RetrogeneDB ID: retro_pabe_1507

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 17:46908026..46908460(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PTP4A2
• Ensembl ID: ENSPPYG00000001606
• Aliases: None
• Description: protein tyrosine phosphatase type IVA, member 2 [Source:HGNC Symbol;Acc:9635]

Sequence

>retro_pabe_1507
ATGAACCGTCTAGCCCCTGTGGAGCTCTCCTATGAGAACATGCATTTTCTGATAACTCACAACCCTACCAATGCTACTCT
CAACAAGTTCACGGAGGAACTTAAGTATGGAGTGACGACTTTGGTTTGAGTTTGTGATGCTACATATGATAAAGCTCCAA
TTGAAAAAGAAGGAATCCACATTCTAGATTGGCCATTTGATGATGGAGCTCCATCCCCTAATCAGATAGTAGATGATTGG
TTAAACCTGTTAAAAAACAAATTTCGTGAAGAGCCAGTTGCTGTGTTGCAGTGCATTGTGTTGCGGAATTGGGAAGGGCA
CCTGTGCTGGTTGCACTTGCTTTGATTGAATGTGGAATGAAGTATAAAGATGCAGTTCAGTTTATAAGACAAAAAAGAAG
GGGAGCATTAAATTCCAAACAGCTGCTTTACTTA

Alignment

ORF - retro_pabe_1507 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.48 %
• Parental protein coverage: 87.43 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MNRPAPVEISYENMRFLITHNPTNATLNKFTEELKKYGVTTLVRVCDATYDKAPVEKEGIHVLDWPFDDG
          MNR.APVE.SYENM.FLITHNPTNATLNKFTEELK.YGVTTLV.VCDATYDKAP.EKEGIH.LDWPFDDG
Retrocopy MNRLAPVELSYENMHFLITHNPTNATLNKFTEELK-YGVTTLV*VCDATYDKAPIEKEGIHILDWPFDDG

Parental  APPPNQIVDDWLNLLKTKFREEP-GCCVAVHCVAGLGRAPVLVALALIECGMKYEDAVQFIRQKRRGAFN
          AP.PNQIVDDWLNLLK.KFREEP..CCVAVHCVA.LGRAPVLVALALIECGMKY.DAVQFIRQKRRGA.N
Retrocopy APSPNQIVDDWLNLLKNKFREEP<SCCVAVHCVAELGRAPVLVALALIECGMKYKDAVQFIRQKRRGALN

Parental  SKQLLYL
          SKQLLYL
Retrocopy SKQLLYL

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
SRP007412_brain_prefrontal_cortex	0.11 RPM	39.26 RPM
SRP007412_cerebellum	0.00 RPM	46.94 RPM
SRP007412_heart	0.00 RPM	58.73 RPM
SRP007412_kidney	0.00 RPM	53.23 RPM
SRP007412_liver	0.00 RPM	45.32 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1507 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1507 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1507 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1754
Pan troglodytes	retro_ptro_1212
Gorilla gorilla	retro_ggor_2251

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 29 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,
Pongo abelii	ENSPPYG00000016743	5 retrocopies	retro_pabe_2058, retro_pabe_255, retro_pabe_2660, retro_pabe_3732, retro_pabe_721,
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,