RetrogeneDB ID: retro_cjac_566

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 1:81982186..81982686(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000011332
• Aliases: None
• Status: KNOWN_PSEUDOGENE

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_566
ATGAACCGTCCAGCCCCTGTGGAGATGTCCTGTGAGAACATGTGTTTTCTGATAACTCACAACCCTACCAGTGCTACTCT
CAGCAAGTTCACAGAGGAACTTAAGAAGTATGAAGTGACGACTTTGGTTCGAGTTTGTGATGTTACACATGATAAAGCTC
CAGTTGAAAAAGAAGGAATCCGGGTTCTAGATTGGCCATTTGATGATGGAGCTCCACCTCCTAATCAGGTAGTAGATGAT
TGGTTAAACCTGTTAAAAACCAAATTTCGTGAAGGGCCAGGTTGCTGTGTTGCAGTGCATTGTGTTGCAGATTGGGAAGG
GCACCTGTGCTGGTTGCCTTTGCTTTGATTGAATGTGGAATGAAGTATGAAGAAGCAGTTCAGTTTATAAGACAAAAAAG
AAGGGGAGCATTCAATTCCAAACAGCTGCTTTACTTGGAGAAATACCGACCTAAGATGCGATTACGCTTCAGAGATACCA
ATGGGCATTGCTGTGTTCAG

Alignment

ORF - retro_cjac_566 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.07 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MNRPAPVEISYENMRFLITHNPTNATLNKFTEELKKYGVTTLVRVCDATYDKAPVEKEGIHVLDWPFDDG
          MNRPAPVE.S.ENM.FLITHNPT.ATL.KFTEELKKY.VTTLVRVCD.T.DKAPVEKEGI.VLDWPFDDG
Retrocopy MNRPAPVEMSCENMCFLITHNPTSATLSKFTEELKKYEVTTLVRVCDVTHDKAPVEKEGIRVLDWPFDDG

Parental  APPPNQIVDDWLNLLKTKFREEPGCCVAVHCVAG-LGRAPVLVALALIECGMKYEDAVQFIRQKRRGAFN
          APPPNQ.VDDWLNLLKTKFRE.PGCCVAVHCVA..LGRAPVLVA.ALIECGMKYE.AVQFIRQKRRGAFN
Retrocopy APPPNQVVDDWLNLLKTKFREGPGCCVAVHCVAD<LGRAPVLVAFALIECGMKYEEAVQFIRQKRRGAFN

Parental  SKQLLYLEKYRPKMRLRFRDTNGHCCVQ
          SKQLLYLEKYRPKMRLRFRDTNGHCCVQ
Retrocopy SKQLLYLEKYRPKMRLRFRDTNGHCCVQ

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	0.04 RPM	117.33 RPM
SRP051959_heart	0.02 RPM	57.99 RPM
SRP051959_kidney	0.11 RPM	55.69 RPM
SRP051959_liver	0.02 RPM	46.85 RPM
SRP051959_lung	0.08 RPM	62.14 RPM
SRP051959_lymph_node	0.00 RPM	60.25 RPM
SRP051959_skeletal_muscle	0.04 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_566 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_566 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_566 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,