RetrogeneDB ID: retro_cjac_3839

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: GL284966.1:29258..29630(-)
• Located in intron of: ENSCJAG00000020703

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMEM254
• Ensembl ID: ENSCJAG00000007670
• Aliases: None
• Description: transmembrane protein 254 [Source:HGNC Symbol;Acc:25804]

Sequence

>retro_cjac_3839
ATGGCTACGGCAGCCGGCGCTGCGGCCTACTTCCAGAGAGGCAGTCTGTTCTGGTTCACAGTCATCACCCTCAGCTTTGG
CTACCACATATGGGTTATCGTCTGGCCTCATAGTATCCCTTATCAGAGCCTTGGGCCTCTGGGCTCTTTCACTCAGTACT
TGGTGGACCACCATCACACCCTCCTGAGCAGTGGGTATTGGCTTGCCTGGCTGATTCATGTGGGAGAGTCCTTGTATGCC
ATAGTATTGTGCAAGCACAAAGGAATCACAAGTGGTCGGGCTTGGCTACTCTGGTTCCTACAGACTTTCCTCTTTAGGAT
AGCGTCTCTCAGCATCTTGACTGCTTACAAACCGAAGCGCCAAAAACAAACT

Alignment

ORF - retro_cjac_3839 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.74 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MATAAGATAYFQRGSLFWFTVITLSFGYHTWVVFWPQSIPYQSLGPLGSFTQYLVDHHHTLLSNGYWLAW
          MATAAGA.AYFQRGSLFWFTVITLSFGYH.WV..WP.SIPYQSLGPLGSFTQYLVDHHHTLLS.GYWLAW
Retrocopy MATAAGAAAYFQRGSLFWFTVITLSFGYHIWVIVWPHSIPYQSLGPLGSFTQYLVDHHHTLLSSGYWLAW

Parental  LIHVGESLYAIVLCKHKGITSGRAQLLWFLQTFLFGIASLSILIAYKPKRQKQT
          LIHVGESLYAIVLCKHKGITSGRA.LLWFLQTFLF.IASLSIL.AYKPKRQKQT
Retrocopy LIHVGESLYAIVLCKHKGITSGRAWLLWFLQTFLFRIASLSILTAYKPKRQKQT

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	4.57 RPM
SRP051959_heart	0.26 RPM	0.51 RPM
SRP051959_kidney	0.38 RPM	1.75 RPM
SRP051959_liver	0.17 RPM	2.99 RPM
SRP051959_lung	0.37 RPM	1.17 RPM
SRP051959_lymph_node	0.34 RPM	0.43 RPM
SRP051959_skeletal_muscle	0.13 RPM	0.17 RPM
SRP051959_spleen	0.61 RPM	0.76 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3839 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3839 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3839 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 28 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000015748	3 retrocopies	retro_cfam_602, retro_cfam_635, retro_cfam_637,
Callithrix jacchus	ENSCJAG00000007670	1 retrocopy	retro_cjac_3839 ,
Dasypus novemcinctus	ENSDNOG00000024625	1 retrocopy	retro_dnov_555,
Felis catus	ENSFCAG00000026147	1 retrocopy	retro_fcat_401,
Myotis lucifugus	ENSMLUG00000007585	16 retrocopies	retro_mluc_1178, retro_mluc_2482, retro_mluc_2491, retro_mluc_2492, retro_mluc_2528, retro_mluc_2532, retro_mluc_2550, retro_mluc_2551, retro_mluc_2552, retro_mluc_2572, retro_mluc_2573, retro_mluc_2583, retro_mluc_2586, retro_mluc_2603, retro_mluc_2623, retro_mluc_766,
Macaca mulatta	ENSMMUG00000003015	1 retrocopy	retro_mmul_1583,
Mus musculus	ENSMUSG00000072676	1 retrocopy	retro_mmus_2102,
Oryctolagus cuniculus	ENSOCUG00000013679	1 retrocopy	retro_ocun_453,
Otolemur garnettii	ENSOGAG00000028898	1 retrocopy	retro_ogar_59,
Tarsius syrichta	ENSTSYG00000006920	1 retrocopy	retro_tsyr_103,
Tursiops truncatus	ENSTTRG00000006122	1 retrocopy	retro_ttru_454,