RetrogeneDB ID: retro_ptro_281

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 1:26530270..26531164(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DPPA2
• Ensembl ID: ENSPTRG00000015199
• Aliases: None
• Description: developmental pluripotency associated 2 [Source:HGNC Symbol;Acc:19197]

Sequence

>retro_ptro_281
ATGTCAGACTCAAATTTGGATAGCAGCAAGAAGAATTTCTTTGAGGGGGAAGTAGTTGATGAGGAAAGTGTGATTTTGAC
ATTGCTGCCAGTTAAAGATGACCCAAATATGGAACAAATGGAACCAAGTGTTTCTTCAACTTCTGATGTCAAACTGGAGA
AACCTATGAAATACAATCAAGGTCATCTACTTCAAACAAATTAACAATTTACAGCTCCACAAAAAGCTAGATGCAAAATA
CCAGCTCTTCCCTTGCCGACCATTTTGCCTCCCATTAATAAGGAGTGTTGGGACACTTTGCGGGACTGGTGCCAACAACT
CAGTTTGAGTACTAATGGCAAGAAAATCGAAGTTTATCTGAGGGTCCATAGGCATGCTTACCCTGAACAACAGCAAGATA
TGCCTGAAATGTCACAAGAGACCAGATTACAGCGGTGTTCAAGGAAACACAAGGCAGTGACCAAGAGAGCAAGGCTTCAG
AAAACTTATGAGATGAATGAGAGAGCAGAAGAGACTAATACAGTCGAAGTGATAACTTCAGCGCAGGGAGCCATGTTGGC
ATCAAGGGCAAGAATTGCTGCAAGAGCTGTTGAGCCTGAGGCTGTGAATTCAAGTTCCATTCCTGTTTCTCTTGAGGCCT
TTTTGATGCAAGGCTCTGGTGTCAGGTGGTGTGTGGTCCATGGCAGACTTCTCTCGGCAGACACAAAGGGTTGAGTATGC
CTGCAGTTTCATGCAGGTCAGGTCTGAGTGCCTACCACTCACAGGAGGATGATTTCTCTCTTCTTGTTACCTGCCTGCAT
TTTCCCATCCCCAGGCACAGAAGATAATATGTTATGCCCCAACTGTGCTAAGAGGAATAAGAAGATGATGAAAAGATTAA
TGACAATAGAGAAG

Alignment

ORF - retro_ptro_281 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.26 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSDANLDSSKKNFLEGEVDDEESVILTLVPVKDDANMEQMEPSVSSTSDVKLEKPKKYNPGHLLQTNEQF
          MSD.NLDSSKKNF.EGEV.DEESVILTL.PVKDD.NMEQMEPSVSSTSDVKLEKP.KYN.GHLLQTN.QF
Retrocopy MSDSNLDSSKKNFFEGEVVDEESVILTLLPVKDDPNMEQMEPSVSSTSDVKLEKPMKYNQGHLLQTN*QF

Parental  TAPQKARCEIPALPLPTILPPINKVCRDTLRDWCQQLGLSTNGKKIEVYLRLHRHAYPEQRQDMPEMSQE
          TAPQKARC.IPALPLPTILPPINK.C.DTLRDWCQQL.LSTNGKKIEVYLR.HRHAYPEQ.QDMPEMSQE
Retrocopy TAPQKARCKIPALPLPTILPPINKECWDTLRDWCQQLSLSTNGKKIEVYLRVHRHAYPEQQQDMPEMSQE

Parental  TRLQRCSRKRKAVTKRARLQRSYEMNERAEETNTVEVITSAPGAMLASWARIAARAVQPKALNSCSIPVS
          TRLQRCSRK.KAVTKRARLQ..YEMNERAEETNTVEVITSA.GAMLAS.ARIAARAV.P.A.NS.SIPVS
Retrocopy TRLQRCSRKHKAVTKRARLQKTYEMNERAEETNTVEVITSAQGAMLASRARIAARAVEPEAVNSSSIPVS

Parental  VEAFLMQASGVRWCVVHGRLLSADTKGWVRLQFHAGQAWVPTTHRRMISLFLLPACIFPSPGIEDNMLCP
          .EAFLMQ.SGVRWCVVHGRLLSADTKG.V.LQFHAGQ..VPTTHRRMISLFLLPACIFPSPG.EDNMLCP
Retrocopy LEAFLMQGSGVRWCVVHGRLLSADTKG*VCLQFHAGQV*VPTTHRRMISLFLLPACIFPSPGTEDNMLCP

Parental  DCAKRNKKMMKRLMTVEK
          .CAKRNKKMMKRLMT.EK
Retrocopy NCAKRNKKMMKRLMTIEK

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	0.00 RPM
SRP007412_cerebellum	0.00 RPM	0.00 RPM
SRP007412_heart	0.00 RPM	0.00 RPM
SRP007412_kidney	0.03 RPM	0.16 RPM
SRP007412_liver	0.00 RPM	0.56 RPM
SRP007412_testis	0.11 RPM	5.59 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_281 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_281 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_281 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_357
Pongo abelii	retro_pabe_346
Macaca mulatta	retro_mmul_475

---

Parental genes homology:

Parental genes homology involve 21 parental genes, and 65 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000020460	2 retrocopies	retro_btau_435, retro_btau_529,
Callithrix jacchus	ENSCJAG00000020168	4 retrocopies	retro_cjac_1378, retro_cjac_1991, retro_cjac_3832, retro_cjac_944,
Dasypus novemcinctus	ENSDNOG00000010745	6 retrocopies	retro_dnov_1248, retro_dnov_1626, retro_dnov_1714, retro_dnov_2462, retro_dnov_2583, retro_dnov_2656,
Erinaceus europaeus	ENSEEUG00000008944	4 retrocopies	retro_eeur_205, retro_eeur_415, retro_eeur_426, retro_eeur_616,
Echinops telfairi	ENSETEG00000007985	4 retrocopies	retro_etel_2051, retro_etel_2058, retro_etel_506, retro_etel_918,
Homo sapiens	ENSG00000163530	3 retrocopies	retro_hsap_1642, retro_hsap_2903, retro_hsap_357,
Microcebus murinus	ENSMICG00000013744	6 retrocopies	retro_mmur_1171, retro_mmur_156, retro_mmur_1634, retro_mmur_213, retro_mmur_598, retro_mmur_955,
Myotis lucifugus	ENSMLUG00000007444	1 retrocopy	retro_mluc_1706,
Macaca mulatta	ENSMMUG00000022112	3 retrocopies	retro_mmul_1550, retro_mmul_342, retro_mmul_475,
Monodelphis domestica	ENSMODG00000018083	3 retrocopies	retro_mdom_1057, retro_mdom_1478, retro_mdom_999,
Mus musculus	ENSMUSG00000072419	7 retrocopies	retro_mmus_1303, retro_mmus_1832, retro_mmus_1847, retro_mmus_2391, retro_mmus_2935, retro_mmus_3699, retro_mmus_394,
Nomascus leucogenys	ENSNLEG00000004020	2 retrocopies	retro_nleu_1329, retro_nleu_633,
Oryctolagus cuniculus	ENSOCUG00000003175	1 retrocopy	retro_ocun_61,
Otolemur garnettii	ENSOGAG00000031228	7 retrocopies	retro_ogar_1678, retro_ogar_1722, retro_ogar_1953, retro_ogar_2404, retro_ogar_2567, retro_ogar_2900, retro_ogar_586,
Ochotona princeps	ENSOPRG00000005059	1 retrocopy	retro_opri_433,
Pongo abelii	ENSPPYG00000013566	3 retrocopies	retro_pabe_1360, retro_pabe_2401, retro_pabe_346,
Pan troglodytes	ENSPTRG00000015199	3 retrocopies	retro_ptro_1113, retro_ptro_1962, retro_ptro_281 ,
Pan troglodytes	ENSPTRG00000015200	2 retrocopies	retro_ptro_1923, retro_ptro_616,
Sarcophilus harrisii	ENSSHAG00000017398	1 retrocopy	retro_shar_542,
Tupaia belangeri	ENSTBEG00000006212	1 retrocopy	retro_tbel_3864,
Tursiops truncatus	ENSTTRG00000009500	1 retrocopy	retro_ttru_1524,