmul_1415, retro_mmul_226, retro_mmul_420 , retro_mmul_765,
Mus musculus	ENSMUSG00000058503	2 retrocopies	retro_mmus_3481, retro_mmus_3519,
Nomascus leucogenys	ENSNLEG00000015333	1 retrocopy	retro_nleu_14,
Pongo abelii	ENSPPYG00000025825	1 retrocopy	retro_pabe_225,
Rattus norvegicus	ENSRNOG00000009163	1 retrocopy	retro_rnor_2891,
Sus scrofa	ENSSSCG00000015317	1 retrocopy	retro_sscr_49,
Ictidomys tridecemlineatus	ENSSTOG00000028195	1 retrocopy	retro_itri_12,
Tupaia belangeri	ENSTBEG00000011674	1 retrocopy	retro_tbel_1,