RetrogeneDB ID: retro_pabe_3409

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 9:49386004..49386597(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PRDX1
• Ensembl ID: ENSPPYG00000001411
• Aliases: None
• Description: peroxiredoxin 1 [Source:HGNC Symbol;Acc:9352]

Sequence

>retro_pabe_3409
ATGTCTTCAGGAAATGCTAAAATTGGGCACCCTGCCTCCAACTTCAAAGCCACAGCCGTTATGTCAGACGGTCAGTTTAA
AGCTATCAGCCTGTCTGACTACAAAGGAAATATGTTGTATTCTTCTTTTACCCGCTTGACTTCACTTTTGTGTGCCCCAC
AGAGATCATTGCTTTCAGTGATACAGAAGAATTTAACAAATTCAACTGCCAAGTGATTGGTGCTTCTGTGGATTCTCACT
TCTGTCAGCTGGCATGTATCCACACCCCTAAGAAACAAGGAGGACTGGGACCCAGGAACATTCCTTTGGCCTCAGACCTG
AAGCGCGCCATTGCTCAGGATTATGGGATCTTAAAGGCTGAAGAAGGCGTCTCATTCAGGGGCCTCTTTATCGTTGATGA
TATGGGTATTCTTCGGCAGATCACTGTAAGTGACCTCCCTGTTGACTGCTCTGCGGATGAGACTTTGAGACTAGTTCAGG
CCTTCCAGTTCACTGACAAACATGGGGAAGTGTGCCCAGCTGGCTGGAAACCTGGCAGTGATACTATCAAGCCTGATGTC
CAAAACAGCAAAGAATATTTCTCCAAGCAGAAG

Alignment

ORF - retro_pabe_3409 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.5 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSSGNAKIGHPAPNFKATAVMPDGQFKDISLSDYKG-KYVVFFFYPLDFTFVCPTEIIAFSDRAEEFKKL
          MSSGNAKIGHPA.NFKATAVM.DGQFK.ISLSDYKG.KYVVFFFYPLDFTFVCPTEIIAFSD..EEF.K.
Retrocopy MSSGNAKIGHPASNFKATAVMSDGQFKAISLSDYKG<KYVVFFFYPLDFTFVCPTEIIAFSD-TEEFNKF

Parental  NCQVIGASVDSHFCHLAWINTPKKQGGLGPMNIPLVSDPKRTIAQDYGVLKADEGISFRGLFIIDDKGIL
          NCQVIGASVDSHFC.LA.I.TPKKQGGLGP.NIPL.SD.KR.IAQDYG.LKA.EG.SFRGLFI.DD.GIL
Retrocopy NCQVIGASVDSHFCQLACIHTPKKQGGLGPRNIPLASDLKRAIAQDYGILKAEEGVSFRGLFIVDDMGIL

Parental  RQITVNDLPVGRSVDETLRLVQAFQFTDKHGEVCPAGWKPGSDTIKPDVQKSKEYFSKQK
          RQITV.DLPV..S.DETLRLVQAFQFTDKHGEVCPAGWKPGSDTIKPDVQ.SKEYFSKQK
Retrocopy RQITVSDLPVDCSADETLRLVQAFQFTDKHGEVCPAGWKPGSDTIKPDVQNSKEYFSKQK

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	1.44 RPM	63.69 RPM
SRP007412_cerebellum	0.36 RPM	59.46 RPM
SRP007412_heart	1.35 RPM	73.12 RPM
SRP007412_kidney	3.65 RPM	253.87 RPM
SRP007412_liver	0.86 RPM	211.95 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3409 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3409 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3409 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 32 parental genes, and 88 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000013632	2 retrocopies	retro_amel_1116, retro_amel_539,
Bos taurus	ENSBTAG00000003642	2 retrocopies	retro_btau_1299, retro_btau_1446,
Canis familiaris	ENSCAFG00000004567	5 retrocopies	retro_cfam_1313, retro_cfam_270, retro_cfam_577, retro_cfam_834, retro_cfam_988,
Choloepus hoffmanni	ENSCHOG00000003358	5 retrocopies	retro_chof_1140, retro_chof_134, retro_chof_1714, retro_chof_2035, retro_chof_2450,
Ciona intestinalis	ENSCING00000003002	1 retrocopy	retro_cint_8,
Callithrix jacchus	ENSCJAG00000004807	2 retrocopies	retro_cjac_1201, retro_cjac_2884,
Cavia porcellus	ENSCPOG00000014137	3 retrocopies	retro_cpor_1079, retro_cpor_290, retro_cpor_398,
Dasypus novemcinctus	ENSDNOG00000018488	1 retrocopy	retro_dnov_2071,
Dipodomys ordii	ENSDORG00000008975	1 retrocopy	retro_dord_727,
Equus caballus	ENSECAG00000008678	1 retrocopy	retro_ecab_81,
Echinops telfairi	ENSETEG00000007922	11 retrocopies	retro_etel_112, retro_etel_1157, retro_etel_1245, retro_etel_1442, retro_etel_1838, retro_etel_2121, retro_etel_2122, retro_etel_308, retro_etel_367, retro_etel_460, retro_etel_556,
Felis catus	ENSFCAG00000028484	1 retrocopy	retro_fcat_1714,
Homo sapiens	ENSG00000117450	1 retrocopy	retro_hsap_4230,
Macropus eugenii	ENSMEUG00000006820	4 retrocopies	retro_meug_1694, retro_meug_1711, retro_meug_2059, retro_meug_662,
Macaca mulatta	ENSMMUG00000006221	1 retrocopy	retro_mmul_762,
Monodelphis domestica	ENSMODG00000002382	2 retrocopies	retro_mdom_1787, retro_mdom_555,
Mus musculus	ENSMUSG00000028691	5 retrocopies	retro_mmus_1466, retro_mmus_1659, retro_mmus_1786, retro_mmus_3129, retro_mmus_3167,
Nomascus leucogenys	ENSNLEG00000014524	2 retrocopies	retro_nleu_1040, retro_nleu_1627,
Oryctolagus cuniculus	ENSOCUG00000005951	2 retrocopies	retro_ocun_1064, retro_ocun_1124,
Otolemur garnettii	ENSOGAG00000002303	4 retrocopies	retro_ogar_1219, retro_ogar_1333, retro_ogar_1588, retro_ogar_486,
Pongo abelii	ENSPPYG00000001411	1 retrocopy	retro_pabe_3409 ,
Pongo abelii	ENSPPYG00000002700	1 retrocopy	retro_pabe_1906,
Pongo abelii	ENSPPYG00000009607	3 retrocopies	retro_pabe_2711, retro_pabe_2892, retro_pabe_988,
Pan troglodytes	ENSPTRG00000000675	1 retrocopy	retro_ptro_2874,
Pteropus vampyrus	ENSPVAG00000015001	1 retrocopy	retro_pvam_179,
Rattus norvegicus	ENSRNOG00000017194	8 retrocopies	retro_rnor_1401, retro_rnor_1488, retro_rnor_1574, retro_rnor_1656, retro_rnor_1736, retro_rnor_2063, retro_rnor_2292, retro_rnor_2401,
Sorex araneus	ENSSARG00000004703	5 retrocopies	retro_sara_153, retro_sara_370, retro_sara_399, retro_sara_633, retro_sara_95,
Sus scrofa	ENSSSCG00000003914	1 retrocopy	retro_sscr_719,
Ictidomys tridecemlineatus	ENSSTOG00000023413	2 retrocopies	retro_itri_631, retro_itri_817,
Tupaia belangeri	ENSTBEG00000015997	4 retrocopies	retro_tbel_3922, retro_tbel_4017, retro_tbel_4024, retro_tbel_4669,
Tarsius syrichta	ENSTSYG00000011031	1 retrocopy	retro_tsyr_1781,
Tursiops truncatus	ENSTTRG00000008858	4 retrocopies	retro_ttru_1350, retro_ttru_1878, retro_ttru_234, retro_ttru_36,