RetrogeneDB ID: retro_pabe_3509

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 9:124203750..124203978(-)
• Located in intron of: ENSPPYG00000019619

Retrocopy information

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

Parental gene information

• Parental gene symbol: DENR
• Ensembl ID: ENSPPYG00000005073
• Aliases: None
• Description: density-regulated protein [Source:HGNC Symbol;Acc:2769]

Sequence

>retro_pabe_3509
ATGGCTGCAGACATTTCTGAATCCAATGGGGCCAAGTGCAAAGGAGACCTACGGAACAGGGCCGAGTTAGATGCTGATTG
CCCACTGTGAGTCCTTCATTGTAGAGTCTGTTCATTACCAACAGGCTACTGTAAATATACGCCTAATGTTGCTAAATGTA
GACAATGGTTAGAGAAGAATTTTCCAAATGAATTTGCAAAACTTACTGTAGAAAATTTACCCAAACAG

Alignment

ORF - retro_pabe_3509 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.92 %
• Parental protein coverage: 50.33 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAADISESSGADCKGDPRNSAKLDADYPLRVLYCGGKCSFPTWYCEYMPDVAKCRQWLEKNFPNEFAKLT
          MAADISES.GA.CKGD.RN.A.LDAD.PL.VL.C...CS.PT.YC.Y.P.VAKCRQWLEKNFPNEFAKLT
Retrocopy MAADISESNGAKCKGDLRNRAELDADCPL*VLHCR-VCSLPTGYCKYTPNVAKCRQWLEKNFPNEFAKLT

Parental  VENSPKQ
          VEN.PKQ
Retrocopy VENLPKQ

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	10.06 RPM
SRP007412_cerebellum	0.00 RPM	4.26 RPM
SRP007412_heart	0.00 RPM	3.49 RPM
SRP007412_kidney	0.00 RPM	4.61 RPM
SRP007412_liver	0.00 RPM	3.49 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3509 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3509 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3509 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 30 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000016012	1 retrocopy	retro_acar_71,
Bos taurus	ENSBTAG00000032433	1 retrocopy	retro_btau_110,
Callithrix jacchus	ENSCJAG00000020488	4 retrocopies	retro_cjac_1665, retro_cjac_2303, retro_cjac_2377, retro_cjac_2627,
Homo sapiens	ENSG00000139726	4 retrocopies	retro_hsap_1028, retro_hsap_1854, retro_hsap_2471, retro_hsap_4313,
Gorilla gorilla	ENSGGOG00000005562	3 retrocopies	retro_ggor_2156, retro_ggor_2883, retro_ggor_813,
Nomascus leucogenys	ENSNLEG00000002186	3 retrocopies	retro_nleu_1465, retro_nleu_2136, retro_nleu_906,
Oryctolagus cuniculus	ENSOCUG00000008150	2 retrocopies	retro_ocun_1325, retro_ocun_1524,
Ochotona princeps	ENSOPRG00000015974	5 retrocopies	retro_opri_1000, retro_opri_1139, retro_opri_1147, retro_opri_133, retro_opri_183,
Pongo abelii	ENSPPYG00000005073	3 retrocopies	retro_pabe_1821, retro_pabe_3509 , retro_pabe_861,
Pan troglodytes	ENSPTRG00000005584	4 retrocopies	retro_ptro_1236, retro_ptro_2921, retro_ptro_2955, retro_ptro_703,