RetrogeneDB ID: retro_cjac_2517

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 5:52315671..52316037(+)
• Located in intron of: ENSCJAG00000019039

Retrocopy information

• Ensembl ID: ENSCJAG00000019046
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: NME1
• Ensembl ID: ENSCJAG00000018395
• Aliases: None
• Description: nucleoside diphosphate kinase A [Source:RefSeq peptide;Acc:NP_001191805]

Sequence

>retro_cjac_2517
AAGCGATTCCGCCTTGTTGGTCTGAAATTCATGCAGGCCTCTGAAGATCTTCTCAAGGAACACTACATCGACCTGAAGGA
CCGTCCATTCTTTGCTGGCCTGGTGAAATACATACACTCAGGGCCGGTAGTTGCCATGGTCTGGGAGGGGCTGAATGTGG
TGAAGACAGCCCGAGTCATGCGCGGGGAGACCAACTCTGCGGACTCCAAGCCTGAGACCATCCGTGGAGACTTCTGCATA
CAAGTCGGCAGGAACATTATACACGGCAGTGATTCCGTGGAGAGTGCAGAGAAGGAGATCAGCTTGTGGTTTCACCCTAA
GGAACTGGTAGATTACAAGAGCTGTGCTCAGAACTGGATGTATGAA

Alignment

ORF - retro_cjac_2517 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.62 %
• Parental protein coverage: 80.26 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KGFRLVGLKFMQASEDLLKEHYIDLKDRPFFAGLVKYMHSGPVVAMVWEGLNVVKTGRVMLGETNPADSK
          K.FRLVGLKFMQASEDLLKEHYIDLKDRPFFAGLVKY.HSGPVVAMVWEGLNVVKT.RVM.GETN.ADSK
Retrocopy KRFRLVGLKFMQASEDLLKEHYIDLKDRPFFAGLVKYIHSGPVVAMVWEGLNVVKTARVMRGETNSADSK

Parental  PGTIRGDFCIQVGRNIIHGSDSVESAEKEIGLWFHPEELVDYKSCAQNWIYE
          P.TIRGDFCIQVGRNIIHGSDSVESAEKEI.LWFHP.ELVDYKSCAQNW.YE
Retrocopy PETIRGDFCIQVGRNIIHGSDSVESAEKEISLWFHPKELVDYKSCAQNWMYE

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
SRP051959_colon	0.69 RPM	46.68 RPM
SRP051959_heart	0.58 RPM	39.69 RPM
SRP051959_kidney	0.60 RPM	68.24 RPM
SRP051959_liver	0.28 RPM	50.62 RPM
SRP051959_lung	0.65 RPM	25.60 RPM
SRP051959_lymph_node	0.73 RPM	38.49 RPM
SRP051959_skeletal_muscle	0.37 RPM	75.19 RPM
SRP051959_spleen	0.92 RPM	42.14 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2517 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2517 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2517 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 33 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000008022	3 retrocopies	retro_amel_1573, retro_amel_390, retro_amel_538,
Callithrix jacchus	ENSCJAG00000018395	5 retrocopies	retro_cjac_1765, retro_cjac_2517 , retro_cjac_2642, retro_cjac_3940, retro_cjac_471,
Erinaceus europaeus	ENSEEUG00000003783	2 retrocopies	retro_eeur_156, retro_eeur_5,
Homo sapiens	ENSG00000011052	1 retrocopy	retro_hsap_1063,
Myotis lucifugus	ENSMLUG00000016929	3 retrocopies	retro_mluc_1422, retro_mluc_1882, retro_mluc_637,
Macaca mulatta	ENSMMUG00000001940	1 retrocopy	retro_mmul_1827,
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,