RetrogeneDB ID: retro_cjac_175

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 12:61086524..61087226(-)
• Located in intron of: ENSCJAG00000007163

Retrocopy information

• Ensembl ID: ENSCJAG00000007239
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000009722
• Aliases: None
• Description: None

Sequence

>retro_cjac_175
CGCGAGGTGTTTGTACTGCTATTTATTTTTGTGAAGAGGCAAATCATGCGCTTTGCAATGAAATCTCGAAGGGGACCTTA
TGTCCCTGTGGGACACAATGCCCCCAAGGACTTGAAAGAGGAGATTGATATTCAACTATCCAGGGTTCAGGATATCCAGT
ATGAACCCCAGCTCCTTGCAGATGATGATGCTAGACTACTACAGCTGGAAACCCAGGGAAATCAAAGTTGCTACAACTAT
CTGTATAGGATGAAAGCTCTGGATGCCATGCGTGCCTCTGAGATCCCATTTCATTCTGAAGGCCGGCATCCCCGTTCCTT
AATGGGCAAGAATTTCCGCTCCTACCTGCTAGATCTACGAAACACTAGTACCCCTTTCAAGGGTGTACGCAAAGCCCTCA
TTGATACCCTGTTGGATGGCTATGAAACAGCCCGCTATGGGACAAGGGTCTTTGGCCTGAATGAGTACCTACGCTATCAA
GAGGCCCTGAGTGAACTGGCCACTGTGGTCAAAGCACGGATTGGGAGCTCTCAGCGACACCACCAGTCAGCAGCCAAAGA
CCTAACTCAGTCCCCCGAAGTCTCCCCAACAACCATCCAAGTGACATACCTCCCCTCCAGTCAGAAGAGTAAATGTGCCA
AGCACTTCCTTGAATTGAAGAGCTTTAAGGACAACTATAACACATTGGAGAGTACTCTGTGA

Alignment

ORF - retro_cjac_175 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.4 %
• Parental protein coverage: 91.3 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VFVLLFIFVKRQIMRFAMKSRRGPHVPVGHNAPKDLKEEIDIRLSRVQDIKYEPQLLADDDARLLQLETQ
          VFVLLFIFVKRQIMRFAMKSRRGP.VPVGHNAPKDLKEEIDI.LSRVQDI.YEPQLLADDDARLLQLETQ
Retrocopy VFVLLFIFVKRQIMRFAMKSRRGPYVPVGHNAPKDLKEEIDIQLSRVQDIQYEPQLLADDDARLLQLETQ

Parental  GNQSCYNYLYRMKALDAIRASEIPFHSEGRHPRSLMGKNFRSYLLDLRNTSTPFKGVRKALIDTLLDGYE
          GNQSCYNYLYRMKALDA.RASEIPFHSEGRHPRSLMGKNFRSYLLDLRNTSTPFKGVRKALIDTLLDGYE
Retrocopy GNQSCYNYLYRMKALDAMRASEIPFHSEGRHPRSLMGKNFRSYLLDLRNTSTPFKGVRKALIDTLLDGYE

Parental  TARYGTGVFGLNEYLRYQEALSELATVVKARIGSSQRHHQSAAKDLTQSPEVSPTTIQVTYLPSSQKSKR
          TARYGT.VFGLNEYLRYQEALSELATVVKARIGSSQRHHQSAAKDLTQSPEVSPTTIQVTYLPSSQKSK.
Retrocopy TARYGTRVFGLNEYLRYQEALSELATVVKARIGSSQRHHQSAAKDLTQSPEVSPTTIQVTYLPSSQKSKC

Parental  AKHFLELKSFKDNYNTLESTL
          AKHFLELKSFKDNYNTLESTL
Retrocopy AKHFLELKSFKDNYNTLESTL

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	0.87 RPM	16.88 RPM
SRP051959_heart	0.93 RPM	26.98 RPM
SRP051959_kidney	0.80 RPM	29.24 RPM
SRP051959_liver	0.63 RPM	26.30 RPM
SRP051959_lung	0.93 RPM	19.88 RPM
SRP051959_lymph_node	1.16 RPM	15.23 RPM
SRP051959_skeletal_muscle	0.79 RPM	40.68 RPM
SRP051959_spleen	1.01 RPM	20.55 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_175 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_175 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_175 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 49 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011865	1 retrocopy	retro_amel_190,
Callithrix jacchus	ENSCJAG00000009722	1 retrocopy	retro_cjac_175 ,
Dasypus novemcinctus	ENSDNOG00000019160	1 retrocopy	retro_dnov_2515,
Dipodomys ordii	ENSDORG00000005454	1 retrocopy	retro_dord_190,
Equus caballus	ENSECAG00000017585	2 retrocopies	retro_ecab_618, retro_ecab_814,
Echinops telfairi	ENSETEG00000001056	15 retrocopies	retro_etel_1138, retro_etel_1318, retro_etel_1388, retro_etel_1633, retro_etel_2182, retro_etel_2205, retro_etel_2206, retro_etel_394, retro_etel_651, retro_etel_719, retro_etel_720, retro_etel_773, retro_etel_842, retro_etel_957, retro_etel_981,
Macropus eugenii	ENSMEUG00000002600	6 retrocopies	retro_meug_1149, retro_meug_1298, retro_meug_1439, retro_meug_1637, retro_meug_213, retro_meug_69,
Myotis lucifugus	ENSMLUG00000013338	1 retrocopy	retro_mluc_537,
Monodelphis domestica	ENSMODG00000017237	3 retrocopies	retro_mdom_1283, retro_mdom_2003, retro_mdom_323,
Mus musculus	ENSMUSG00000027942	6 retrocopies	retro_mmus_1014, retro_mmus_1018, retro_mmus_1020, retro_mmus_1107, retro_mmus_1792, retro_mmus_490,
Otolemur garnettii	ENSOGAG00000012008	2 retrocopies	retro_ogar_2563, retro_ogar_38,
Ochotona princeps	ENSOPRG00000007244	2 retrocopies	retro_opri_426, retro_opri_586,
Pongo abelii	ENSPPYG00000000785	2 retrocopies	retro_pabe_3590, retro_pabe_969,
Pteropus vampyrus	ENSPVAG00000002717	1 retrocopy	retro_pvam_696,
Rattus norvegicus	ENSRNOG00000017758	1 retrocopy	retro_rnor_139,
Sarcophilus harrisii	ENSSHAG00000012915	1 retrocopy	retro_shar_740,
Tupaia belangeri	ENSTBEG00000013866	1 retrocopy	retro_tbel_177,
Tarsius syrichta	ENSTSYG00000012777	1 retrocopy	retro_tsyr_91,
Tursiops truncatus	ENSTTRG00000015824	1 retrocopy	retro_ttru_923,