RetrogeneDB ID: retro_pabe_3072

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 7:73688599..73689204(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NPM1
• Ensembl ID: ENSPPYG00000016037
• Aliases: None
• Description: nucleophosmin [Source:RefSeq peptide;Acc:NP_001125077]

Sequence

>retro_pabe_3072
GAGCTAAACACTGACAAAGTTTGTCACTTTAACGTGAATAATGATGAAAAAACTACAGTTATCTTTAAGAATAGTCAGTT
TAGGGGCTGATGCATAGGATGAATCGCACATTGTTGAAGCAGAGGCAATGAATTATAAAGGCGGTCCAATTGAAATAACA
CTGGCACTTTGAAAATGTCTGTACAGCCAGTCAGTGGTTTCCCTTAGGGGCTTTAAAATACCACCACCCATGGTCTTATG
GTTGAAGTGTGGTTCACGGCCAGGGCATATTAGGGGACAGCACTTAGTAGCTGTGGAGGAAGAGGCAGAGTGAGAAGATG
AAGAGGAAGAGAATATGAAGCTCTTAAGTATACCTGGAAAGCGATCTGCCCCTAGAAATGGTAGTGAGGTTCCACAGAAG
AAAAGGAAAACATGCTGCTGATGAAGATGATAATAATAGAGACGACGAAGATGAAGATGATGATTTTAATTATGATGAAA
CTGAAAAAATATCTCCAGTGAAGAAGTCTATATGAGATACTCCAGCCAAAAATGCACAAACATCAAACCAGAAGGAAAAA
GACTCAACACCAGCAACACCAACACCAGAAGGTCAAGAATCATTC

Alignment

ORF - retro_pabe_3072 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.24 %
• Parental protein coverage: 75.55 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  ELKADKDYHFKVDNDENEH-QLSLRTVSLGAGAKDELHIVEAEAMNYEGSPIKVTLATLK-MSVQPTVSL
          EL..DK..HF.V.N......QLSLR.VSLGA.A.DE.HIVEAEAMNY.G.PI..TLA..K....Q..VSL
Retrocopy ELNTDKVCHFNV-NNDEKT>QLSLRIVSLGADA*DESHIVEAEAMNYKGGPIEITLAL*KCLYSQSVVSL

Parental  GGFEITPPVVLRLKCGSGPVHISGQHLVAVEEDAESEDEEEEDVKLLSISGKRSAPGGGSKVPQKKVKL-
          .GF.I.PP.VL.LKCGS.P.HI.GQHLVAVEE.AE.EDEEEE..KLLSI.GKRSAP..GS.VPQKK.K..
Retrocopy RGFKIPPPMVLWLKCGSRPGHIRGQHLVAVEEEAE*EDEEEENMKLLSIPGKRSAPRNGSEVPQKKRKT>

Parental  AADEDDDDDDEDDDDEDDDDDDFDDEEAEEKAPVKKSIRDTPAKNAQKSNQNGKDSKPSSTPRSKGQESF
          AADE..DD...DD.DEDDD...F...E.E...PVKKSI.DTPAKNAQ.SNQ..KDS.P..TP...GQESF
Retrocopy AADE--DDNNRDDEDEDDD---FNYDETEKISPVKKSI*DTPAKNAQTSNQKEKDSTP-ATPTPEGQESF

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	35.28 RPM
SRP007412_cerebellum	0.00 RPM	26.27 RPM
SRP007412_heart	0.00 RPM	46.66 RPM
SRP007412_kidney	0.00 RPM	60.76 RPM
SRP007412_liver	0.00 RPM	48.96 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3072 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3072 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3072 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3817

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 97 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000003910	1 retrocopy	retro_amel_983,
Bos taurus	ENSBTAG00000015316	2 retrocopies	retro_btau_538, retro_btau_56,
Canis familiaris	ENSCAFG00000016912	3 retrocopies	retro_cfam_22, retro_cfam_286, retro_cfam_900,
Callithrix jacchus	ENSCJAG00000019334	13 retrocopies	retro_cjac_1559, retro_cjac_1682, retro_cjac_1696, retro_cjac_1733, retro_cjac_2075, retro_cjac_2351, retro_cjac_2368, retro_cjac_2533, retro_cjac_2605, retro_cjac_3270, retro_cjac_3416, retro_cjac_4117, retro_cjac_838,
Equus caballus	ENSECAG00000021950	4 retrocopies	retro_ecab_1016, retro_ecab_1100, retro_ecab_393, retro_ecab_544,
Felis catus	ENSFCAG00000030268	3 retrocopies	retro_fcat_156, retro_fcat_376, retro_fcat_720,
Homo sapiens	ENSG00000181163	30 retrocopies	retro_hsap_1275, retro_hsap_129, retro_hsap_1526, retro_hsap_1580, retro_hsap_1593, retro_hsap_1621, retro_hsap_2226, retro_hsap_2375, retro_hsap_2478, retro_hsap_2856, retro_hsap_2862, retro_hsap_3355, retro_hsap_3460, retro_hsap_3609, retro_hsap_3636, retro_hsap_3718, retro_hsap_3776, retro_hsap_3808, retro_hsap_3817, retro_hsap_3822, retro_hsap_3962, retro_hsap_4666, retro_hsap_4753, retro_hsap_4785, retro_hsap_614, retro_hsap_638, retro_hsap_690, retro_hsap_717, retro_hsap_785, retro_hsap_961,
Gorilla gorilla	ENSGGOG00000007220	12 retrocopies	retro_ggor_1543, retro_ggor_1660, retro_ggor_1976, retro_ggor_2453, retro_ggor_2454, retro_ggor_2539, retro_ggor_2559, retro_ggor_2571, retro_ggor_2681, retro_ggor_2959, retro_ggor_560, retro_ggor_591,
Macaca mulatta	ENSMMUG00000015781	1 retrocopy	retro_mmul_203,
Mus musculus	ENSMUSG00000057113	5 retrocopies	retro_mmus_1301, retro_mmus_1798, retro_mmus_3131, retro_mmus_539, retro_mmus_550,
Otolemur garnettii	ENSOGAG00000013616	14 retrocopies	retro_ogar_1554, retro_ogar_1623, retro_ogar_1671, retro_ogar_1776, retro_ogar_2015, retro_ogar_2168, retro_ogar_2207, retro_ogar_2461, retro_ogar_2605, retro_ogar_2832, retro_ogar_3037, retro_ogar_536, retro_ogar_595, retro_ogar_614,
Pongo abelii	ENSPPYG00000002589	1 retrocopy	retro_pabe_706,
Pongo abelii	ENSPPYG00000016037	7 retrocopies	retro_pabe_2405, retro_pabe_3072 , retro_pabe_3261, retro_pabe_3627, retro_pabe_3699, retro_pabe_486, retro_pabe_532,
Pteropus vampyrus	ENSPVAG00000002211	1 retrocopy	retro_pvam_851,