RetrogeneDB ID: retro_cjac_3940

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: GL286358.1:14178..14630(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000011081
• 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_3940
ATGGCCAACTGTGAGCATACCTTCATTGCCGTCAATTCACCTGGGGTCCAGTGGGGTCTTGTGGGAGAGATTATCAAGTG
TTTTGAGCAGAAGGGATTCTGCCTTGTTGGTCTGAAATTCATGCAAGCTTCTGAAGACCTTCTCAAGGAACACTACATCG
ACCTGAAGGACCATCCATTCTTGCCGGCCTGGTGAAATACATGCACTCAGGGCTGGTAGTTGCCATGGTCTGGGAGGGGC
TGAACGTGGTGAAGACAGGCCGAGTCAGGCTCGGGGAGACCAACCCTGCAGACTCCAAGCCTGGGACCCTCCGTGGAGAC
TTCCACATGCAAGTTGGCAGGAACATTATACAGGGCAGCGATTCTGTGGAGAGTGCGGAGGAGATCAGCTTGTGGTTTCA
CCCTGAGGAACTGGTAGATTATAAGAGCTGTGCTCAGAACTGGATGTATGAA

Alignment

ORF - retro_cjac_3940 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.93 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MANCERTFIAIKPDGVQRGLVGEIIKRFEQKGFRLVGLKFMQASEDLLKEHYIDLKDRPFF-AGLVKYMH
          MANCE.TFIA....GVQ.GLVGEIIK.FEQKGF.LVGLKFMQASEDLLKEHYIDLKD.PF..AGLVKYMH
Retrocopy MANCEHTFIAVNSPGVQWGLVGEIIKCFEQKGFCLVGLKFMQASEDLLKEHYIDLKDHPFL<AGLVKYMH

Parental  SGPVVAMVWEGLNVVKTGRVMLGETNPADSKPGTIRGDFCIQVGRNIIHGSDSVESAEKEIGLWFHPEEL
          SG.VVAMVWEGLNVVKTGRV.LGETNPADSKPGT.RGDF..QVGRNII.GSDSVESAE.EI.LWFHPEEL
Retrocopy SGLVVAMVWEGLNVVKTGRVRLGETNPADSKPGTLRGDFHMQVGRNIIQGSDSVESAE-EISLWFHPEEL

Parental  VDYKSCAQNWIYE
          VDYKSCAQNW.YE
Retrocopy VDYKSCAQNWMYE

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	0.13 RPM	46.68 RPM
SRP051959_heart	0.09 RPM	39.69 RPM
SRP051959_kidney	0.27 RPM	68.24 RPM
SRP051959_liver	3.25 RPM	50.62 RPM
SRP051959_lung	0.10 RPM	25.60 RPM
SRP051959_lymph_node	0.11 RPM	38.49 RPM
SRP051959_skeletal_muscle	0.02 RPM	75.19 RPM
SRP051959_spleen	0.11 RPM	42.14 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3940 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3940 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3940 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,