RetrogeneDB ID: retro_cjac_1775

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 2:38219458..38219844(+)
• Located in intron of: ENSCJAG00000031434

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000005200
• Aliases: None
• Description: None

Sequence

>retro_cjac_1775
GCAGAAGCAACCAAGAATGTGCTGAACAGTATTCACTTTGATCCTGAGAACCCACAGACACTGAGACTAAAATTTGCCAA
AGTCAACACCAAGATGGCCAACAGCAAGCTAGTGGCAACTCCAAATCCAACCAACGTGTACTCTGCCCTAGGAGCACACT
TCATTGCATGGAACCCATATAACCTGAGGGGGCTGCTCTGATCACTGCATCCCCAGAGACCTGGGCCCCCTACCCTTTGT
ATAACACAGAGTTGACCCCAGCCATCCCCCATGCTGCATTCACCTACCCAGCTGCCACTGCTGCTGCTGCCGCCCTCCAT
GCTCAGATGCCCTGGTACCTTTCCTCTGACACCACCCAGCAAAGATGGAAGTATCCTAAGTTTTGT

Alignment

ORF - retro_cjac_1775 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.46 %
• Parental protein coverage: 71.27 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  AEAAKNALNGIRFDPENPQTLRLEFAKANTKMAKSKLMATPNPSNMHPALGAHLIARDPYDLMG-AALIP
          AEA.KN.LN.I.FDPENPQTLRL.FAK.NTKMA.SKL.ATPNP.N...ALGAH.IA..PY.L.G.AALI.
Retrocopy AEATKNVLNSIHFDPENPQTLRLKFAKVNTKMANSKLVATPNPTNVYSALGAHFIAWNPYNLRG<AALIT

Parental  ASPEAWAPYPLYTTELTPAISHAAFTYPAATAAAAALHAQVRWYPSSDTTQQGWKYRQFC
          ASPE.WAPYPLY.TELTPAI.HAAFTYPAATAAAAALHAQ..WY.SSDTTQQ.WKY..FC
Retrocopy ASPETWAPYPLYNTELTPAIPHAAFTYPAATAAAAALHAQMPWYLSSDTTQQRWKYPKFC

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	0.00 RPM	1.71 RPM
SRP051959_heart	0.00 RPM	4.24 RPM
SRP051959_kidney	0.00 RPM	0.69 RPM
SRP051959_liver	0.00 RPM	0.22 RPM
SRP051959_lung	0.00 RPM	1.29 RPM
SRP051959_lymph_node	0.00 RPM	0.57 RPM
SRP051959_skeletal_muscle	0.00 RPM	0.66 RPM
SRP051959_spleen	0.00 RPM	0.59 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1775 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1775 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1775 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 39 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000011037	1 retrocopy	retro_btau_1674,
Callithrix jacchus	ENSCJAG00000005200	2 retrocopies	retro_cjac_1775 , retro_cjac_298,
Callithrix jacchus	ENSCJAG00000012366	1 retrocopy	retro_cjac_2705,
Dipodomys ordii	ENSDORG00000004025	1 retrocopy	retro_dord_438,
Homo sapiens	ENSG00000166831	2 retrocopies	retro_hsap_2513, retro_hsap_3613,
Gorilla gorilla	ENSGGOG00000008984	1 retrocopy	retro_ggor_2438,
Loxodonta africana	ENSLAFG00000018725	6 retrocopies	retro_lafr_344, retro_lafr_393, retro_lafr_445, retro_lafr_481, retro_lafr_550, retro_lafr_859,
Macaca mulatta	ENSMMUG00000013270	1 retrocopy	retro_mmul_1837,
Monodelphis domestica	ENSMODG00000010487	1 retrocopy	retro_mdom_571,
Mus musculus	ENSMUSG00000032387	9 retrocopies	retro_mmus_2671, retro_mmus_3408, retro_mmus_3410, retro_mmus_3429, retro_mmus_3431, retro_mmus_3437, retro_mmus_3562, retro_mmus_3588, retro_mmus_3596,
Nomascus leucogenys	ENSNLEG00000012505	1 retrocopy	retro_nleu_2209,
Otolemur garnettii	ENSOGAG00000026017	1 retrocopy	retro_ogar_3254,
Pongo abelii	ENSPPYG00000006553	1 retrocopy	retro_pabe_2963,
Pan troglodytes	ENSPTRG00000007165	2 retrocopies	retro_ptro_1458, retro_ptro_2441,
Sus scrofa	ENSSSCG00000004549	1 retrocopy	retro_sscr_851,
Ictidomys tridecemlineatus	ENSSTOG00000010055	2 retrocopies	retro_itri_1512, retro_itri_556,
Tarsius syrichta	ENSTSYG00000008996	3 retrocopies	retro_tsyr_1433, retro_tsyr_171, retro_tsyr_445,
Tursiops truncatus	ENSTTRG00000011840	3 retrocopies	retro_ttru_1046, retro_ttru_1212, retro_ttru_1790,