RetrogeneDB ID: retro_sscr_1186

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: X:24997490..24997852(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PTP4A2
• Ensembl ID: ENSSSCG00000003605
• Aliases: None
• Description: protein tyrosine phosphatase type IVA, member 2 [Source:HGNC Symbol;Acc:9635]

Sequence

>retro_sscr_1186
ATGACCTGCCCTGCTCCTGTAAAGACTGCATACAGGAATATGAGATTTCTGATCACCCATAGCCCAACCAATGCCTCCTT
ACAGGAACTTAAGAAGAACAGAGTTACCACCATAGTAAGAATATGTGAAGCAATTTATAATATTGCCATTTTGGAGAAAG
AAAGCATCCAGGTTCTGGACAGGCCTTTTGATGGTGCACCATCATCCAGTCAAATTGTTGATAAATGTTAAAACTTGTAA
AAAAGAAATTTCCTGAAGATCCTGGTTGTTGCATTGCGGTCCACTGTGCTGCAGGTCATAGAGGAGCCCCAGTGCTGGCT
GCCCTGACATTACAGCAAGAAACTTTTATATTTGGGGATGCT

Alignment

ORF - retro_sscr_1186 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.27 %
• Parental protein coverage: 75.45 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MNRPAPVEISYENMRFLITHNPTNATLNKFTEELKKYGVTTLVRVCDATYDKAPVEKEGIHVLDWPFDDG
          M..PAPV...Y.NMRFLITH.PTNA.L.....ELKK..VTT.VR.C.A.Y..A..EKE.I.VLD.PF.DG
Retrocopy MTCPAPVKTAYRNMRFLITHSPTNASL----QELKKNRVTTIVRICEAIYNIAILEKESIQVLDRPF-DG

Parental  APPPNQIVDD-WLNLLKTKFREEPGCCVAVHCVAGLGRAPVLVALALIECGMKYEDA
          AP...QIVD...L.L.K.KF.E.PGCC.AVHC.AG...APVL.AL.L........DA
Retrocopy APSSSQIVDK<MLKLVKKKFPEDPGCCIAVHCAAGHRGAPVLAALTLQQETFIFGDA

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
SRP014902_placenta	0.00 RPM	95.70 RPM
SRP014902_testis	0.00 RPM	44.13 RPM
SRP018288_heart	0.00 RPM	174.58 RPM
SRP018288_kidney	0.00 RPM	47.87 RPM
SRP018288_liver	0.00 RPM	41.74 RPM
SRP018288_lung	0.00 RPM	116.08 RPM
SRP018856_adipose	0.00 RPM	32.19 RPM
SRP035408_brain	0.00 RPM	88.71 RPM
SRP035408_liver	0.00 RPM	69.43 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_1186 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_1186 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_1186 has 5 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4798
Pan troglodytes	retro_ptro_3190
Gorilla gorilla	retro_ggor_2986
Pongo abelii	retro_pabe_3732
Equus caballus	retro_ecab_10

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000039121	1 retrocopy	retro_btau_638,
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,