RetrogeneDB ID: retro_pabe_1830

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 20:51716754..51717173(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SUMO1
• Ensembl ID: ENSPPYG00000013083
• Aliases: None
• Description: Small ubiquitin-related modifier 1 [Source:UniProtKB/Swiss-Prot;Acc:Q5R6J4]

Sequence

>retro_pabe_1830
GCCGCCATGGTGTCGTGCTGTGACGAAGGGAGATGGCATTGTAAACGCCGGAGCGAGGTTCTGCCTACCCCGAGACTGCT
GCTGTTCTGAGACCTGCAGGTGAATGCCCCATTACCATGTCTGACCAGGAGGCAAAACCTTCAACTGAGCATTTGGGAGA
TAAGATAAAAGATGAAGCTATTAAACTCAGGGTTATTGGACAGGATAGCAGTGAGATTCATTTCAAAGTGAAAATGACAA
CACCTCTCAAGAAGCTCAAGAAATCGTACTGTCAGAGACAGGGCGTTCCAGTGAATTCCCTCAGGTTTCTCTTTGAAGGT
CAGAGAATTGCTGATAATCATACTCCAGAAGAACTGGGAATGGAGGAAGAAGATGTGATTGAGGTTTATCAGGAACAAAT
CGCAGGTCATTCAACAGTT

Alignment

ORF - retro_pabe_1830 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.56 %
• Parental protein coverage: 63.76 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  AAAVLCCGEGR-GFVNPGARFCLP-EAAAVRRPPGEATVIMSDQEAKPSTEDLGDKKEGEYIKLKVIGQD
          AA.V.CC.EGR.G.VN.GARFCLP.E.AAV.RP.GE....MSDQEAKPSTE.LGDK...E.IKL.VIGQD
Retrocopy AAMVSCCDEGR>GIVNAGARFCLP>ETAAVLRPAGECPITMSDQEAKPSTEHLGDKIKDEAIKLRVIGQD

Parental  SSEIHFKVKMTTHLKKLKESYCQRQGVPMNSLRFLFEGQRIADNHTPKELGMEEEDVIEVYQEQTGGHST
          SSEIHFKVKMTT.LKKLK.SYCQRQGVP.NSLRFLFEGQRIADNHTP.ELGMEEEDVIEVYQEQ..GHST
Retrocopy SSEIHFKVKMTTPLKKLKKSYCQRQGVPVNSLRFLFEGQRIADNHTPEELGMEEEDVIEVYQEQIAGHST

Parental  V
          V
Retrocopy V

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	43.85 RPM
SRP007412_cerebellum	0.00 RPM	39.52 RPM
SRP007412_heart	0.00 RPM	16.59 RPM
SRP007412_kidney	0.00 RPM	40.24 RPM
SRP007412_liver	0.00 RPM	32.87 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1830 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1830 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1830 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2489
Gorilla gorilla	retro_ggor_1550
Macaca mulatta	retro_mmul_313
Callithrix jacchus	retro_cjac_2610

---

Parental genes homology:

Parental genes homology involve 29 parental genes, and 118 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000013225	5 retrocopies	retro_amel_1068, retro_amel_233, retro_amel_236, retro_amel_315, retro_amel_49,
Bos taurus	ENSBTAG00000009859	6 retrocopies	retro_btau_112, retro_btau_1512, retro_btau_1705, retro_btau_357, retro_btau_363, retro_btau_499,
Canis familiaris	ENSCAFG00000012431	8 retrocopies	retro_cfam_1226, retro_cfam_1253, retro_cfam_139, retro_cfam_1815, retro_cfam_1912, retro_cfam_2048, retro_cfam_386, retro_cfam_985,
Choloepus hoffmanni	ENSCHOG00000009739	2 retrocopies	retro_chof_190, retro_chof_2068,
Callithrix jacchus	ENSCJAG00000004961	3 retrocopies	retro_cjac_1686, retro_cjac_1932, retro_cjac_2610,
Cavia porcellus	ENSCPOG00000012143	1 retrocopy	retro_cpor_1279,
Dasypus novemcinctus	ENSDNOG00000015868	10 retrocopies	retro_dnov_1070, retro_dnov_1324, retro_dnov_1610, retro_dnov_1623, retro_dnov_1826, retro_dnov_1876, retro_dnov_2068, retro_dnov_2330, retro_dnov_2423, retro_dnov_997,
Equus caballus	ENSECAG00000024693	4 retrocopies	retro_ecab_199, retro_ecab_365, retro_ecab_570, retro_ecab_935,
Erinaceus europaeus	ENSEEUG00000013161	6 retrocopies	retro_eeur_40, retro_eeur_404, retro_eeur_428, retro_eeur_644, retro_eeur_645, retro_eeur_651,
Felis catus	ENSFCAG00000031005	6 retrocopies	retro_fcat_1520, retro_fcat_218, retro_fcat_26, retro_fcat_472, retro_fcat_6, retro_fcat_862,
Homo sapiens	ENSG00000116030	5 retrocopies	retro_hsap_2007, retro_hsap_240, retro_hsap_2489, retro_hsap_262, retro_hsap_897,
Gorilla gorilla	ENSGGOG00000026439	5 retrocopies	retro_ggor_1451, retro_ggor_1550, retro_ggor_299, retro_ggor_311, retro_ggor_725,
Loxodonta africana	ENSLAFG00000022855	5 retrocopies	retro_lafr_111, retro_lafr_1148, retro_lafr_189, retro_lafr_540, retro_lafr_951,
Microcebus murinus	ENSMICG00000008968	5 retrocopies	retro_mmur_1177, retro_mmur_1300, retro_mmur_1493, retro_mmur_1554, retro_mmur_1602,
Myotis lucifugus	ENSMLUG00000007504	2 retrocopies	retro_mluc_1346, retro_mluc_188,
Macaca mulatta	ENSMMUG00000005240	7 retrocopies	retro_mmul_1108, retro_mmul_2035, retro_mmul_2081, retro_mmul_313, retro_mmul_373, retro_mmul_450, retro_mmul_855,
Mustela putorius furo	ENSMPUG00000000335	2 retrocopies	retro_mputfur_257, retro_mputfur_33,
Mus musculus	ENSMUSG00000026021	5 retrocopies	retro_mmus_1594, retro_mmus_2129, retro_mmus_2135, retro_mmus_252, retro_mmus_2962,
Nomascus leucogenys	ENSNLEG00000006997	4 retrocopies	retro_nleu_277, retro_nleu_384, retro_nleu_855, retro_nleu_865,
Otolemur garnettii	ENSOGAG00000030345	1 retrocopy	retro_ogar_215,
Procavia capensis	ENSPCAG00000006870	1 retrocopy	retro_pcap_136,
Pongo abelii	ENSPPYG00000013083	3 retrocopies	retro_pabe_11, retro_pabe_1830 , retro_pabe_775,
Pongo abelii	ENSPPYG00000029777	2 retrocopies	retro_pabe_164, retro_pabe_84,
Pan troglodytes	ENSPTRG00000012817	1 retrocopy	retro_ptro_119,
Rattus norvegicus	ENSRNOG00000016133	2 retrocopies	retro_rnor_2015, retro_rnor_813,
Sorex araneus	ENSSARG00000008205	8 retrocopies	retro_sara_130, retro_sara_429, retro_sara_433, retro_sara_456, retro_sara_487, retro_sara_679, retro_sara_758, retro_sara_763,
Sarcophilus harrisii	ENSSHAG00000011968	1 retrocopy	retro_shar_375,
Ictidomys tridecemlineatus	ENSSTOG00000025405	4 retrocopies	retro_itri_1193, retro_itri_1232, retro_itri_216, retro_itri_668,
Tursiops truncatus	ENSTTRG00000000642	4 retrocopies	retro_ttru_1646, retro_ttru_1652, retro_ttru_309, retro_ttru_399,