RetrogeneDB ID: retro_hsap_3355

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 5:93018968..93019423(-)
• Located in intron of: ENSG00000113391

Retrocopy information

• Ensembl ID: ENSG00000249353
• Aliases: None
• 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_3355
ATGGAAGATTCGATGGACATGGACATGAGCCCCCTGAGGCCCCAGAACTATCTTTTCGGTTGTGAACTAAAGGCCGACAA
AGATGATCACTTTAAGGTGGATAATGATGAAAATGAGCGCCAGTTATCCTTAAGAACGGCCAGTTTAGGGCTGGTGCAAA
GGATGAACTGCACATTGTTGAAGCAGAGGCCATGAATTACGAAGGCAGTCCAATTAAAGTAACACTGGCAACTTTGAAAA
TGTCTGTACAGCCAACAGTTTCCCTTGGGGGCTTTGAAATAACACCACCAGTGGTCTTAAGGTTGAAGTGTGGTTCAGGG
CCAGTGCATATTAGTGGACAGCACTTAGTAGCTGTGGAGGAAGATGCAGAGTCAGAAGATGAAGAGGAGGAGGATGTGAA
ACTCTGAAGTATATCTGGAAAGCGGTCTGCCCCTGGAGGTGGTAGCAAGGTTCCA

Alignment

ORF - retro_hsap_3355 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.73 %
• Parental protein coverage: 58.69 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MEDSMDMDMSPLRPQNYLFGCELKADKDYHFKVDNDENEHQLSLRTVSLG-AGAKDELHIVEAEAMNYEG
          MEDSMDMDMSPLRPQNYLFGCELKADKD.HFKVDNDENE.QLSLRT.SLG.AGAKDELHIVEAEAMNYEG
Retrocopy MEDSMDMDMSPLRPQNYLFGCELKADKDDHFKVDNDENERQLSLRTASLG<AGAKDELHIVEAEAMNYEG

Parental  SPIKVTLATLKMSVQPTVSLGGFEITPPVVLRLKCGSGPVHISGQHLVAVEEDAESEDEEEEDVKLLSIS
          SPIKVTLATLKMSVQPTVSLGGFEITPPVVLRLKCGSGPVHISGQHLVAVEEDAESEDEEEEDVKL.SIS
Retrocopy SPIKVTLATLKMSVQPTVSLGGFEITPPVVLRLKCGSGPVHISGQHLVAVEEDAESEDEEEEDVKL*SIS

Parental  GKRSAPGGGSKVP
          GKRSAPGGGSKVP
Retrocopy GKRSAPGGGSKVP

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	0.74 RPM	332.62 RPM
bodymap2_adrenal	1.06 RPM	422.00 RPM
bodymap2_brain	0.59 RPM	165.16 RPM
bodymap2_breast	0.47 RPM	239.26 RPM
bodymap2_colon	1.37 RPM	676.89 RPM
bodymap2_heart	0.24 RPM	159.13 RPM
bodymap2_kidney	0.60 RPM	255.78 RPM
bodymap2_liver	0.09 RPM	151.05 RPM
bodymap2_lung	0.81 RPM	383.42 RPM
bodymap2_lymph_node	0.79 RPM	324.63 RPM
bodymap2_ovary	1.93 RPM	913.07 RPM
bodymap2_prostate	1.20 RPM	560.29 RPM
bodymap2_skeletal_muscle	0.56 RPM	231.70 RPM
bodymap2_testis	0.89 RPM	446.48 RPM
bodymap2_thyroid	0.55 RPM	478.22 RPM
bodymap2_white_blood_cells	0.81 RPM	368.83 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_3355 was not detected

EST

No EST(s) were mapped for retro_hsap_3355 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_156754	342 libraries	431 libraries	973 libraries	69 libraries	14 libraries

The graphical summary, for retro_hsap_3355 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_3355 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_3355 has 0 orthologous retrocopies within eutheria group .

---

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,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	4.88 RPM
CEU_NA11843	5.80 RPM
CEU_NA11930	6.75 RPM
CEU_NA12004	4.60 RPM
CEU_NA12400	4.88 RPM
CEU_NA12751	3.50 RPM
CEU_NA12760	5.88 RPM
CEU_NA12827	6.08 RPM
CEU_NA12872	4.82 RPM
CEU_NA12873	5.55 RPM
FIN_HG00183	6.12 RPM
FIN_HG00277	6.36 RPM
FIN_HG00315	5.02 RPM
FIN_HG00321	4.68 RPM
FIN_HG00328	4.28 RPM
FIN_HG00338	4.73 RPM
FIN_HG00349	9.53 RPM
FIN_HG00375	5.70 RPM
FIN_HG00377	5.95 RPM
FIN_HG00378	5.21 RPM
GBR_HG00099	5.52 RPM
GBR_HG00111	4.54 RPM
GBR_HG00114	4.23 RPM
GBR_HG00119	4.48 RPM
GBR_HG00131	10.66 RPM
GBR_HG00133	3.76 RPM
GBR_HG00134	3.54 RPM
GBR_HG00137	3.60 RPM
GBR_HG00142	4.95 RPM
GBR_HG00143	4.95 RPM
TSI_NA20512	4.24 RPM
TSI_NA20513	5.78 RPM
TSI_NA20518	12.35 RPM
TSI_NA20532	6.67 RPM
TSI_NA20538	5.30 RPM
TSI_NA20756	6.46 RPM
TSI_NA20765	4.48 RPM
TSI_NA20771	5.73 RPM
TSI_NA20786	2.96 RPM
TSI_NA20798	4.24 RPM
YRI_NA18870	5.18 RPM
YRI_NA18907	3.92 RPM
YRI_NA18916	4.06 RPM
YRI_NA19093	2.39 RPM
YRI_NA19099	4.10 RPM
YRI_NA19114	4.27 RPM
YRI_NA19118	4.14 RPM
YRI_NA19213	3.66 RPM
YRI_NA19214	3.71 RPM
YRI_NA19223	3.52 RPM

---

Indel association:

No indels were associated with its genomic coordinates. Based on Kabza et al. 2015 (PubMed).