RetrogeneDB ID: retro_ptro_2108

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 4:167305788..167306331(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ANP32A
• Ensembl ID: ENSPTRG00000007219
• Aliases: None
• Description: Acidic (Leucine-rich) nuclear phosphoprotein 32 family, member A [Source:UniProtKB/TrEMBL;Acc:K7BJB7]

Sequence

>retro_ptro_2108
GGCAGACGGATTCATTCAGAGCTGCGGAACAGGGCGCCCTCTGATGTGAAAGAACTTGCCCTGGACAAGAGTCGGTCGAA
TGAAGGCAAACTCGAAGCCCTCACAGAAGAATTTGAAGAACTGGAATTCTTAAGTACAATCAACGGAGGCCTCACCTCAA
TCTCAGACTTAACAAAGTTAAAGTTAAGAAAGCTTGAACTAAGAGTCTCAGGGGGCCTGGAAGTATTGGCAGAAAAGTGT
CCAAACCTCACGCATCTAAATTTAAGTGGCAACAAAATTAAAGACCTCAGCACAATAGAGCCACTGAAACAGTTAGAAAA
CCTCAAGAGCTTAGACCTTTTCAATTGCAAGGTAACCAACCTGAACGACTTCCGAGAAAACGTGTTCAAGCTCCTCCTGC
AACTCACATATCTCGACAGCTGTTACTGGGACCACAAGGAGGCCCCTGACTCAGATATTAAGGGCTACGTGGAGGGCCTG
GATGACGAGGAGGAAGGTGAGGATGAGGAGGAGTATGATGAAGATGCTCAGGTAGTGGAAGAT

Alignment

ORF - retro_ptro_2108 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.41 %
• Parental protein coverage: 74.19 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GRRIHLELRNRTPSDVKELVLDNSRSNEGKLEGLTDEFEELEFLSTINVGLTSIANLPKLNKLKKLELSD
          GRRIH.ELRNR.PSDVKEL.LD.SRSNEGKLE.LT.EFEELEFLSTIN.GLTSI..L.KL.KL.KLEL..
Retrocopy GRRIHSELRNRAPSDVKELALDKSRSNEGKLEALTEEFEELEFLSTINGGLTSISDLTKL-KLRKLEL--

Parental  NRVSGGLEVLAEKCPNLTHLNLSGNKIKDLSTIEPLKKLENLKSLDLFNCEVTNLNDYRENVFKLLPQLT
          .RVSGGLEVLAEKCPNLTHLNLSGNKIKDLSTIEPLK.LENLKSLDLFNC.VTNLND.RENVFKLL.QLT
Retrocopy -RVSGGLEVLAEKCPNLTHLNLSGNKIKDLSTIEPLKQLENLKSLDLFNCKVTNLNDFRENVFKLLLQLT

Parental  YLDGYDRDDKEAPDSD-AGYVEGLDDEEEDEDEEEYDEDAQVVED
          YLD....D.KEAPDSD..GYVEGLDDEEE.EDEEEYDEDAQVVED
Retrocopy YLDSCYWDHKEAPDSDIKGYVEGLDDEEEGEDEEEYDEDAQVVED

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	0.13 RPM	85.55 RPM
SRP007412_cerebellum	0.11 RPM	142.39 RPM
SRP007412_heart	0.03 RPM	78.11 RPM
SRP007412_kidney	0.00 RPM	92.71 RPM
SRP007412_liver	0.03 RPM	62.56 RPM
SRP007412_testis	0.00 RPM	24.87 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2108 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2108 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2108 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3117
Pongo abelii	retro_pabe_2575
Macaca mulatta	retro_mmul_1985

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 28 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,
Homo sapiens	ENSG00000140350	3 retrocopies	retro_hsap_1479, retro_hsap_3117, retro_hsap_48,
Gorilla gorilla	ENSGGOG00000015417	1 retrocopy	retro_ggor_1134,
Loxodonta africana	ENSLAFG00000022560	1 retrocopy	retro_lafr_679,
Nomascus leucogenys	ENSNLEG00000013347	2 retrocopies	retro_nleu_15, retro_nleu_2383,
Otolemur garnettii	ENSOGAG00000003058	1 retrocopy	retro_ogar_2596,
Ochotona princeps	ENSOPRG00000015394	2 retrocopies	retro_opri_302, retro_opri_563,
Pan troglodytes	ENSPTRG00000007219	2 retrocopies	retro_ptro_2108 , retro_ptro_758,
Pan troglodytes	ENSPTRG00000021172	3 retrocopies	retro_ptro_1073, retro_ptro_1075, retro_ptro_40,
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,