RetrogeneDB ID: retro_hsap_1441

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 14:74006027..74006427(-)
• Located in intron of: ENSG00000187105

Retrocopy information

• Ensembl ID: ENSG00000258408
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: NT5C
• Ensembl ID: ENSG00000125458
• Aliases: NT5C, DNT, DNT1, HEL74, P5N2, PN-I, PN-II, UMPH2, cdN, dNT-1
• Description: 5', 3'-nucleotidase, cytosolic [Source:HGNC Symbol;Acc:17144]

Sequence

>retro_hsap_1441
GGCATCCTGTGGGGCTTCAGCCGCCGCTTCTCAGGGAGCTGCATGTGACACTGCAGCAGCACCGCAGCTTCCTGGTCTGG
AAGCAGTACCTCACCCTGCTGCCGGACCTGGTGGATAAAGTGGCCCATGGGTGTGAAGCCCTAGGCTTTTCCCTAGTCTT
GAAGCCCAACCCCAGAGGGCCTTGCAAGAGATGAAGCACATGCAAAACACCGAGGTCTTCACACTGCACCAGCCCCTGCC
AAAGTATGACCACTGTGTGGGTGAGAAGCACCGCTGGGTAGAGCAGCACCTGGAGTCCCAGCTTGTGGAGTGAATTATCC
TGACAATGGACAAGACCGTGGTCTTTGGGGACTTGCTCACTGATGACAAGGATACCATTCGAGGCCAAGAGGAGAGGCCA

Alignment

ORF - retro_hsap_1441 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.14 %
• Parental protein coverage: 67.66 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  GLLRGFRRRFP-EEPHVPLEQRRGFLAREQYRALRPDLADKVASVYEAPGF-FLDLEPIPGALDAVREMN
          G.L.GF.RRF...E.HV.L.Q.R.FL...QY..L.PDL.DKVA...EA.GF.F..LE..P....A..EM.
Retrocopy GILWGFSRRFS<RELHVTLQQHRSFLVWKQYLTLLPDLVDKVAHGCEALGF<FPSLEAQPQR--ALQEMK

Parental  DLPDTQVFICTSPLLKYHHCVGEKYRWVEQHLGPQFVERIILTRDKTVVLGDLLIDDKDTVRGQEETP
          ....T.VF....PL.KY.HCVGEK.RWVEQHL..Q.VE.IILT.DKTVV.GDLL.DDKDT.RGQEE.P
Retrocopy HMQNTEVFTLHQPLPKYDHCVGEKHRWVEQHLESQLVE*IILTMDKTVVFGDLLTDDKDTIRGQEERP

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	0.04 RPM	10.04 RPM
bodymap2_adrenal	0.02 RPM	15.74 RPM
bodymap2_brain	0.00 RPM	4.78 RPM
bodymap2_breast	0.00 RPM	7.76 RPM
bodymap2_colon	0.00 RPM	8.04 RPM
bodymap2_heart	0.00 RPM	3.34 RPM
bodymap2_kidney	0.06 RPM	10.11 RPM
bodymap2_liver	0.00 RPM	3.91 RPM
bodymap2_lung	0.00 RPM	9.35 RPM
bodymap2_lymph_node	0.00 RPM	14.03 RPM
bodymap2_ovary	0.06 RPM	9.37 RPM
bodymap2_prostate	0.00 RPM	15.74 RPM
bodymap2_skeletal_muscle	0.00 RPM	7.26 RPM
bodymap2_testis	0.06 RPM	7.64 RPM
bodymap2_thyroid	0.02 RPM	13.69 RPM
bodymap2_white_blood_cells	0.00 RPM	6.28 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_1441 was not detected

EST

No EST(s) were mapped for retro_hsap_1441 retrocopy.

TSS

No TSS is located nearby retro_hsap_1441 retrocopy 5' end.

Lab

retro_hsap_1441 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_1441 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009175	1 retrocopy	retro_amel_1684,
Callithrix jacchus	ENSCJAG00000014578	1 retrocopy	retro_cjac_810,
Felis catus	ENSFCAG00000031408	2 retrocopies	retro_fcat_1016, retro_fcat_606,
Homo sapiens	ENSG00000125458	2 retrocopies	retro_hsap_1441 , retro_hsap_1442,
Gorilla gorilla	ENSGGOG00000004740	2 retrocopies	retro_ggor_1061, retro_ggor_1109,
Microcebus murinus	ENSMICG00000017488	1 retrocopy	retro_mmur_1088,
Mustela putorius furo	ENSMPUG00000013985	1 retrocopy	retro_mputfur_1352,
Nomascus leucogenys	ENSNLEG00000000601	2 retrocopies	retro_nleu_1083, retro_nleu_1416,
Pongo abelii	ENSPPYG00000008619	1 retrocopy	retro_pabe_1195,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.00 RPM
CEU_NA11843	0.00 RPM
CEU_NA11930	0.00 RPM
CEU_NA12004	0.00 RPM
CEU_NA12400	0.00 RPM
CEU_NA12751	0.00 RPM
CEU_NA12760	0.00 RPM
CEU_NA12827	0.00 RPM
CEU_NA12872	0.00 RPM
CEU_NA12873	0.00 RPM
FIN_HG00183	0.00 RPM
FIN_HG00277	0.00 RPM
FIN_HG00315	0.03 RPM
FIN_HG00321	0.00 RPM
FIN_HG00328	0.00 RPM
FIN_HG00338	0.00 RPM
FIN_HG00349	0.00 RPM
FIN_HG00375	0.00 RPM
FIN_HG00377	0.00 RPM
FIN_HG00378	0.00 RPM
GBR_HG00099	0.00 RPM
GBR_HG00111	0.00 RPM
GBR_HG00114	0.00 RPM
GBR_HG00119	0.00 RPM
GBR_HG00131	0.00 RPM
GBR_HG00133	0.02 RPM
GBR_HG00134	0.00 RPM
GBR_HG00137	0.00 RPM
GBR_HG00142	0.00 RPM
GBR_HG00143	0.00 RPM
TSI_NA20512	0.00 RPM
TSI_NA20513	0.00 RPM
TSI_NA20518	0.00 RPM
TSI_NA20532	0.03 RPM
TSI_NA20538	0.00 RPM
TSI_NA20756	0.00 RPM
TSI_NA20765	0.00 RPM
TSI_NA20771	0.00 RPM
TSI_NA20786	0.00 RPM
TSI_NA20798	0.00 RPM
YRI_NA18870	0.00 RPM
YRI_NA18907	0.00 RPM
YRI_NA18916	0.00 RPM
YRI_NA19093	0.00 RPM
YRI_NA19099	0.00 RPM
YRI_NA19114	0.00 RPM
YRI_NA19118	0.00 RPM
YRI_NA19213	0.02 RPM
YRI_NA19214	0.00 RPM
YRI_NA19223	0.00 RPM

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Indel association:

The presence of retro_hsap_1441 across human populations is associated with 1 indel. The percentage values indicate the frequencies of retro_hsap_1441 presence in various populations. Based on Kabza et al. 2015 (PubMed).

#	Indel coordinates	AFR, African			AMR, Ad Mixed American			EUR, European					EAS, East Asian
		ASW	YRI	LWK	MXL	PUR	CLM	CEU	IBS	GBR	FIN	TSI	JPT	CHB	CHS
1.	14:73997050..74024400	62.3	71.59	67.01	56.82	56.36	46.67	47.06	60.71	58.43	41.4	55.1	14.04	15.46	20.5

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Indel #1, located at the genomic coordinates 14:73997050..74024400.