RetrogeneDB ID: retro_ptro_1876

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 3:37722570..37723105(-)
• Located in intron of: ENSPTRG00000014745

Retrocopy information

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

Parental gene information

• Parental gene symbol: UBE2F
• Ensembl ID: ENSPTRG00000013081
• Aliases: None
• Description: None

Sequence

>retro_ptro_1876
CTGACACCTGTAAGCAAACTGAAGTGCGATGACAGTCTCAAAGGGTCTGGGACGTCAGCCATAGCATCCGGCCCCAGTCA
GAGGGTTCTGTGAGAGACGAGTTGATTGTTAAAGAGGTTGCAGAGCTTGAGCTTATTTACCTTGTACATGTCAAGAGTAT
TTCCTGATCTAAAAAGCTTCATTGCTTTCTGCTGACTGTAACCCCAGACGAGGGTTACTACTAGGGTGGAAAATTTCAGC
TCGAAACTGGACTTCCTGATGCATACAATGTGGTGCCTTCCAAAGTGAAATGCCTGACCAGGATCTGGTACCCTAACATC
ACAGAGATAGGGGAAATATGTCTAAAGTTTACTGAGGACATTCGATTGACAGCACTGGCTGGGCTCCCACGAGAACGTTA
AAGGATGTTATTTGGAGATTAAATTATTTGTTTACTAATCTTCTGAATTTTGACGATCCACTGAATGTTGAAGCTGCAGA
ACATCATTTGTAGGACAAGGAGGACTACTTGAATAAAGTCGATGACTACATCAAG

Alignment

ORF - retro_ptro_1876 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.05 %
• Parental protein coverage: 97.3 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  LTLASKLKRDDGLKGSRTAATASDSTRRV-SVRDKLLVKEVAELE-ANLPCTCKVHF-PD-PNKLHCFQL
          LT..SKLK.DD.LKGS.T.A.AS....RV.SVRD.L.VKEVAELE.A.LPCTC...F.PD...KLHCF.L
Retrocopy LTPVSKLKCDDSLKGSGTSAIASGPSQRV<SVRDELIVKEVAELE<AYLPCTCQEYF<PD<SKKLHCFLL

Parental  TVTPDEGYYQGGKFQFETEVPDAYNMVPPKVKCLTKIWHPNITETGEICLSLLRE-HSIDGTGWAPTRTL
          TVTPDEGYY.GGKFQ.ET..PDAYN.VP.KVKCLT.IW.PNITE.GEICL......HSID.TGWAPTRTL
Retrocopy TVTPDEGYY*GGKFQLETGLPDAYNVVPSKVKCLTRIWYPNITEIGEICLKFTED<HSIDSTGWAPTRTL

Parental  KDVVWGLNSLFTDLLNFDDPLNIEAAEHHLRDKEDFRNKVDDYIK
          KDV.W.LN.LFT.LLNFDDPLN.EAAEHHL.DKED..NKVDDYIK
Retrocopy KDVIWRLNYLFTNLLNFDDPLNVEAAEHHL*DKEDYLNKVDDYIK

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	0.25 RPM	31.57 RPM
SRP007412_cerebellum	0.22 RPM	34.59 RPM
SRP007412_heart	0.29 RPM	19.64 RPM
SRP007412_kidney	0.60 RPM	22.88 RPM
SRP007412_liver	1.21 RPM	19.80 RPM
SRP007412_testis	0.21 RPM	21.81 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1876 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1876 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1876 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Gorilla gorilla	retro_ggor_1930

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Parental genes homology:

Parental genes homology involve 24 parental genes, and 59 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000008551	1 retrocopy	retro_amel_572,
Bos taurus	ENSBTAG00000026114	2 retrocopies	retro_btau_1698, retro_btau_948,
Canis familiaris	ENSCAFG00000012363	1 retrocopy	retro_cfam_1275,
Callithrix jacchus	ENSCJAG00000000476	3 retrocopies	retro_cjac_2378, retro_cjac_2980, retro_cjac_3219,
Cavia porcellus	ENSCPOG00000006368	1 retrocopy	retro_cpor_1122,
Dasypus novemcinctus	ENSDNOG00000000506	2 retrocopies	retro_dnov_1301, retro_dnov_132,
Equus caballus	ENSECAG00000011687	1 retrocopy	retro_ecab_158,
Echinops telfairi	ENSETEG00000009230	1 retrocopy	retro_etel_1534,
Homo sapiens	ENSG00000184182	2 retrocopies	retro_hsap_2439, retro_hsap_2773,
Gorilla gorilla	ENSGGOG00000010709	3 retrocopies	retro_ggor_1518, retro_ggor_1519, retro_ggor_1930,
Microcebus murinus	ENSMICG00000012075	5 retrocopies	retro_mmur_1014, retro_mmur_114, retro_mmur_1365, retro_mmur_584, retro_mmur_815,
Myotis lucifugus	ENSMLUG00000001286	5 retrocopies	retro_mluc_1237, retro_mluc_1674, retro_mluc_1747, retro_mluc_1789, retro_mluc_2627,
Macaca mulatta	ENSMMUG00000018482	4 retrocopies	retro_mmul_1450, retro_mmul_1585, retro_mmul_254, retro_mmul_628,
Mustela putorius furo	ENSMPUG00000000101	1 retrocopy	retro_mputfur_782,
Mus musculus	ENSMUSG00000034343	3 retrocopies	retro_mmus_2161, retro_mmus_255, retro_mmus_845,
Nomascus leucogenys	ENSNLEG00000011152	2 retrocopies	retro_nleu_1340, retro_nleu_677,
Otolemur garnettii	ENSOGAG00000005308	7 retrocopies	retro_ogar_1109, retro_ogar_1995, retro_ogar_2491, retro_ogar_2551, retro_ogar_2715, retro_ogar_639, retro_ogar_761,
Pongo abelii	ENSPPYG00000013315	3 retrocopies	retro_pabe_1395, retro_pabe_1785, retro_pabe_2242,
Pan troglodytes	ENSPTRG00000013081	2 retrocopies	retro_ptro_1410, retro_ptro_1876 ,
Rattus norvegicus	ENSRNOG00000019953	1 retrocopy	retro_rnor_2696,
Sus scrofa	ENSSSCG00000027723	3 retrocopies	retro_sscr_291, retro_sscr_423, retro_sscr_542,
Tarsius syrichta	ENSTSYG00000011510	3 retrocopies	retro_tsyr_1718, retro_tsyr_1944, retro_tsyr_2133,
Tursiops truncatus	ENSTTRG00000011528	2 retrocopies	retro_ttru_1297, retro_ttru_1455,
Vicugna pacos	ENSVPAG00000010485	1 retrocopy	retro_vpac_361,