RetrogeneDB ID: retro_cjac_3249

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 9:105065997..105066599(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: OSTF1
• Ensembl ID: ENSCJAG00000012808
• Aliases: None
• Description: None

Sequence

>retro_cjac_3249
ATGTTGAAGCTGCCACCGAAACCGGTCAAACCAGGGCAAGATAAAGTCTTCAGAACCCTCTATATGTTGGAACCCAGAGC
TCCAGATGAACTATGCTTTGAGGAAGGCGATATCATCTATGTTACTGACATGAATTATGCCAGTTGGTAGAAAGGTACCT
CCAAAGGCAGCACTGGACTGATTCCAAGCAACTATGTGGCTGAGCAGGCAGAATCCATAGACAATCCATTGCGTGAAGGA
GCCAAAAGAGGCAACTTGTGTTAGTTGCCAGCGTTTTCGGACAACTGAGTGGGTGTTAATGGCTGAGACAAAGCCAGAAG
CATTGCCTTAGACTAGGCTTGTCATGGGGATCTCAGAAATACAGTGGCAATGCTATTTACTCAACCAAGTACTGAACTGA
GCCATAGAACAAGTTGGGAGACACAGCTGTGCATGCTGCTGCCTGGAAGGGTTATGCAGATATTGTCCAGTTGCTTCTGG
CAAAAGGTGTTCTGGCAGACAGAAGAAACAATGAGAGGATGCTGGCTTTGGGCAATGCTGCCCGTGCATCTCTCCAGAGA
AAGAAACAGGGGACAGATGCAGTTCAAACATTAAGCAATGCT

Alignment

ORF - retro_cjac_3249 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.68 %
• Parental protein coverage: 95.33 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSKPPPKPVKPGQVKVFRALYTFEPRTPDELYFEEGDIIYITDMSDTNWWKGTSKGRTGLIPSNYVAEQA
          M.K.PPKPVKPGQ.KVFR.LY..EPR.PDEL.FEEGDIIY.TDM....W.KGTSKG.TGLIPSNYVAEQA
Retrocopy MLKLPPKPVKPGQDKVFRTLYMLEPRAPDELCFEEGDIIYVTDMNYASW*KGTSKGSTGLIPSNYVAEQA

Parental  ESIDNPLHEAAKRGNLSWLRECLDNRVGVNGLDKAGSTALYWACHGGHKDIVEMLFTQPNIELNQQ-NKL
          ESIDNPL.E.AKRGNL..L....DN.VGVNG.DKA.S.AL..ACHG.....V.MLFTQP..EL....NKL
Retrocopy ESIDNPLREGAKRGNLC*LPAFSDN*VGVNG*DKARSIALD*ACHGDLRNTVAMLFTQPSTELSHR<NKL

Parental  GDTALHAAAWKGYADIVQLLLAKGARTDLRNNEKKLALDMATNAACASLLKKKQGTDAVRTLSNA
          GDTA.HAAAWKGYADIVQLLLAKG...D.RNNE..LAL....NAA.ASL..KKQGTDAV.TLSNA
Retrocopy GDTAVHAAAWKGYADIVQLLLAKGVLADRRNNERMLALG---NAARASLQRKKQGTDAVQTLSNA

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	31.28 RPM
SRP051959_heart	0.00 RPM	16.26 RPM
SRP051959_kidney	0.00 RPM	28.60 RPM
SRP051959_liver	0.00 RPM	24.39 RPM
SRP051959_lung	0.00 RPM	32.94 RPM
SRP051959_lymph_node	0.00 RPM	45.61 RPM
SRP051959_skeletal_muscle	0.00 RPM	7.51 RPM
SRP051959_spleen	0.00 RPM	57.35 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3249 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3249 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3249 has 5 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1058
Pan troglodytes	retro_ptro_720
Gorilla gorilla	retro_ggor_836
Pongo abelii	retro_pabe_883
Macaca mulatta	retro_mmul_836

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000007953	1 retrocopy	retro_cjac_858,
Callithrix jacchus	ENSCJAG00000012808	1 retrocopy	retro_cjac_3249 ,
Cavia porcellus	ENSCPOG00000007226	1 retrocopy	retro_cpor_1049,
Dipodomys ordii	ENSDORG00000002933	1 retrocopy	retro_dord_698,
Erinaceus europaeus	ENSEEUG00000008320	2 retrocopies	retro_eeur_545, retro_eeur_683,
Felis catus	ENSFCAG00000022374	1 retrocopy	retro_fcat_1869,
Homo sapiens	ENSG00000134996	1 retrocopy	retro_hsap_1058,
Gorilla gorilla	ENSGGOG00000011920	1 retrocopy	retro_ggor_836,
Macaca mulatta	ENSMMUG00000010401	1 retrocopy	retro_mmul_836,
Nomascus leucogenys	ENSNLEG00000001854	1 retrocopy	retro_nleu_2502,
Otolemur garnettii	ENSOGAG00000002603	1 retrocopy	retro_ogar_2962,
Pongo abelii	ENSPPYG00000019300	1 retrocopy	retro_pabe_883,
Pan troglodytes	ENSPTRG00000021031	1 retrocopy	retro_ptro_720,
Rattus norvegicus	ENSRNOG00000012156	2 retrocopies	retro_rnor_936, retro_rnor_937,
Sus scrofa	ENSSSCG00000005273	1 retrocopy	retro_sscr_979,
Tursiops truncatus	ENSTTRG00000003081	1 retrocopy	retro_ttru_492,