RetrogeneDB ID: retro_ptro_566

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 11:98188005..98188798(+)
• Located in intron of: ENSPTRG00000004201

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPA2
• Ensembl ID: ENSPTRG00000000420
• Aliases: None
• Description: replication protein A2, 32kDa [Source:HGNC Symbol;Acc:10290]

Sequence

>retro_ptro_566
GGATTTGAAAGCTATAGCAGCAACTCATAGGGCAGCCGGTGAACACACGCAGTCCCCAGTAGGCTTTGGATCGCGGGCAC
CTTCTTAGGCAGAAAAGAAATCAAGAGCCAGAGCACAGCACATTGAACCCCACACTATATCTCAGCTGCTTTCTGCCACT
TTGATTGATGAAGTGTTCAAAATTGGCAATGCTGAGATTTCACAAATCACTCTTGTAGGGATCATCAGACATGCAGAGAA
GACTTCAACCAACATTGTTTACAAACTAGATGACATGACAGCTGCACCCATGAATGTTCGCCAGTGGGTTGACACAGATG
ACACCAGCAGTGAAAACACTGTAGTTCCTCCAGAAACATATGTGAAAGTGGCAGGCCACCTGAGATCTTTTCAGAACAAA
AAGAGCCTGGTAGCCTTTATAAATCATGCTCCTGGAAGATATGAATGAGTTCACCATACATATTCTGGAAGTGATCGATG
CACGCATGATCACAAAGCGAACAGCCAGCCCTCAGCAGAGAGAGCACCTATCAGCAATCCAGGGAAGAGTGAAGCAGCGT
ACTTTCGTGGGAATAGCTTCATGCCAGCAAATGGCCTCCCTGTGGCCCAAAATCAGGTGTTGAATGTGATTAAGTCTTGC
CCAAGACCTGAGGGACTGAACTTTCAGGATCTCAAGAACTAGCTCAAACGCATGTCTGTATCCCCAGTCAAGCAAGCTGT
GGATTTTCTGAGCAATGAGGGGCATGTCTATTCTACTGTGGAGGATGATCATTTTAAATCCACAGATGCAGAA

Alignment

ORF - retro_ptro_566 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.34 %
• Parental protein coverage: 74.65 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  GFENYGSSYGG-AGGYTQSPGGFGSPAPSQAEKKSRARAQHIVPCTISQLLSATLVDEVFRIGNVEISQV
          GFE.Y.S...G.AG..TQSP.GFGS.APS.AEKKSRARAQHI.P.TISQLLSATL.DEVF.IGN.EISQ.
Retrocopy GFESYSSNS*G>AGEHTQSPVGFGSRAPS*AEKKSRARAQHIEPHTISQLLSATLIDEVFKIGNAEISQI

Parental  TIVGIIRHAEKAPTNIVYKIDDMTAAPMDVRQWVDTDDTSSENTVVPPETYVKVAGHLRSFQNKKSLVAF
          T.VGIIRHAEK..TNIVYK.DDMTAAPM.VRQWVDTDDTSSENTVVPPETYVKVAGHLRSFQNKKSLVAF
Retrocopy TLVGIIRHAEKTSTNIVYKLDDMTAAPMNVRQWVDTDDTSSENTVVPPETYVKVAGHLRSFQNKKSLVAF

Parental  K-IMPLEDMNEFTTHILEVINAHMVLSKANSQP-SAGRAPISNPGMSEAGNFGGNSFMPANGLTVAQNQV
          ..IM.LEDMNEFT.HILEVI.A.M...K....P.SA.RAPISNPG.SEA..F.GNSFMPANGL.VAQNQV
Retrocopy I>IMLLEDMNEFTIHILEVIDARMI-TKRTASP<SAERAPISNPGKSEAAYFRGNSFMPANGLPVAQNQV

Parental  LNLIKACPRPEGLNFQDLKNQLKHMSVSSIKQAVDFLSNEGHIYSTVDDDHFKSTDAE
          LN.IK.CPRPEGLNFQDLKN.LK.MSVS..KQAVDFLSNEGH.YSTV.DDHFKSTDAE
Retrocopy LNVIKSCPRPEGLNFQDLKN*LKRMSVSPVKQAVDFLSNEGHVYSTVEDDHFKSTDAE

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	0.00 RPM	8.58 RPM
SRP007412_cerebellum	0.00 RPM	18.39 RPM
SRP007412_heart	0.00 RPM	14.81 RPM
SRP007412_kidney	0.03 RPM	20.61 RPM
SRP007412_liver	0.00 RPM	16.89 RPM
SRP007412_testis	0.00 RPM	56.06 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_566 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_566 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_566 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_815
Gorilla gorilla	retro_ggor_668
Pongo abelii	retro_pabe_728
Macaca mulatta	retro_mmul_1081

---

Parental genes homology:

Parental genes homology involve 14 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000006225	5 retrocopies	retro_btau_1093, retro_btau_1228, retro_btau_1359, retro_btau_406, retro_btau_633,
Callithrix jacchus	ENSCJAG00000009473	1 retrocopy	retro_cjac_225,
Homo sapiens	ENSG00000117748	2 retrocopies	retro_hsap_704, retro_hsap_815,
Gorilla gorilla	ENSGGOG00000015287	2 retrocopies	retro_ggor_599, retro_ggor_668,
Loxodonta africana	ENSLAFG00000014387	1 retrocopy	retro_lafr_519,
Macaca mulatta	ENSMMUG00000018172	2 retrocopies	retro_mmul_1081, retro_mmul_2172,
Nomascus leucogenys	ENSNLEG00000009702	3 retrocopies	retro_nleu_1409, retro_nleu_250, retro_nleu_2511,
Oryctolagus cuniculus	ENSOCUG00000016194	1 retrocopy	retro_ocun_1180,
Otolemur garnettii	ENSOGAG00000015583	2 retrocopies	retro_ogar_1838, retro_ogar_2066,
Pongo abelii	ENSPPYG00000001651	2 retrocopies	retro_pabe_523, retro_pabe_728,
Pan troglodytes	ENSPTRG00000000420	1 retrocopy	retro_ptro_566 ,
Pteropus vampyrus	ENSPVAG00000001449	1 retrocopy	retro_pvam_166,
Ictidomys tridecemlineatus	ENSSTOG00000004433	2 retrocopies	retro_itri_1257, retro_itri_773,
Tursiops truncatus	ENSTTRG00000007507	1 retrocopy	retro_ttru_873,