RetrogeneDB ID: retro_ptro_1236

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 17:62085328..62085724(-)
• Located in intron of: ENSPTRG00000009511

Retrocopy information

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

Parental gene information

• Parental gene symbol: DENR
• Ensembl ID: ENSPTRG00000005584
• Aliases: None
• Description: density-regulated protein [Source:HGNC Symbol;Acc:2769]

Sequence

>retro_ptro_1236
AATGAATTTGAAAAACTTACTGTAGAAAATTCACCCAATCAAGAAGTGGAATTAGTAAGGGTCAAGGAATAGCAGGGGAA
GGGGAGAAGAAAAAACAGAAGAGAGGTGGAAGGGGTCAAATAAAACCAAAAAAGGAGACTGTACCATAAAAGGTTATTAT
AGCCAAAATTCCCAGAGCAAAGAAGAAATATGTAAAAACAGTGTGTGGCTTTGCAACTTTTGAAGTTGATCTTAAAGAAG
CACAAAGATTTTTCTGCTCAAAAATTCTCCTGTGGTACCTCAGTAACAGGGGAGGATGAAATTATTCAGGAAGACTCTAC
GGATGGCATAATTGATTTCATTCAGAAAAAACAGCCAGAGGTGGATGATGACAGCATCGAAGATCTTGAAGAAGTA

Alignment

ORF - retro_ptro_1236 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.88 %
• Parental protein coverage: 67.68 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  NEFAKLTVENSPKQE-AGISEGQGTAGEEEEKKKQKRGGRGQIKQKKKTVPQKVTIAKIPRAKKKYVTRV
          NEF.KLTVENSP.QE..GIS.GQG.AGE..EKKKQKRGGRGQIK.KK.TVP.KV.IAKIPRAKKKYV..V
Retrocopy NEFEKLTVENSPNQE<SGISKGQGIAGEG-EKKKQKRGGRGQIKPKKETVP*KVIIAKIPRAKKKYVKTV

Parental  CGLATFEIDLKEAQRFF-AQKFSCGASVTGEDEIIIQGDFTDDIIDVIQEKWPEVDDDSIEDLGEV
          CG.ATFE.DLKEAQRFF.AQKFSCG.SVTGEDE.IIQ.D.TD.IID.IQ.K.PEVDDDSIEDL.EV
Retrocopy CGFATFEVDLKEAQRFF>AQKFSCGTSVTGEDE-IIQEDSTDGIIDFIQKKQPEVDDDSIEDLEEV

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	15.60 RPM
SRP007412_cerebellum	0.00 RPM	21.22 RPM
SRP007412_heart	0.00 RPM	21.42 RPM
SRP007412_kidney	0.00 RPM	20.14 RPM
SRP007412_liver	0.00 RPM	17.55 RPM
SRP007412_testis	0.00 RPM	20.34 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1236 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1236 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1236 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1854
Gorilla gorilla	retro_ggor_2156
Callithrix jacchus	retro_cjac_2627

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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,