RetrogeneDB ID: retro_hsap_1526

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 15:92829057..92829539(+)
• Located in intron of: ENSG00000260661

Retrocopy information

• Ensembl ID: ENSG00000258925
• Aliases: NPM1P5, NG5-4, NPMP5
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: NPM1
• Ensembl ID: ENSG00000181163
• Aliases: NPM1, B23, NPM
• Description: nucleophosmin (nucleolar phosphoprotein B23, numatrin) [Source:HGNC Symbol;Acc:7910]

Sequence

>retro_hsap_1526
ATGGAAGATTCGATGGGCATGTATGTGGACATGAGCCCCCTGAGGCCCCAGAACTATCTTTTCGGTTGTGAACTAAAGGC
CGACAAAGATTACCACTTTAAGGTGGATAATGATGAAAATGGACACCAGTTATTTTTAAGAACAGTCAGTTTAGGGGCGG
GTGCAAAGGATGAATTGGACATTGTCGAAGAGAGGCAATGAATTACGAAGGCAGTCCAATTAAAGTAACACTGGCAACTT
TGAAAATGTCTGTACAGCCAACGGTTTCCCTTGGGGACTCTGAAATAACACCACCAGTGATCTTACGGTTGAAGTGTGGT
TCAGGGCCAGTGCATATTAGTGGACAGCACTTAGTAGCTGTGGAGGAAGACGCAGAGTCAGAAGACGAAGAGGAGGAGGA
TGTGAGACTCTTAAGTATATCTGGAAAGCGGTCTGCCACTGGAGGTGGTAGCAAGGTTCCACAGAAACAAGTAAAACTTG
CT

Alignment

ORF - retro_hsap_1526 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.36 %
• Parental protein coverage: 54.08 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MEDSMDM--DMSPLRPQNYLFGCELKADKDYHFKVDNDENEHQLSLRTVSLGAGAKDELHIVEA-EAMNY
          MEDSM.M..DMSPLRPQNYLFGCELKADKDYHFKVDNDEN.HQL.LRTVSLGAGAKDEL.IVE..EAMNY
Retrocopy MEDSMGMYVDMSPLRPQNYLFGCELKADKDYHFKVDNDENGHQLFLRTVSLGAGAKDELDIVEE<EAMNY

Parental  EGSPIKVTLATLKMSVQPTVSLGGFEITPPVVLRLKCGSGPVHISGQHLVAVEEDAESEDEEEEDVKLLS
          EGSPIKVTLATLKMSVQPTVSLG..EITPPV.LRLKCGSGPVHISGQHLVAVEEDAESEDEEEEDV.LLS
Retrocopy EGSPIKVTLATLKMSVQPTVSLGDSEITPPVILRLKCGSGPVHISGQHLVAVEEDAESEDEEEEDVRLLS

Parental  ISGKRSAPGGGSKVPQKKVKLA
          ISGKRSA.GGGSKVPQK.VKLA
Retrocopy ISGKRSATGGGSKVPQKQVKLA

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
bodymap2_adipose	0.00 RPM	332.62 RPM
bodymap2_adrenal	0.00 RPM	422.00 RPM
bodymap2_brain	0.00 RPM	165.16 RPM
bodymap2_breast	0.00 RPM	239.26 RPM
bodymap2_colon	0.00 RPM	676.89 RPM
bodymap2_heart	0.00 RPM	159.13 RPM
bodymap2_kidney	0.06 RPM	255.78 RPM
bodymap2_liver	0.00 RPM	151.05 RPM
bodymap2_lung	0.00 RPM	383.42 RPM
bodymap2_lymph_node	0.02 RPM	324.63 RPM
bodymap2_ovary	0.10 RPM	913.07 RPM
bodymap2_prostate	0.00 RPM	560.29 RPM
bodymap2_skeletal_muscle	0.00 RPM	231.70 RPM
bodymap2_testis	0.02 RPM	446.48 RPM
bodymap2_thyroid	0.02 RPM	478.22 RPM
bodymap2_white_blood_cells	0.00 RPM	368.83 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_hsap_1526 was not detected

EST

No EST(s) were mapped for retro_hsap_1526 retrocopy.

TSS

TSS No.	TSS Name	TSS expression level (Expr) in TPM range:
		no expression	0 < Expr ≤ 1	1 < Expr ≤ 5	5 < Expr ≤ 10	Expr > 10
TSS #1	TSS_48071	150 libraries	121 libraries	943 libraries	466 libraries	149 libraries

The graphical summary, for retro_hsap_1526 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1829 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)

Lab

retro_hsap_1526 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_1526 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 93 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,
Felis catus	ENSFCAG00000030268	3 retrocopies	retro_fcat_156, retro_fcat_376, retro_fcat_720,
Homo sapiens	ENSG00000107833	1 retrocopy	retro_hsap_792,
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	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,