RetrogeneDB ID: retro_cjac_3047

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 8:12459998..12460296(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000014008
• Aliases: None
• Description: None

Sequence

>retro_cjac_3047
ATTGGAGTAAAATGCTATTCAGCCTACAGAGCTGGTCAAAAGCTTTTGATCTGTTCAATCCAAGCTTCAAGTCTACCTGT
CAATGCTTTGTGAAGTATATTGAGCTGCAGAAACTTAAAGAAACAGATGAAGACAAGTTATTTGTAGAAACAGGGAAGGC
TTTATTGCAGAAGGTGTCATTTTAAGATGAGTAGGAGAAGCAAGGACTCAACAGGGAGATAGTCACGTTTCCTGGAAATC
TGAACACATGAGTGTCAGACCCCAAACTGCATTGAAAGAAAACCAGCTTCAGAAAGAA

Alignment

ORF - retro_cjac_3047 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.79 %
• Parental protein coverage: 52.91 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  IRAKFYSAYGSGQR-AFDLFNPNFKSTCQRFVEKYTELQKLGETDEEKLFVETGKALL-AEGIILRRVGE
          I..K.YSAY..GQ..AFDLFNP.FKSTCQ.FV.KY.ELQKL.ETDE.KLFVETGKALL.AEG.ILR.VGE
Retrocopy IGVKCYSAYRAGQK<AFDLFNPSFKSTCQCFV-KYIELQKLKETDEDKLFVETGKALL<AEGVILR*VGE

Parental  ARTQQ-QGHVSQKSEHLSVRPQTTSEEDEPQKE
          ARTQQ...HVS.KSEH.SVRPQT...E...QKE
Retrocopy ARTQQGDSHVSWKSEHMSVRPQTALKENQLQKE

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	6.39 RPM
SRP051959_heart	0.11 RPM	8.86 RPM
SRP051959_kidney	0.09 RPM	9.96 RPM
SRP051959_liver	0.06 RPM	8.86 RPM
SRP051959_lung	0.11 RPM	7.40 RPM
SRP051959_lymph_node	0.27 RPM	9.41 RPM
SRP051959_skeletal_muscle	0.04 RPM	12.38 RPM
SRP051959_spleen	0.27 RPM	8.93 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3047 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3047 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3047 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000014008	1 retrocopy	retro_cjac_3047 ,
Cavia porcellus	ENSCPOG00000008761	1 retrocopy	retro_cpor_1175,
Felis catus	ENSFCAG00000005711	1 retrocopy	retro_fcat_963,
Homo sapiens	ENSG00000181610	1 retrocopy	retro_hsap_3727,
Macaca mulatta	ENSMMUG00000001913	1 retrocopy	retro_mmul_1691,
Mustela putorius furo	ENSMPUG00000015372	1 retrocopy	retro_mputfur_1274,
Nomascus leucogenys	ENSNLEG00000008072	1 retrocopy	retro_nleu_1972,
Pongo abelii	ENSPPYG00000025941	1 retrocopy	retro_pabe_3131,
Pan troglodytes	ENSPTRG00000009440	1 retrocopy	retro_ptro_2523,
Tarsius syrichta	ENSTSYG00000009862	1 retrocopy	retro_tsyr_2077,