RetrogeneDB ID: retro_pabe_1120

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 14:60878000..60878551(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PSMA3
• Ensembl ID: ENSPPYG00000005855
• Aliases: None
• Description: proteasome (prosome, macropain) subunit, alpha type, 3 [Source:HGNC Symbol;Acc:9532]

Sequence

>retro_pabe_1120
TTGGATCAGAATGTTGGAATGCTGGCAGCAGGTTTGTTGGCAGATGCTTGTTCTTTAGCAGACATAGCAAGAGAAGAAGT
TTCCAACTTTAAATCTGACTTTGGCTATAACCCTCCACTAAAACATCTTGCAAACAGAGTGGACATGTATGTACATGCAT
ATACACTCTACAGTGCTGTTAGATCTTTTGCCTTCAGTTTCGTGTTAGGGTCTTACAGTATGAATGACAGTGCACAATTT
TCCATGATTGACTCATCAGGTGTTTTATATGGTTATTGGGCCTGTGCCACTGGCAAAGCCAGGCAAGCTGTAAAACAGAA
ATAGAAAAGCTTCAGATGAAAGAAATGACCTGCTATGATACTGTTAAAGAAGTTGCTCAAGTAATTTACATAGTACATGA
TGACGTTAAGGATAAAGCTTACAAACTCAGCTGGGTTAGTGGTTTAACTAAAGGAAGACATGAAATTGTTTCAAAAGATA
TAAGAGAATAAGCAGATAAATATGCTAAAGAATCCTTGAGTGAAGAAGACAAGTCAGATGATGATAATATG

Alignment

ORF - retro_pabe_1120 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.01 %
• Parental protein coverage: 72.94 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VDRHVGMAVAGLLADARSLADIAREEASNFRSNFGYNIPLKHLADRVAMYVHAYTLYSAVRPFGCSFMLG
          .D..VGM..AGLLADA.SLADIAREE.SNF.S.FGYN.PLKHLA.RV.MYVHAYTLYSAVR.F..SF.LG
Retrocopy LDQNVGMLAAGLLADACSLADIAREEVSNFKSDFGYNPPLKHLANRVDMYVHAYTLYSAVRSFAFSFVLG

Parental  SYSVNDGAQLYMIDPSGVSYGYWGCAIGKARQA-AKTEIEKLQMKEMTCRDIVKEVAKIIYIVHDEVKDK
          SYS.ND.AQ..MID.SGV.YGYW.CA.GKARQA..KTEIEKLQMKEMTC.D.VKEVA..IYIVHD.VKDK
Retrocopy SYSMNDSAQFSMIDSSGVLYGYWACATGKARQA<CKTEIEKLQMKEMTCYDTVKEVAQVIYIVHDDVKDK

Parental  AFELELSWVGELTNGRHEIVPKDIREEAEKYAKESLKEEDESDDDNM
          A....LSWV..LT.GRHEIV.KDIRE.A.KYAKESL.EED.SDDDNM
Retrocopy AY--KLSWVSGLTKGRHEIVSKDIRE*ADKYAKESLSEEDKSDDDNM

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	18.19 RPM
SRP007412_cerebellum	0.00 RPM	30.16 RPM
SRP007412_heart	0.00 RPM	20.05 RPM
SRP007412_kidney	0.00 RPM	26.02 RPM
SRP007412_liver	0.00 RPM	29.10 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1120 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1120 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1120 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1348
Pan troglodytes	retro_ptro_923
Gorilla gorilla	retro_ggor_1049
Macaca mulatta	retro_mmul_2187

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Parental genes homology:

Parental genes homology involve 21 parental genes, and 55 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000015287	1 retrocopy	retro_cfam_1331,
Callithrix jacchus	ENSCJAG00000018732	1 retrocopy	retro_cjac_3974,
Dasypus novemcinctus	ENSDNOG00000004077	27 retrocopies	retro_dnov_1089, retro_dnov_1115, retro_dnov_1156, retro_dnov_1240, retro_dnov_1252, retro_dnov_1285, retro_dnov_1347, retro_dnov_1473, retro_dnov_1542, retro_dnov_1604, retro_dnov_1650, retro_dnov_1662, retro_dnov_1783, retro_dnov_1785, retro_dnov_1791, retro_dnov_1880, retro_dnov_1896, retro_dnov_198, retro_dnov_2030, retro_dnov_2125, retro_dnov_2128, retro_dnov_2334, retro_dnov_2507, retro_dnov_2578, retro_dnov_447, retro_dnov_765, retro_dnov_992,
Dipodomys ordii	ENSDORG00000002167	1 retrocopy	retro_dord_402,
Homo sapiens	ENSG00000100567	1 retrocopy	retro_hsap_1348,
Gorilla gorilla	ENSGGOG00000015814	1 retrocopy	retro_ggor_1049,
Macaca mulatta	ENSMMUG00000003509	2 retrocopies	retro_mmul_2187, retro_mmul_564,
Monodelphis domestica	ENSMODG00000007839	1 retrocopy	retro_mdom_544,
Mustela putorius furo	ENSMPUG00000006126	2 retrocopies	retro_mputfur_1549, retro_mputfur_414,
Mus musculus	ENSMUSG00000060073	3 retrocopies	retro_mmus_1277, retro_mmus_1463, retro_mmus_2810,
Nomascus leucogenys	ENSNLEG00000013092	1 retrocopy	retro_nleu_1831,
Oryctolagus cuniculus	ENSOCUG00000010316	1 retrocopy	retro_ocun_667,
Otolemur garnettii	ENSOGAG00000000382	2 retrocopies	retro_ogar_1764, retro_ogar_2857,
Ochotona princeps	ENSOPRG00000002835	2 retrocopies	retro_opri_67, retro_opri_991,
Pongo abelii	ENSPPYG00000005855	2 retrocopies	retro_pabe_1120 , retro_pabe_339,
Pan troglodytes	ENSPTRG00000006390	1 retrocopy	retro_ptro_923,
Rattus norvegicus	ENSRNOG00000007851	1 retrocopy	retro_rnor_183,
Sorex araneus	ENSSARG00000002670	2 retrocopies	retro_sara_437, retro_sara_573,
Ictidomys tridecemlineatus	ENSSTOG00000013539	1 retrocopy	retro_itri_1317,
Tupaia belangeri	ENSTBEG00000016910	1 retrocopy	retro_tbel_1947,
Tursiops truncatus	ENSTTRG00000013526	1 retrocopy	retro_ttru_545,