RetrogeneDB ID: retro_pabe_2650

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 5:76403905..76404125(+)
• Located in intron of: ENSPPYG00000015566

Retrocopy information

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

Parental gene information

• Parental gene symbol: PDCD5
• Ensembl ID: ENSPPYG00000009817
• Aliases: None
• Description: programmed cell death protein 5 [Source:RefSeq peptide;Acc:NP_001125439]

Sequence

>retro_pabe_2650
CGGCCCAGGTAAAGTAACTTAGCACTTGTAAAGACTAAAAAAACTAAAGCAATAGAGAATTACCTTATACAGATGACAAG
ATATGGACAACTAAGTGAGAAGGTATCAGAACTAGGTTTAATAGAAATCCTTTAAAAAAGTAAGCCGACAAACAGAAAAG
ACAACAACAGTGAAATTCAACAGAAGAAAAGTAATGGACTCTGATGAAGATAAGGATTAT

Alignment

ORF - retro_pabe_2650 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.14 %
• Parental protein coverage: 58.4 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RARLSNLALVKPEKTKAVENYLIQMARYGQLSEKVSEQGLIEIL-KKVSQQTDKTTTVKFNRRKVMDSDE
          R.R.SNLALVK..KTKA.ENYLIQM.RYGQLSEKVSE.GLIEIL.KKVS.QT.KTTTVKFNRRKVMDSDE
Retrocopy RPR*SNLALVKTKKTKAIENYLIQMTRYGQLSEKVSELGLIEIL>KKVSRQTEKTTTVKFNRRKVMDSDE

Parental  DDDY
          D.DY
Retrocopy DKDY

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	24.77 RPM
SRP007412_cerebellum	0.00 RPM	15.56 RPM
SRP007412_heart	0.03 RPM	20.50 RPM
SRP007412_kidney	0.00 RPM	23.60 RPM
SRP007412_liver	0.00 RPM	18.33 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2650 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2650 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2650 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3194
Pan troglodytes	retro_ptro_2250
Gorilla gorilla	retro_ggor_1334
Macaca mulatta	retro_mmul_2015

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Parental genes homology:

Parental genes homology involve 25 parental genes, and 44 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000007555	3 retrocopies	retro_cfam_1659, retro_cfam_535, retro_cfam_838,
Callithrix jacchus	ENSCJAG00000018410	6 retrocopies	retro_cjac_1020, retro_cjac_1959, retro_cjac_2855, retro_cjac_2937, retro_cjac_3841, retro_cjac_3942,
Cavia porcellus	ENSCPOG00000000159	2 retrocopies	retro_cpor_1024, retro_cpor_816,
Dasypus novemcinctus	ENSDNOG00000004010	3 retrocopies	retro_dnov_283, retro_dnov_408, retro_dnov_899,
Equus caballus	ENSECAG00000019406	1 retrocopy	retro_ecab_1007,
Erinaceus europaeus	ENSEEUG00000001182	1 retrocopy	retro_eeur_276,
Homo sapiens	ENSG00000105185	1 retrocopy	retro_hsap_3194,
Gorilla gorilla	ENSGGOG00000006169	1 retrocopy	retro_ggor_1334,
Macropus eugenii	ENSMEUG00000007777	1 retrocopy	retro_meug_1855,
Myotis lucifugus	ENSMLUG00000007141	1 retrocopy	retro_mluc_1497,
Macaca mulatta	ENSMMUG00000015395	1 retrocopy	retro_mmul_2015,
Monodelphis domestica	ENSMODG00000012326	4 retrocopies	retro_mdom_1012, retro_mdom_1693, retro_mdom_411, retro_mdom_893,
Mus musculus	ENSMUSG00000030417	1 retrocopy	retro_mmus_519,
Oryctolagus cuniculus	ENSOCUG00000013220	1 retrocopy	retro_ocun_828,
Otolemur garnettii	ENSOGAG00000025274	3 retrocopies	retro_ogar_3143, retro_ogar_479, retro_ogar_592,
Ochotona princeps	ENSOPRG00000016642	1 retrocopy	retro_opri_604,
Pongo abelii	ENSPPYG00000009817	1 retrocopy	retro_pabe_2650 ,
Pan troglodytes	ENSPTRG00000010791	1 retrocopy	retro_ptro_2250,
Rattus norvegicus	ENSRNOG00000013250	1 retrocopy	retro_rnor_167,
Rattus norvegicus	ENSRNOG00000050827	1 retrocopy	retro_rnor_1116,
Sarcophilus harrisii	ENSSHAG00000006705	1 retrocopy	retro_shar_354,
Sus scrofa	ENSSSCG00000002860	2 retrocopies	retro_sscr_1098, retro_sscr_278,
Ictidomys tridecemlineatus	ENSSTOG00000025794	3 retrocopies	retro_itri_1151, retro_itri_1645, retro_itri_563,
Tursiops truncatus	ENSTTRG00000003999	2 retrocopies	retro_ttru_1291, retro_ttru_1472,
Vicugna pacos	ENSVPAG00000012046	1 retrocopy	retro_vpac_383,