RetrogeneDB ID: retro_pabe_3370

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 8:133662916..133663242(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SOD1
• Ensembl ID: ENSPPYG00000011354
• Aliases: None
• Description: superoxide dismutase [Source:RefSeq peptide;Acc:NP_001125441]

Sequence

>retro_pabe_3370
TTCCATGTTCATCAGTTTGCAAATAATATACAAGGCTGTACCAGTGCAGGTCCTCACTTTAATCCACTATCCCCAAAATA
CGGTGGACCAAAGGATCAAGAGAGGCATGTTGAACACCTGGGCAATGTGACTGCTGGCAAAGATGGTGCAACGATGTGTC
TATTGAAGATTCTATGATCTCACTCTCAGGAGGCCACTCCATCATTGGCCACGCAATGGTTGTCCATGAAAAACCAGATG
ACTTGGGCAAAGATAGAAATGAAGAAAGTACAAAGATGAGAAATGCTGGAAGTTATTTGGCTTGTGGTGTATTTGGGAAT
TCCCAG

Alignment

ORF - retro_pabe_3370 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.73 %
• Parental protein coverage: 83.85 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  FHVHEFGDNTVGCTSAGPHFNPLSRKHGGPKDEERHVGDLGNVTADKDGVA-SVSIEDSVISLSGDHCII
          FHVH.F..N..GCTSAGPHFNPLS.K.GGPKD.ERHV..LGNVTA.KDG....VSIEDS.ISLSG.H.II
Retrocopy FHVHQFANNIQGCTSAGPHFNPLSPKYGGPKDQERHVEHLGNVTAGKDGAT<DVSIEDSMISLSGGHSII

Parental  GRTLVVHEKADDLGKGGNEESTKTGNAGSRLACGVIGIAQ
          G...VVHEK.DDLGK..NEESTK..NAGS.LACGV.G..Q
Retrocopy GHAMVVHEKPDDLGKDRNEESTKMRNAGSYLACGVFGNSQ

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	171.01 RPM
SRP007412_cerebellum	0.00 RPM	163.80 RPM
SRP007412_heart	0.03 RPM	115.27 RPM
SRP007412_kidney	0.20 RPM	350.86 RPM
SRP007412_liver	0.06 RPM	396.11 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3370 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3370 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3370 has 5 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4117
Pan troglodytes	retro_ptro_2796
Gorilla gorilla	retro_ggor_2763
Macaca mulatta	retro_mmul_2372
Callithrix jacchus	retro_cjac_1477

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Parental genes homology:

Parental genes homology involve 26 parental genes, and 65 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000018854	1 retrocopy	retro_btau_40,
Canis familiaris	ENSCAFG00000008859	1 retrocopy	retro_cfam_1515,
Callithrix jacchus	ENSCJAG00000008983	3 retrocopies	retro_cjac_1477, retro_cjac_1986, retro_cjac_652,
Dasypus novemcinctus	ENSDNOG00000006512	1 retrocopy	retro_dnov_816,
Dipodomys ordii	ENSDORG00000013850	3 retrocopies	retro_dord_217, retro_dord_41, retro_dord_603,
Erinaceus europaeus	ENSEEUG00000015905	1 retrocopy	retro_eeur_305,
Felis catus	ENSFCAG00000002225	2 retrocopies	retro_fcat_1260, retro_fcat_422,
Homo sapiens	ENSG00000142168	3 retrocopies	retro_hsap_1637, retro_hsap_3591, retro_hsap_4117,
Gorilla gorilla	ENSGGOG00000015554	4 retrocopies	retro_ggor_1238, retro_ggor_2421, retro_ggor_2690, retro_ggor_2763,
Latimeria chalumnae	ENSLACG00000013736	1 retrocopy	retro_lcha_51,
Loxodonta africana	ENSLAFG00000010708	1 retrocopy	retro_lafr_127,
Microcebus murinus	ENSMICG00000005253	2 retrocopies	retro_mmur_378, retro_mmur_573,
Macaca mulatta	ENSMMUG00000001711	2 retrocopies	retro_mmul_1563, retro_mmul_2372,
Monodelphis domestica	ENSMODG00000021041	1 retrocopy	retro_mdom_1376,
Mus musculus	ENSMUSG00000022982	1 retrocopy	retro_mmus_2742,
Nomascus leucogenys	ENSNLEG00000003545	3 retrocopies	retro_nleu_1324, retro_nleu_302, retro_nleu_584,
Otolemur garnettii	ENSOGAG00000014646	3 retrocopies	retro_ogar_27, retro_ogar_3364, retro_ogar_702,
Ochotona princeps	ENSOPRG00000007008	1 retrocopy	retro_opri_1190,
Pongo abelii	ENSPPYG00000011354	2 retrocopies	retro_pabe_1353, retro_pabe_3370 ,
Pan troglodytes	ENSPTRG00000013847	3 retrocopies	retro_ptro_1107, retro_ptro_2431, retro_ptro_2796,
Pteropus vampyrus	ENSPVAG00000005216	2 retrocopies	retro_pvam_281, retro_pvam_563,
Sarcophilus harrisii	ENSSHAG00000004195	1 retrocopy	retro_shar_278,
Ictidomys tridecemlineatus	ENSSTOG00000004434	1 retrocopy	retro_itri_1342,
Tupaia belangeri	ENSTBEG00000007333	4 retrocopies	retro_tbel_2131, retro_tbel_3531, retro_tbel_3611, retro_tbel_429,
Tarsius syrichta	ENSTSYG00000011342	17 retrocopies	retro_tsyr_1055, retro_tsyr_1064, retro_tsyr_1082, retro_tsyr_1112, retro_tsyr_1143, retro_tsyr_1176, retro_tsyr_1262, retro_tsyr_1275, retro_tsyr_1295, retro_tsyr_1369, retro_tsyr_1378, retro_tsyr_1590, retro_tsyr_2107, retro_tsyr_365, retro_tsyr_402, retro_tsyr_823, retro_tsyr_831,
Vicugna pacos	ENSVPAG00000012396	1 retrocopy	retro_vpac_168,