RetrogeneDB ID: retro_pabe_3164

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 7:98050171..98050670(-)
• Located in intron of: ENSPPYG00000017865

Retrocopy information

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

Parental gene information

• Parental gene symbol: UFC1
• Ensembl ID: ENSPPYG00000000610
• Aliases: None
• Description: ubiquitin-fold modifier conjugating enzyme 1 [Source:HGNC Symbol;Acc:26941]

Sequence

>retro_pabe_3164
ATGGCAGATGAGGCCACCTGACATGTTGTGTCTAAGACTCTGGCACTGAAGACTAATGCAGGACCCCAAGATTGGGAGTT
GTGGGTGCAGTGATTGAAGGAGGACTATCAGTCCCTTATCTGGTACGTGGAGAACAACAAGAATGGCGACAACGATGGTT
CCAACTGGAGTCCAGCAAGGTAGGGACTCAGTGGTTTGGAAAATGTTGGTATATCCGTGACCTCCTGAAATGTGAGTTTG
ATGTCAAGTTTGCAATTCCTATCATATATCTTACTACTGCCCCAGAAATTGCAGTCCCCGAGCTGGATGGAAAGACAGCA
AAGATGTACAGAGGTGGCAAAATTGCCTGACAGATCATTTCAAGTCTTTGTGGGACAGGAACGTACCCAAATTTGAACTA
GCTCATTTCATGGCTCTGGGGCTGGGTCCATGGCTGGCAGCGGAAATCCCTGATCTGATTCAGAAGGGGATGTTCCAGCA
CAAAGAGAAATGTAACCAA

Alignment

ORF - retro_pabe_3164 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.47 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MADEATRRVVSEIPVLKTNAGPRDRELWVQRLKEEYQSLIRYVENNKNADND-WFRLESNKEGTRWFGKC
          MADEAT..VVS....LKTNAGP.D.ELWVQ.LKE.YQSLI.YVENNKN.DND.WF.LES.K.GT.WFGKC
Retrocopy MADEAT*HVVSKTLALKTNAGPQDWELWVQ*LKEDYQSLIWYVENNKNGDND<WFQLESSKVGTQWFGKC

Parental  WYIHDLLKYEFDIEFDIPITYPTTAPEIAVPELDGKTAKMYRGGKI-CLTDHFKPLWARNVPKFGLAHLM
          WYI.DLLK.EFD..F.IPI.Y.TTAPEIAVPELDGKTAKMYRGGKI.CLTDHFK.LW.RNVPKF.LAH.M
Retrocopy WYIRDLLKCEFDVKFAIPIIYLTTAPEIAVPELDGKTAKMYRGGKI<CLTDHFKSLWDRNVPKFELAHFM

Parental  ALGLGPWLAVEIPDLIQKGVIQHKEKCNE
          ALGLGPWLA.EIPDLIQKG..QHKEKCN.
Retrocopy ALGLGPWLAAEIPDLIQKGMFQHKEKCNQ

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	31.90 RPM
SRP007412_cerebellum	0.00 RPM	19.82 RPM
SRP007412_heart	0.00 RPM	12.22 RPM
SRP007412_kidney	0.00 RPM	31.49 RPM
SRP007412_liver	0.00 RPM	27.69 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3164 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3164 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3164 has 5 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3753
Pan troglodytes	retro_ptro_2547
Gorilla gorilla	retro_ggor_2525
Macaca mulatta	retro_mmul_1727
Callithrix jacchus	retro_cjac_3146

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Parental genes homology:

Parental genes homology involve 23 parental genes, and 35 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000015545	1 retrocopy	retro_amel_1221,
Callithrix jacchus	ENSCJAG00000005303	3 retrocopies	retro_cjac_2546, retro_cjac_3146, retro_cjac_4122,
Danio rerio	ENSDARG00000022340	1 retrocopy	retro_drer_22,
Dasypus novemcinctus	ENSDNOG00000013733	1 retrocopy	retro_dnov_1943,
Echinops telfairi	ENSETEG00000015730	4 retrocopies	retro_etel_1042, retro_etel_562, retro_etel_714, retro_etel_83,
Felis catus	ENSFCAG00000009829	1 retrocopy	retro_fcat_1217,
Homo sapiens	ENSG00000143222	1 retrocopy	retro_hsap_3753,
Gorilla gorilla	ENSGGOG00000007486	1 retrocopy	retro_ggor_2525,
Loxodonta africana	ENSLAFG00000026969	1 retrocopy	retro_lafr_473,
Macropus eugenii	ENSMEUG00000004417	1 retrocopy	retro_meug_423,
Myotis lucifugus	ENSMLUG00000004543	1 retrocopy	retro_mluc_716,
Macaca mulatta	ENSMMUG00000022632	2 retrocopies	retro_mmul_1727, retro_mmul_2273,
Mustela putorius furo	ENSMPUG00000014243	1 retrocopy	retro_mputfur_854,
Nomascus leucogenys	ENSNLEG00000014049	1 retrocopy	retro_nleu_1893,
Oryctolagus cuniculus	ENSOCUG00000002389	1 retrocopy	retro_ocun_1304,
Otolemur garnettii	ENSOGAG00000026679	4 retrocopies	retro_ogar_1385, retro_ogar_2156, retro_ogar_3496, retro_ogar_496,
Ochotona princeps	ENSOPRG00000010906	3 retrocopies	retro_opri_319, retro_opri_509, retro_opri_773,
Pongo abelii	ENSPPYG00000000610	1 retrocopy	retro_pabe_3164 ,
Pan troglodytes	ENSPTRG00000001572	1 retrocopy	retro_ptro_2547,
Pteropus vampyrus	ENSPVAG00000005519	2 retrocopies	retro_pvam_1161, retro_pvam_814,
Sus scrofa	ENSSSCG00000006363	1 retrocopy	retro_sscr_171,
Tupaia belangeri	ENSTBEG00000016276	1 retrocopy	retro_tbel_2810,
Tarsius syrichta	ENSTSYG00000010824	1 retrocopy	retro_tsyr_1751,