RetrogeneDB ID: retro_pabe_2204

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 3:23430209..23430624(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: H3F3B
• Ensembl ID: ENSPPYG00000000168
• Aliases: None
• Description: Histone H3 [Source:UniProtKB/TrEMBL;Acc:H2N3J5]

Sequence

>retro_pabe_2204
ATGGCTTGTACAAAGCGCACTGCCTGCAAATCGACCGGTAAAGCAGCCAGGAAGCAACGGGGTACAAAAGCCGCTCACAA
GAGTGCGCCCTCTACTGGAAGGGGTGAAGAAAACCTTATCGTTACAGGCCTGGTACTGTGGCACTCCCGTGAAATCAGAC
GTTATCAGAAGGCCACTGAAACTTCTGATTCGCCATCTTCGCTTTCAGCATCTGGTGCAAGAAATTGCTCAGGGCTTGAA
AACAGATCTACGCTTCCAGAGTGCAACCTATGGGTGCTCTGCAGGGAGGCAAGTGAGGCCTATCTGGGTTGGCCTTTTTG
AAGACAGCAATCTGTGTGCTATCCACCCCAAACGTGCAAACGATTTATGCCAAAAGACATTCCAGCTAGCATGCCGCATA
CATGGAAGACGTGCT

Alignment

ORF - retro_pabe_2204 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.61 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  MARTKQTARKSTGGKAPRKQLATKAARKSAPSTG-GVKK-PHRYRPGTVAL-REIRRYQKSTE-LLIRKL
          MA.TK.TA.KSTG.KA.RKQ..TKAA.KSAPSTG.GVKK.P.RYRPGTVAL.REIRRYQK.TE.LLIR.L
Retrocopy MACTKRTACKSTG-KAARKQRGTKAAHKSAPSTG>GVKK>PYRYRPGTVAL>REIRRYQKATE>LLIRHL

Parental  PFQRLVREIAQDFKTDLRFQSAA-IGALQ-EASEAYL-VGLFEDTNLCAIHAKRVT-IMPKDIQLARRIR
          .FQ.LV.EIAQ..KTDLRFQSA...GALQ.EASEAYL.VGLFED.NLCAIH.KR......K..QLA.RI.
Retrocopy RFQHLVQEIAQGLKTDLRFQSAT>MGALQ>EASEAYL>VGLFEDSNLCAIHPKRANDLCQKTFQLACRIH

Parental  GERA
          G.RA
Retrocopy GRRA

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	20.24 RPM
SRP007412_cerebellum	0.00 RPM	22.01 RPM
SRP007412_heart	0.00 RPM	24.50 RPM
SRP007412_kidney	0.00 RPM	37.65 RPM
SRP007412_liver	0.00 RPM	30.02 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2204 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2204 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2204 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 115 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000024561	3 retrocopies	retro_btau_156, retro_btau_204, retro_btau_47,
Canis familiaris	ENSCAFG00000004916	2 retrocopies	retro_cfam_1117, retro_cfam_622,
Canis familiaris	ENSCAFG00000016119	4 retrocopies	retro_cfam_168, retro_cfam_1845, retro_cfam_650, retro_cfam_673,
Dipodomys ordii	ENSDORG00000008132	9 retrocopies	retro_dord_238, retro_dord_283, retro_dord_43, retro_dord_589, retro_dord_678, retro_dord_685, retro_dord_719, retro_dord_765, retro_dord_774,
Erinaceus europaeus	ENSEEUG00000013796	1 retrocopy	retro_eeur_2,
Felis catus	ENSFCAG00000003617	4 retrocopies	retro_fcat_1085, retro_fcat_1953, retro_fcat_592, retro_fcat_830,
Felis catus	ENSFCAG00000030424	5 retrocopies	retro_fcat_1251, retro_fcat_1532, retro_fcat_1533, retro_fcat_2011, retro_fcat_674,
Gorilla gorilla	ENSGGOG00000022526	11 retrocopies	retro_ggor_1179, retro_ggor_1809, retro_ggor_1837, retro_ggor_1919, retro_ggor_2003, retro_ggor_2837, retro_ggor_2956, retro_ggor_3082, retro_ggor_393, retro_ggor_736, retro_ggor_944,
Gadus morhua	ENSGMOG00000014306	1 retrocopy	retro_gmor_9,
Macaca mulatta	ENSMMUG00000031483	9 retrocopies	retro_mmul_108, retro_mmul_147, retro_mmul_201, retro_mmul_213, retro_mmul_215, retro_mmul_286, retro_mmul_337, retro_mmul_346, retro_mmul_7,
Mus musculus	ENSMUSG00000016559	18 retrocopies	retro_mmus_1058, retro_mmus_1188, retro_mmus_1269, retro_mmus_1535, retro_mmus_1635, retro_mmus_2021, retro_mmus_2083, retro_mmus_2377, retro_mmus_2771, retro_mmus_2867, retro_mmus_2972, retro_mmus_3002, retro_mmus_3144, retro_mmus_3477, retro_mmus_3667, retro_mmus_896, retro_mmus_961, retro_mmus_962,
Nomascus leucogenys	ENSNLEG00000001577	2 retrocopies	retro_nleu_25, retro_nleu_35,
Otolemur garnettii	ENSOGAG00000024312	11 retrocopies	retro_ogar_1086, retro_ogar_1790, retro_ogar_1863, retro_ogar_2364, retro_ogar_2463, retro_ogar_2581, retro_ogar_2746, retro_ogar_3415, retro_ogar_478, retro_ogar_842, retro_ogar_955,
Otolemur garnettii	ENSOGAG00000025933	14 retrocopies	retro_ogar_1285, retro_ogar_1364, retro_ogar_1449, retro_ogar_1575, retro_ogar_1576, retro_ogar_2200, retro_ogar_2316, retro_ogar_2449, retro_ogar_2634, retro_ogar_3235, retro_ogar_42, retro_ogar_733, retro_ogar_937, retro_ogar_952,
Pongo abelii	ENSPPYG00000000168	14 retrocopies	retro_pabe_1285, retro_pabe_2151, retro_pabe_2204 , retro_pabe_2252, retro_pabe_2391, retro_pabe_2679, retro_pabe_2722, retro_pabe_2805, retro_pabe_2938, retro_pabe_3078, retro_pabe_323, retro_pabe_3420, retro_pabe_3637, retro_pabe_3697,
Pongo abelii	ENSPPYG00000008636	1 retrocopy	retro_pabe_2662,
Pteropus vampyrus	ENSPVAG00000008459	2 retrocopies	retro_pvam_218, retro_pvam_52,
Rattus norvegicus	ENSRNOG00000003220	4 retrocopies	retro_rnor_121, retro_rnor_191, retro_rnor_336, retro_rnor_44,