RetrogeneDB ID: retro_pabe_2401

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 3:197974864..197975338(-)
• Located in intron of: ENSPPYG00000014418

Retrocopy information

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

Parental gene information

• Parental gene symbol: DPPA2
• Ensembl ID: ENSPPYG00000013566
• Aliases: None
• Description: developmental pluripotency associated 2 [Source:HGNC Symbol;Acc:19197]

Sequence

>retro_pabe_2401
ATGTCAGACTCAAATTTGGATAGCAGCAAGAAGAATTTCTTTGAGGGAGGAAGTAGCTGATGAGGGAAGCGTGATTTTGA
CATTGGTGCCAGTTAAAGATGACCCGAATATGGAACAAATGGAACCAAGTGTTTCTTCAACTTCTGATGTCAAACTGGAG
AAGCCTAAGAAATACAATCAAGGTCATCACTTCAAACACATTAACAATTTACAGCTCCACAAAAAGCTGGTGCAAAATAC
CAGCCCTTCCCTTGCCGACCACTTTGCCTCCCATTAATAAGGTGTGTCGGGACACTTAGCGGGACTGGTGTCAACAACTT
GGTTTGAGTGCTAATGGCAAGAAAATAGAAGTTTATCTGAGGCTCTGGTAGGCATGCTTTCCCTGAACAACAGCAAGATA
CGCCTGAAACGTCACAAGAGACCAGATTACAGCGATGTTCGAGGAAACACAAGGCAGTGACCGAGAGAGCAAGA

Alignment

ORF - retro_pabe_2401 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.42 %
• Parental protein coverage: 52.67 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MSDANLDSSKKNFFEG-EVDDEESVILTLVPVKDDANMEQMEPSVSSTSDVKLEKPKKYNQGH-LLQTNE
          MSD.NLDSSKKNFFEG.EV.DE.SVILTLVPVKDD.NMEQMEPSVSSTSDVKLEKPKKYNQGH..LQT..
Retrocopy MSDSNLDSSKKNFFEG>EVADEGSVILTLVPVKDDPNMEQMEPSVSSTSDVKLEKPKKYNQGH<SLQTH*

Parental  QFTAPQKAR-CKIPALPLPTILPPINKVCRDTLRDWCQQLGLSTNGKKIEVYLRL-HRHAYPEQRQDMPE
          QFTAPQKA..CKIPALPLPT.LPPINKVCRDT.RDWCQQLGLS.NGKKIEVYLRL..RHA.PEQ.QD.PE
Retrocopy QFTAPQKAG<CKIPALPLPTTLPPINKVCRDT*RDWCQQLGLSANGKKIEVYLRL>GRHAFPEQQQDTPE

Parental  MSQETRLQRCSRKRKAVTKRAR
          .SQETRLQRCSRK.KAVT.RAR
Retrocopy TSQETRLQRCSRKHKAVTERAR

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	0.00 RPM	0.20 RPM
SRP007412_liver	0.03 RPM	0.00 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2401 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2401 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2401 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2903
Pan troglodytes	retro_ptro_1962
Macaca mulatta	retro_mmul_1550
Callithrix jacchus	retro_cjac_1378

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Parental genes homology:

Parental genes homology involve 21 parental genes, and 66 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	ENSPPYG00000013565	3 retrocopies	retro_pabe_2316, retro_pabe_2349, retro_pabe_770,
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,
Sarcophilus harrisii	ENSSHAG00000017398	1 retrocopy	retro_shar_542,
Tupaia belangeri	ENSTBEG00000006212	1 retrocopy	retro_tbel_3864,
Tursiops truncatus	ENSTTRG00000009500	1 retrocopy	retro_ttru_1524,