RetrogeneDB ID: retro_cjac_203

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 12:78197350..78197917(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000022808
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000019467
• Aliases: None
• Description: None

Sequence

>retro_cjac_203
ATGGCTGCCTGCGCTTTTGCTGGTGCGGTGAAAACAGCTTCAGGAATCCTACGGCCCCTAAATATTTTGGCATCTTCAAC
CTATCGAAACTGTGTCAAGAATGCCTCTCTTATTTCTGCATTGTCCACTGGACGTTTTGGTCACATTCAGACATCAGTTG
TTTCCTCCACTTCCAGACTTATCACATCTGAGAAAAACCTGACATGTGGGCGTACTTCAGTGACCCTTAATAGAGTGGCC
CCCTTGCTTCCAAGTGTCCTGAAGCTACCAGTCAGATCTCTAACATACTTCAGTACACGAAAAGGCAAGAGAAAGACTGT
GAAAGCTGTCATCTACAGGTTTCTTCGACTTCATTGTGGACTTTGGGTGAGAAGAAAGGCTGGTTATAAGAAAAAACTAT
GGAAAAAGGAACCTGTGAGAAAAAAGCGACTGAGGGAATTTGTATTCTGCAATAAAACCCAGAGTAAACTCTTAGATAAA
ATGACGACGTCCTTCTGGAAGAGGCGAAACTGGTATGTCGACGATCCTTATCAGAAGTATCATGATCGAACAAATCTGAA
AGTATAG

Alignment

ORF - retro_cjac_203 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 100.0 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAACAFAGAVKTASGILRPLNILASSTYRNCVKNASLISALSTGRFGHIQTSVVSSTSRLITSEKNLTCG
          MAACAFAGAVKTASGILRPLNILASSTYRNCVKNASLISALSTGRFGHIQTSVVSSTSRLITSEKNLTCG
Retrocopy MAACAFAGAVKTASGILRPLNILASSTYRNCVKNASLISALSTGRFGHIQTSVVSSTSRLITSEKNLTCG

Parental  RTSVTLNRVAPLLPSVLKLPVRSLTYFSTRKGKRKTVKAVIYRFLRLHCGLWVRRKAGYKKKLWKKEPVR
          RTSVTLNRVAPLLPSVLKLPVRSLTYFSTRKGKRKTVKAVIYRFLRLHCGLWVRRKAGYKKKLWKKEPVR
Retrocopy RTSVTLNRVAPLLPSVLKLPVRSLTYFSTRKGKRKTVKAVIYRFLRLHCGLWVRRKAGYKKKLWKKEPVR

Parental  KKRLREFVFCNKTQSKLLDKMTTSFWKRRNWYVDDPYQKYHDRTNLKV
          KKRLREFVFCNKTQSKLLDKMTTSFWKRRNWYVDDPYQKYHDRTNLKV
Retrocopy KKRLREFVFCNKTQSKLLDKMTTSFWKRRNWYVDDPYQKYHDRTNLKV

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	0.02 RPM	7.37 RPM
SRP051959_heart	0.04 RPM	15.91 RPM
SRP051959_kidney	0.00 RPM	12.27 RPM
SRP051959_liver	0.02 RPM	10.09 RPM
SRP051959_lung	0.02 RPM	9.65 RPM
SRP051959_lymph_node	0.05 RPM	10.87 RPM
SRP051959_skeletal_muscle	0.15 RPM	23.59 RPM
SRP051959_spleen	0.02 RPM	11.62 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_203 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_203 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_203 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 38 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000019467	1 retrocopy	retro_cjac_203 ,
Dasypus novemcinctus	ENSDNOG00000008329	1 retrocopy	retro_dnov_404,
Homo sapiens	ENSG00000132313	4 retrocopies	retro_hsap_3424, retro_hsap_4784, retro_hsap_595, retro_hsap_681,
Gorilla gorilla	ENSGGOG00000026769	3 retrocopies	retro_ggor_2315, retro_ggor_2979, retro_ggor_526,
Macropus eugenii	ENSMEUG00000004773	1 retrocopy	retro_meug_1703,
Mus musculus	ENSMUSG00000052962	1 retrocopy	retro_mmus_1777,
Nomascus leucogenys	ENSNLEG00000002756	4 retrocopies	retro_nleu_1103, retro_nleu_1362, retro_nleu_2217, retro_nleu_781,
Otolemur garnettii	ENSOGAG00000004048	1 retrocopy	retro_ogar_2600,
Pongo abelii	ENSPPYG00000012214	5 retrocopies	retro_pabe_1817, retro_pabe_2837, retro_pabe_3724, retro_pabe_541, retro_pabe_595,
Pan troglodytes	ENSPTRG00000012152	4 retrocopies	retro_ptro_2325, retro_ptro_3185, retro_ptro_438, retro_ptro_489,
Rattus norvegicus	ENSRNOG00000008546	1 retrocopy	retro_rnor_1399,
Tupaia belangeri	ENSTBEG00000015366	10 retrocopies	retro_tbel_1143, retro_tbel_146, retro_tbel_2647, retro_tbel_289, retro_tbel_2892, retro_tbel_3789, retro_tbel_3828, retro_tbel_428, retro_tbel_4379, retro_tbel_627,
Tarsius syrichta	ENSTSYG00000007713	2 retrocopies	retro_tsyr_1128, retro_tsyr_264,