RetrogeneDB ID: retro_pabe_2575

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 4:170577775..170578311(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPPYG00000015169
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: ANP32A
• Ensembl ID: ENSPPYG00000006595
• Aliases: None
• Description: acidic (leucine-rich) nuclear phosphoprotein 32 family, member A [Source:HGNC Symbol;Acc:13233]

Sequence

>retro_pabe_2575
GGCAGACGGATTCATTTAGAGCTGTGGAACAGGGCGCCCTCTGATGTGAAAGAACTTGCCCTGGACAACAGTCGGTCGAA
TGAAGGCAAACTCAAAGGCCTCACAGATGAATCTGAAGAACTGGAATTCTTAAGTACAATCAACGGAGGCCTCACCTCGA
TCTCAAACTTACCAAAGTTAAAGTTAAGAAAGCTTGAACTAAGAGTCTCAGGGGGCCTGGAAGTATTGGCAGAAAAGTGT
CCAAACCTCACGCATCTAAATTTAAGTGGCAACAAAATTAAAGACCTCAGCACAACAGAGCCACTGAAAAAGTTAGAAAA
CCTCAAGAGCTTAGACCTTTTCAATTGCGAAGTAACCAACCTGAACGACTACCGAGAAAACGTGTTCAAGCTTCTCCTGC
AACTCACATATCTCGACGGCTGTTACCGGGACCACAAGGAGGCCCCTGACTCGGATACTGAGGGCTACGTGGAGGGCCTG
GATGACGAGGAGGAGGATGAGGATGAGGAGGAGTATGACGAAGAGCTCAGGTAGTG

Alignment

ORF - retro_pabe_2575 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.13 %
• Parental protein coverage: 74.09 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GRRIHLELRNRTPSDVKELVLDNSRSNEGKLEGLTDEFEELEFLSTINVGLTSIANLPKLNKLKKLELSD
          GRRIHLEL.NR.PSDVKEL.LDNSRSNEGKL.GLTDE.EELEFLSTIN.GLTSI.NLPKL.KL.KLEL..
Retrocopy GRRIHLELWNRAPSDVKELALDNSRSNEGKLKGLTDESEELEFLSTINGGLTSISNLPKL-KLRKLEL--

Parental  NRVSGGLEVLAEKCPNLTHLNLSGNKIKDLSTIEPLKKLENLKSLDLFNCEVTNLNDYRENVFKLLPQLT
          .RVSGGLEVLAEKCPNLTHLNLSGNKIKDLST.EPLKKLENLKSLDLFNCEVTNLNDYRENVFKLL.QLT
Retrocopy -RVSGGLEVLAEKCPNLTHLNLSGNKIKDLSTTEPLKKLENLKSLDLFNCEVTNLNDYRENVFKLLLQLT

Parental  YLDGYDRDDKEAPDSDAEGYVEGLDDEEEDEDEEEYDED-AQVV
          YLDG..RD.KEAPDSD.EGYVEGLDDEEEDEDEEEYDE..AQVV
Retrocopy YLDGCYRDHKEAPDSDTEGYVEGLDDEEEDEDEEEYDEE<AQVV

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	0.06 RPM	94.49 RPM
SRP007412_cerebellum	0.00 RPM	140.69 RPM
SRP007412_heart	0.00 RPM	86.16 RPM
SRP007412_kidney	0.03 RPM	107.89 RPM
SRP007412_liver	0.00 RPM	71.24 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2575 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2575 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2575 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3117
Pan troglodytes	retro_ptro_2108
Macaca mulatta	retro_mmul_1985

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000002339	2 retrocopies	retro_cjac_3305, retro_cjac_3799,
Dasypus novemcinctus	ENSDNOG00000015360	5 retrocopies	retro_dnov_1199, retro_dnov_1250, retro_dnov_1696, retro_dnov_836, retro_dnov_956,
Dipodomys ordii	ENSDORG00000008611	1 retrocopy	retro_dord_240,
Felis catus	ENSFCAG00000015773	1 retrocopy	retro_fcat_1188,
Loxodonta africana	ENSLAFG00000022560	1 retrocopy	retro_lafr_679,
Macaca mulatta	ENSMMUG00000022717	1 retrocopy	retro_mmul_1985,
Otolemur garnettii	ENSOGAG00000003058	1 retrocopy	retro_ogar_2596,
Ochotona princeps	ENSOPRG00000015394	2 retrocopies	retro_opri_302, retro_opri_563,
Pongo abelii	ENSPPYG00000006595	2 retrocopies	retro_pabe_210, retro_pabe_2575 ,
Pongo abelii	ENSPPYG00000019430	2 retrocopies	retro_pabe_1312, retro_pabe_1316,
Rattus norvegicus	ENSRNOG00000045651	1 retrocopy	retro_rnor_1043,
Sarcophilus harrisii	ENSSHAG00000010906	1 retrocopy	retro_shar_540,
Tupaia belangeri	ENSTBEG00000016417	2 retrocopies	retro_tbel_4078, retro_tbel_4595,