RetrogeneDB ID: retro_cjac_3052

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 8:22659567..22660100(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000031878
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: NPM3
• Ensembl ID: ENSCJAG00000017650
• Aliases: None
• Description: nucleophosmin/nucleoplasmin 3 [Source:HGNC Symbol;Acc:7931]

Sequence

>retro_cjac_3052
ATGGCCGCCGGCACTGCAGATACCTTAGCGTTTTTGAGTCAGGAGAGCCGAACGCGGGCCGGGGGTGTCGGGAGCCCGCG
AGTCCCGGCCCCGGTCACTATGGACAGTTTTTTCTTTGGCTGTGAGCTCTCCGGCCACACCCGCTCCTTCACCTTTAAGG
TAGAGGAAGAGGATGATGCAGAGCACGTGCTGGCACTGACCATGCTCTGCCTCACCGAGGGAGCCAAAGATGAGTGTAAT
GTGGTAGAAGTTGTGGCCCGGAACCATGATCATCAGGAGATCGCAGTCCCTGTGGCCAACCTCAAGCTGTCCTGCCAACC
CATGCCTCAGCCTGGATGATTTCCAGCTCCAACCACCTGTAACTTTCCGCCTGAAGTCGGGCTCTGGCCGTGTGGATCAC
TGGGCGGCACCAGATTGTTATGATGAGCAATGATGTTTCTGAGGAGGAGATCGAGGAAGAGGAAGAGGACAGTGAGGAGG
AGGAAGCTGAGCTGTGCCCCATCCTTCCTGCCAAAAAGCAGAGGGGCAGGCCC

Alignment

ORF - retro_cjac_3052 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.33 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAAGTADALAFLSQESRTRAGGLGSPRVPAPVTMDSFFFGCELSGHTRSFTFKVEEEDDAEHVLALTMLC
          MAAGTAD.LAFLSQESRTRAGG.GSPRVPAPVTMDSFFFGCELSGHTRSFTFKVEEEDDAEHVLALTMLC
Retrocopy MAAGTADTLAFLSQESRTRAGGVGSPRVPAPVTMDSFFFGCELSGHTRSFTFKVEEEDDAEHVLALTMLC

Parental  LTEGAKDECNVVEVVARNHDHQEIAVPVANLKLSCQPMLSLDDFQLQPPVTFRLKSGSGP-VRITGRHQI
          LTEGAKDECNVVEVVARNHDHQEIAVPVANLKLSCQPM.....F.......F....G..P.V.ITGRHQI
Retrocopy LTEGAKDECNVVEVVARNHDHQEIAVPVANLKLSCQPMPQPG*FPAPTTCNFPPEVGLWP<VWITGRHQI

Parental  VMMSNDVSEEEIEEEEEDSEEEEAELCPILPAKKQRGRP
          VMMSNDVSE...............ELCPILPAKKQRGRP
Retrocopy VMMSNDVSEXXXXXXXXXXXXXXXELCPILPAKKQRGRP

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	0.04 RPM	4.06 RPM
SRP051959_heart	0.02 RPM	2.58 RPM
SRP051959_kidney	0.00 RPM	3.59 RPM
SRP051959_liver	0.02 RPM	1.95 RPM
SRP051959_lung	0.00 RPM	3.04 RPM
SRP051959_lymph_node	0.05 RPM	5.59 RPM
SRP051959_skeletal_muscle	0.02 RPM	1.86 RPM
SRP051959_spleen	0.00 RPM	4.83 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3052 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3052 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3052 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 38 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017639	2 retrocopies	retro_amel_1233, retro_amel_90,
Bos taurus	ENSBTAG00000016335	1 retrocopy	retro_btau_1164,
Canis familiaris	ENSCAFG00000009919	2 retrocopies	retro_cfam_1968, retro_cfam_2064,
Callithrix jacchus	ENSCJAG00000017650	2 retrocopies	retro_cjac_2491, retro_cjac_3052 ,
Callithrix jacchus	ENSCJAG00000019334	13 retrocopies	retro_cjac_1559, retro_cjac_1682, retro_cjac_1696, retro_cjac_1733, retro_cjac_2075, retro_cjac_2351, retro_cjac_2368, retro_cjac_2533, retro_cjac_2605, retro_cjac_3270, retro_cjac_3416, retro_cjac_4117, retro_cjac_838,
Cavia porcellus	ENSCPOG00000006301	1 retrocopy	retro_cpor_1315,
Dasypus novemcinctus	ENSDNOG00000018876	1 retrocopy	retro_dnov_1279,
Dipodomys ordii	ENSDORG00000003491	1 retrocopy	retro_dord_577,
Felis catus	ENSFCAG00000007178	1 retrocopy	retro_fcat_1906,
Homo sapiens	ENSG00000107833	1 retrocopy	retro_hsap_792,
Macropus eugenii	ENSMEUG00000003465	2 retrocopies	retro_meug_20, retro_meug_25,
Microcebus murinus	ENSMICG00000011739	1 retrocopy	retro_mmur_126,
Myotis lucifugus	ENSMLUG00000004961	1 retrocopy	retro_mluc_2333,
Macaca mulatta	ENSMMUG00000015774	1 retrocopy	retro_mmul_1072,
Mustela putorius furo	ENSMPUG00000016894	2 retrocopies	retro_mputfur_750, retro_mputfur_759,
Mus musculus	ENSMUSG00000056209	2 retrocopies	retro_mmus_2756, retro_mmus_3479,
Ochotona princeps	ENSOPRG00000009229	2 retrocopies	retro_opri_1019, retro_opri_92,
Pongo abelii	ENSPPYG00000002589	1 retrocopy	retro_pabe_706,
Pan troglodytes	ENSPTRG00000002875	1 retrocopy	retro_ptro_551,