RetrogeneDB ID: retro_cjac_3257

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 9:124064451..124064830(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PTP4A2
• Ensembl ID: ENSCJAG00000006539
• Aliases: None
• Description: protein tyrosine phosphatase type IVA, member 2 [Source:HGNC Symbol;Acc:9635]

Sequence

>retro_cjac_3257
TTGGTTTGAGTGTGTGATGCTACATTTGGTAGAATTCCAGCTGAAAAAGAAGGAATCCACATTTTACATTGGCCGTTTAA
CAATGGAGCTCACCACCTAATCAGATAGCAGATGATTGGCTGAAGCTGTTAAGCACCGATTTTCGTGAAAAGCCAGGTTG
CTGTGTTGCAGTGCATTGTGTTGTGGGATTGGGAGGGAAGGGCACCTGTGCTGGCTGCACCTGCTCTGACTGAATATGGA
ATTATGTATGAAGACAGTTTGGTTTACAAGACGAAAAAGAAGGGCAGCATTCTATTCTAAACAGCTGCTTTACTTGGAGA
AATACCGACCTAAGATGCGATTACACTTCAGAGATACCGATGGGCATTGCTGTGTTCAG

Alignment

ORF - retro_cjac_3257 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.44 %
• Parental protein coverage: 75.45 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LVRVCDATYDKAPVEKEGIHVLDWPFDDGA-PPPNQIVDDWLNLLKTKFREEPGCCVAVHCVAGL-GRAP
          LV.VCDAT....P.EKEGIH.L.WPF..GA..PPNQI.DDWL.LL.T.FRE.PGCCVAVHCV.GL.GR..
Retrocopy LV*VCDATFGRIPAEKEGIHILHWPFNNGA<SPPNQIADDWLKLLSTDFREKPGCCVAVHCVVGL<GREG

Parental  VLVALALIECGMKY-EDAVQFIRQKRRGAFNSKQLLYLEKYRPKMRLRFRDTNGHCCVQ
          .L..L.L....M......V.F.R.KRR.AF.SKQLLYLEKYRPKMRL.FRDT.GHCCVQ
Retrocopy HLCWLHLL*LNMELCMKTVWFTRRKRRAAFYSKQLLYLEKYRPKMRLHFRDTDGHCCVQ

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	117.33 RPM
SRP051959_heart	0.05 RPM	57.99 RPM
SRP051959_kidney	0.04 RPM	55.69 RPM
SRP051959_liver	0.00 RPM	46.85 RPM
SRP051959_lung	0.00 RPM	62.14 RPM
SRP051959_lymph_node	0.00 RPM	60.25 RPM
SRP051959_skeletal_muscle	0.09 RPM	69.73 RPM
SRP051959_spleen	0.02 RPM	89.31 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3257 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3257 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3257 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000039121	1 retrocopy	retro_btau_638,
Callithrix jacchus	ENSCJAG00000001743	3 retrocopies	retro_cjac_2812, retro_cjac_4144, retro_cjac_910,
Callithrix jacchus	ENSCJAG00000006539	2 retrocopies	retro_cjac_3257 , retro_cjac_566,
Homo sapiens	ENSG00000184007	4 retrocopies	retro_hsap_1069, retro_hsap_1754, retro_hsap_4331, retro_hsap_944,
Mus musculus	ENSMUSG00000028788	2 retrocopies	retro_mmus_1894, retro_mmus_2432,
Nomascus leucogenys	ENSNLEG00000002137	3 retrocopies	retro_nleu_2880, retro_nleu_2956, retro_nleu_3015,
Oryctolagus cuniculus	ENSOCUG00000002060	1 retrocopy	retro_ocun_1673,
Otolemur garnettii	ENSOGAG00000029603	1 retrocopy	retro_ogar_3341,
Pongo abelii	ENSPPYG00000001606	3 retrocopies	retro_pabe_1507, retro_pabe_808, retro_pabe_890,
Rattus norvegicus	ENSRNOG00000050044	1 retrocopy	retro_rnor_305,
Sus scrofa	ENSSSCG00000003605	1 retrocopy	retro_sscr_1186,
Ictidomys tridecemlineatus	ENSSTOG00000002775	2 retrocopies	retro_itri_1165, retro_itri_152,
Tupaia belangeri	ENSTBEG00000006790	1 retrocopy	retro_tbel_4601,
Tursiops truncatus	ENSTTRG00000016571	2 retrocopies	retro_ttru_1396, retro_ttru_1402,