RetrogeneDB ID: retro_mmul_1827

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 4:29845315..29845772(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMMUG00000011686
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: MMU.3162
• Ensembl ID: ENSMMUG00000001940
• Aliases: None
• Description: nucleoside diphosphate kinase A [Source:RefSeq peptide;Acc:NP_001191444]

Sequence

>retro_mmul_1827
ATGGCCAACTGTGAGCGTACCTTCATTGCGATCAAACCAGATAGGGTCCAGCGGGGTCTTGTCGGAGAGATTATCAAGCA
TTTTGAGCAGAAAGGATTCCGCCTTGTTGGTCTGAAATTCATGCCAGCTTCTGAAGACCTTCTCAAGGAACACTACATTG
ACCTGAAGGGACGTCCATTCTTTGTTGGCCTGGTGAAATACATGCACTCAGGGGCCCGTGGTTGCCATGGTCTGGGAGGG
GCTGAATGTGGTGAAGACAGGCCGAGTCATGCTCGGGGAGACCAACTCTGCAGACTCCAAGCCTGGGACCATCCATGGAG
ACTTCTGCATACAAGTTGGCAGGAACATTATACATGGCAGTGATTCCGTGGAGAGTGCAGAGAACGAGATCAGCTTGTGG
TTTCACCCTGAGGAACTGGTAGACTACACGAGCTGTGTTCAGAACTGGATCTATGAA

Alignment

ORF - retro_mmul_1827 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.81 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MANCERTFIAIKPDGVQRGLVGEIIKRFEQKGFRLVGLKFMQASEDLLKEHYIDLKDRPFFAGLVKYMHS
          MANCERTFIAIKPD.VQRGLVGEIIK.FEQKGFRLVGLKFM.ASEDLLKEHYIDLK.RPFF.GLVKYMHS
Retrocopy MANCERTFIAIKPDRVQRGLVGEIIKHFEQKGFRLVGLKFMPASEDLLKEHYIDLKGRPFFVGLVKYMHS

Parental  -GPVVAMVWEGLNVVKTGRVMLGETNPADSKPGTIRGDFCIQVGRNIIHGSDSVESAEKEISLWFHPEEL
          .GPVVAMVWEGLNVVKTGRVMLGETN.ADSKPGTI.GDFCIQVGRNIIHGSDSVESAE.EISLWFHPEEL
Retrocopy >GPVVAMVWEGLNVVKTGRVMLGETNSADSKPGTIHGDFCIQVGRNIIHGSDSVESAENEISLWFHPEEL

Parental  VDYMSCAQNWIYE
          VDY.SC.QNWIYE
Retrocopy VDYTSCVQNWIYE

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	0.11 RPM	110.03 RPM
SRP007412_brain_prefrontal_cortex	0.79 RPM	170.24 RPM
SRP007412_cerebellum	0.58 RPM	60.57 RPM
SRP007412_heart	0.12 RPM	158.40 RPM
SRP007412_kidney	0.12 RPM	159.03 RPM
SRP007412_liver	0.36 RPM	140.72 RPM
SRP007412_testis	0.38 RPM	30.23 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1827 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1827 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1827 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 48 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000008022	3 retrocopies	retro_amel_1573, retro_amel_390, retro_amel_538,
Bos taurus	ENSBTAG00000047186	1 retrocopy	retro_btau_1329,
Callithrix jacchus	ENSCJAG00000018395	5 retrocopies	retro_cjac_1765, retro_cjac_2517, retro_cjac_2642, retro_cjac_3940, retro_cjac_471,
Equus caballus	ENSECAG00000021658	1 retrocopy	retro_ecab_404,
Erinaceus europaeus	ENSEEUG00000003783	2 retrocopies	retro_eeur_156, retro_eeur_5,
Felis catus	ENSFCAG00000006742	5 retrocopies	retro_fcat_1083, retro_fcat_1117, retro_fcat_1475, retro_fcat_216, retro_fcat_663,
Homo sapiens	ENSG00000011052	1 retrocopy	retro_hsap_1063,
Loxodonta africana	ENSLAFG00000007784	1 retrocopy	retro_lafr_636,
Myotis lucifugus	ENSMLUG00000016929	3 retrocopies	retro_mluc_1422, retro_mluc_1882, retro_mluc_637,
Macaca mulatta	ENSMMUG00000000612	1 retrocopy	retro_mmul_1221,
Macaca mulatta	ENSMMUG00000001940	1 retrocopy	retro_mmul_1827 ,
Monodelphis domestica	ENSMODG00000012580	1 retrocopy	retro_mdom_1811,
Mustela putorius furo	ENSMPUG00000015573	4 retrocopies	retro_mputfur_1236, retro_mputfur_1590, retro_mputfur_327, retro_mputfur_912,
Rattus norvegicus	ENSRNOG00000002671	8 retrocopies	retro_rnor_1129, retro_rnor_1610, retro_rnor_1708, retro_rnor_1784, retro_rnor_1966, retro_rnor_2646, retro_rnor_2951, retro_rnor_628,
Sarcophilus harrisii	ENSSHAG00000014470	3 retrocopies	retro_shar_130, retro_shar_554, retro_shar_781,
Sus scrofa	ENSSSCG00000017591	1 retrocopy	retro_sscr_854,
Tupaia belangeri	ENSTBEG00000013053	6 retrocopies	retro_tbel_1271, retro_tbel_1386, retro_tbel_2497, retro_tbel_294, retro_tbel_4620, retro_tbel_820,
Tursiops truncatus	ENSTTRG00000007433	1 retrocopy	retro_ttru_1821,