RetrogeneDB ID: retro_hsap_3580

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 6:36059768..36060134(-)
• Located in intron of: ENSG00000112062

Retrocopy information

• Ensembl ID: ENSG00000237719
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: NUDT5
• Ensembl ID: ENSG00000165609
• Aliases: NUDT5, YSA1, YSA1H, YSAH1, hYSAH1
• Description: nudix (nucleoside diphosphate linked moiety X)-type motif 5 [Source:HGNC Symbol;Acc:8052]

Sequence

>retro_hsap_3580
CTCATAGAAGATGGTGAAACCCCAGGAGCAGCTGCTCTTTGGGAGCTTGAGGAAGAAACTGGCTACAAAGGGGACGCTGC
TGAATGTTCTCCAGTGGTCTATATGGACCCAGGTTTGTCAAACTGTACCACACACATCGTGACAGTAATCATTAACGGAG
ATGACGCAGAAAATGTAAGGCCCAAGCCAAAGCCAGGGGATGGAGAATTTGTGGAAGTCATTTCGTTACCCAAGAATGAC
CTGCTGCAGGGACTCGATGCTCTCGTAGCTGAAAAACATCTTACAGTGGATGCCAAAGTCTATTCCCATGCTCTAGCACT
GAAACATGCAAATGTGAAGCCATCTGAAGTGCCCGTCCTGAAATTT

Alignment

ORF - retro_hsap_3580 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.89 %
• Parental protein coverage: 55.71 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LIDDGETPEAAALRELEEETGYKGDIAECSPAVCMDPGLSNCTIHIVTVTINGDDAENARPKPKPGDGEF
          LI.DGETP.AAAL.ELEEETGYKGD.AECSP.V.MDPGLSNCT.HIVTV.INGDDAEN.RPKPKPGDGEF
Retrocopy LIEDGETPGAAALWELEEETGYKGDAAECSPVVYMDPGLSNCTTHIVTVIINGDDAENVRPKPKPGDGEF

Parental  VEVISLPKNDLLQRLDALVAEEHLTVDARVYSYALALKHANAKPFEVPFLKF
          VEVISLPKNDLLQ.LDALVAE.HLTVDA.VYS.ALALKHAN.KP.EVP.LKF
Retrocopy VEVISLPKNDLLQGLDALVAEKHLTVDAKVYSHALALKHANVKPSEVPVLKF

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	0.20 RPM	33.69 RPM
bodymap2_adrenal	0.76 RPM	37.83 RPM
bodymap2_brain	0.30 RPM	20.16 RPM
bodymap2_breast	0.08 RPM	38.17 RPM
bodymap2_colon	0.00 RPM	24.46 RPM
bodymap2_heart	0.07 RPM	7.92 RPM
bodymap2_kidney	0.00 RPM	54.39 RPM
bodymap2_liver	0.00 RPM	73.70 RPM
bodymap2_lung	0.00 RPM	25.23 RPM
bodymap2_lymph_node	0.20 RPM	45.34 RPM
bodymap2_ovary	0.13 RPM	36.24 RPM
bodymap2_prostate	0.00 RPM	28.68 RPM
bodymap2_skeletal_muscle	0.00 RPM	3.66 RPM
bodymap2_testis	0.00 RPM	29.51 RPM
bodymap2_thyroid	0.70 RPM	32.75 RPM
bodymap2_white_blood_cells	0.06 RPM	46.11 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_3580 was not detected

EST

No EST(s) were mapped for retro_hsap_3580 retrocopy.

TSS

No TSS is located nearby retro_hsap_3580 retrocopy 5' end.

Lab

retro_hsap_3580 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_3580 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_2427
Gorilla gorilla	retro_ggor_2415
Pongo abelii	retro_pabe_2949
Macaca mulatta	retro_mmul_1828

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000019509	2 retrocopies	retro_btau_1326, retro_btau_1438,
Canis familiaris	ENSCAFG00000004794	2 retrocopies	retro_cfam_435, retro_cfam_612,
Equus caballus	ENSECAG00000023658	1 retrocopy	retro_ecab_647,
Echinops telfairi	ENSETEG00000006403	1 retrocopy	retro_etel_946,
Felis catus	ENSFCAG00000025093	1 retrocopy	retro_fcat_350,
Homo sapiens	ENSG00000165609	1 retrocopy	retro_hsap_3580 ,
Gorilla gorilla	ENSGGOG00000006325	1 retrocopy	retro_ggor_2415,
Loxodonta africana	ENSLAFG00000012052	1 retrocopy	retro_lafr_226,
Myotis lucifugus	ENSMLUG00000010453	2 retrocopies	retro_mluc_1263, retro_mluc_2073,
Macaca mulatta	ENSMMUG00000017141	1 retrocopy	retro_mmul_1828,
Nomascus leucogenys	ENSNLEG00000012298	1 retrocopy	retro_nleu_2838,
Oryctolagus cuniculus	ENSOCUG00000009308	1 retrocopy	retro_ocun_862,
Otolemur garnettii	ENSOGAG00000005816	2 retrocopies	retro_ogar_2071, retro_ogar_2988,
Pongo abelii	ENSPPYG00000002091	2 retrocopies	retro_pabe_2949, retro_pabe_3040,
Pan troglodytes	ENSPTRG00000002294	1 retrocopy	retro_ptro_2427,
Rattus norvegicus	ENSRNOG00000017741	1 retrocopy	retro_rnor_1672,
Sus scrofa	ENSSSCG00000011113	1 retrocopy	retro_sscr_143,
Tursiops truncatus	ENSTTRG00000007394	2 retrocopies	retro_ttru_209, retro_ttru_495,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.19 RPM
CEU_NA11843	0.03 RPM
CEU_NA11930	0.46 RPM
CEU_NA12004	0.04 RPM
CEU_NA12400	0.11 RPM
CEU_NA12751	0.15 RPM
CEU_NA12760	0.18 RPM
CEU_NA12827	0.09 RPM
CEU_NA12872	0.05 RPM
CEU_NA12873	0.22 RPM
FIN_HG00183	0.22 RPM
FIN_HG00277	0.18 RPM
FIN_HG00315	0.11 RPM
FIN_HG00321	0.15 RPM
FIN_HG00328	0.19 RPM
FIN_HG00338	0.04 RPM
FIN_HG00349	0.06 RPM
FIN_HG00375	0.05 RPM
FIN_HG00377	0.05 RPM
FIN_HG00378	0.04 RPM
GBR_HG00099	0.12 RPM
GBR_HG00111	0.09 RPM
GBR_HG00114	0.18 RPM
GBR_HG00119	0.22 RPM
GBR_HG00131	0.57 RPM
GBR_HG00133	0.24 RPM
GBR_HG00134	0.24 RPM
GBR_HG00137	0.22 RPM
GBR_HG00142	0.17 RPM
GBR_HG00143	0.03 RPM
TSI_NA20512	0.08 RPM
TSI_NA20513	0.27 RPM
TSI_NA20518	0.06 RPM
TSI_NA20532	0.27 RPM
TSI_NA20538	0.05 RPM
TSI_NA20756	0.03 RPM
TSI_NA20765	0.48 RPM
TSI_NA20771	0.20 RPM
TSI_NA20786	0.05 RPM
TSI_NA20798	0.19 RPM
YRI_NA18870	0.10 RPM
YRI_NA18907	0.03 RPM
YRI_NA18916	0.11 RPM
YRI_NA19093	0.00 RPM
YRI_NA19099	0.00 RPM
YRI_NA19114	0.10 RPM
YRI_NA19118	0.04 RPM
YRI_NA19213	0.12 RPM
YRI_NA19214	0.15 RPM
YRI_NA19223	0.24 RPM

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Indel association:

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