RetrogeneDB ID: retro_pabe_1

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: X:135587216..135588083(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPPYG00000020760
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: E2F6
• Ensembl ID: ENSPPYG00000012646
• Aliases: None
• Description: E2F transcription factor 6 [Source:HGNC Symbol;Acc:3120]

Sequence

>retro_pabe_1
ATGAGTCAGCAGCAGCCTGCAGGAAAGTTGACTGACCTGCCCATTAACCCGGCGGAGGAGACAGTTCGCCGCCGAGACGC
CACCAATGCGGAGTGCCCATTGCCATCAACAATAAGGATTAATTCCAAAGATGATGTACAACCTGAGTCTAAAAGAGAAA
CTGTAAATATGAAACCTCATAATAAGACATCACTGGCTTGTACAACGCGAAAATTTATAGATATTCTCAAATCGGCTCCT
GGAGGTGTTCTTAACTTAAGCCAGGTAGCAGCAAAACTGGCAGTACACAGACGAAGAATATATGACATCATCAGTGTCTT
ACAAGGAGTCAAACTAATTGAAAAAACATCTAATAACCATATTCAGTGGATTGGACCTGATTTTAATTCTGGAGCAACAC
CCGAAGAAAAGAAGCTAGAGGAGGAACTTTCCAAATTATCAGCAACAGAAGATGCCTTGGATAAGTTAATTGAAGATTGT
TCTCAGCAACTGTGTGAGTTAACAAATGACCACGAATTGGGAAAGCGAGCATATGTGACGCATGAAGACATTCACAACTT
GGAACACTTCCAGGAACAGACCATTTTTGTAGCTAAATCGCCAGTAGAAATCACACTGGAAATTCCAGTTTCTGAAGACT
CTTTCTCATTACGTATAAATAACACCGACAGACCTGTTAACGCCTATTTGCGTCTATCGAGGAAGGATTACGAAGCTAAC
TACACGTCTGAGGGTGCCGGGACTTCATCTGAGGGTGCCGGGACTTCATCTGAGAGCACTGGGACTTCATCTGAGAGCAG
ACATCCAGAACGCCCTGAAAAAGAAGAAAATCCTCAGCAAAGTGAAGAATTGCTTGACATGAGCAAC

Alignment

ORF - retro_pabe_1 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.69 %
• Parental protein coverage: 73.98 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSQQRPARKLPSLLLDPTEETVRRRCRDPINVEGLLPSKIRINLEDNVQYVSMRKALKVKRPRFDVSLVY
          MSQQ.PA.KL..L...P.EETVRRR..D..N.E..LPS.IRIN..D.VQ..S.R.....K.P....SL..
Retrocopy MSQQQPAGKLTDLPINPAEETVRRR--DATNAECPLPSTIRINSKDDVQPESKRETVNMK-PHNKTSLAC

Parental  LTRKFMDLVRSAPGGILDLNKVATKLGVRKRRVYDITNVLDGIDLVEKKSKNHIRWIGSDLSNFGAVPQQ
          .TRKF.D...SAPGG.L.L..VA.KL.V..RR.YDI..VL.G..L.EK.S.NHI.WIG.D..N.GA.P..
Retrocopy TTRKFIDILKSAPGGVLNLSQVAAKLAVHRRRIYDIISVLQGVKLIEKTSNNHIQWIGPDF-NSGATPEE

Parental  KKLQEELSDLSAMEDALDELIKDCAQQLFELTDDKENERLAY
          KKL.EELS.LSA.EDALD.LI.DC.QQL.ELT.D.E....AY
Retrocopy KKLEEELSKLSATEDALDKLIEDCSQQLCELTNDHELGKRAY

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	0.06 RPM	4.42 RPM
SRP007412_cerebellum	0.00 RPM	4.38 RPM
SRP007412_heart	0.03 RPM	3.85 RPM
SRP007412_kidney	0.00 RPM	2.75 RPM
SRP007412_liver	0.00 RPM	2.05 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Callithrix jacchus	retro_cjac_178

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000048286	1 retrocopy	retro_btau_1820,
Callithrix jacchus	ENSCJAG00000006910	1 retrocopy	retro_cjac_178,
Dasypus novemcinctus	ENSDNOG00000000258	1 retrocopy	retro_dnov_187,
Homo sapiens	ENSG00000169016	4 retrocopies	retro_hsap_2542, retro_hsap_2547, retro_hsap_2572, retro_hsap_4906,
Macropus eugenii	ENSMEUG00000007957	4 retrocopies	retro_meug_1169, retro_meug_860, retro_meug_882, retro_meug_893,
Myotis lucifugus	ENSMLUG00000003384	1 retrocopy	retro_mluc_864,
Macaca mulatta	ENSMMUG00000023225	1 retrocopy	retro_mmul_87,
Nomascus leucogenys	ENSNLEG00000014134	1 retrocopy	retro_nleu_2351,
Pongo abelii	ENSPPYG00000012646	1 retrocopy	retro_pabe_1 ,
Pongo abelii	ENSPPYG00000016269	2 retrocopies	retro_pabe_1447, retro_pabe_2137,
Pan troglodytes	ENSPTRG00000011661	2 retrocopies	retro_ptro_1484, retro_ptro_3272,
Ictidomys tridecemlineatus	ENSSTOG00000003316	1 retrocopy	retro_itri_135,