RetrogeneDB ID: retro_hsap_379

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 1:47131581..47131921(-)
• Located in intron of: ENSG00000123472

Retrocopy information

• Ensembl ID: ENSG00000233647
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: NENF
• Ensembl ID: ENSG00000117691
• Aliases: NENF, CIR2, SCIRP10, SPUF
• Description: neudesin neurotrophic factor [Source:HGNC Symbol;Acc:30384]

Sequence

>retro_hsap_379
GAAGAAAAACATCCCATCTACATGACAGTGAAGGGAGTGGTGTTTTATGTCACCTCCAGAAAGGAATTTTATGGAAGAAG
GGGCCCCCTATAATGCATTGACCAGGAAAGTCCACCAGAGGGATAGCCAAGATGTCCCTGGGTCCTCCAGACCTCACCCA
TGAAACTCTGGGTCTCATGGCCAAAGAGCTGGAATCCCTGGATGATATCTTCACCAAAGTGTACAAAACCAAATATCCCA
TGGTTAGCTACACAGTCTGAAGAATTCTTAATAGGGACAGCACCCCAGCCTGGACTTCAAACCTGAAGACCAACCCCATT
TTGACATAAACAATGTGTTC

Alignment

ORF - retro_hsap_379 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.5 %
• Parental protein coverage: 66.28 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  EEDQPIYLAVKGVVFDVTSGKEFYGR-GAPYNALT-GKDSTRGVAKMSLDPADLTHDTTGLTAKELEALD
          EE..PIY..VKGVVF.VTS.KEFYGR.GAPYNALT.GK.STRG.AKMSL.P.DLTH.T.GL.AKELE.LD
Retrocopy EEKHPIYMTVKGVVFYVTSRKEFYGR>GAPYNALT>GK-STRGIAKMSLGPPDLTHETLGLMAKELESLD

Parental  EVFTKVYKAKYPIVGYTARRILNEDGS-PNLDFKPEDQPHFDIKDEF
          ..FTKVYK.KYP.V.YT..RILN.D...P.LDFKPEDQPHFDI...F
Retrocopy DIFTKVYKTKYPMVSYTV*RILNRDST<PSLDFKPEDQPHFDINNVF

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	25.01 RPM
bodymap2_adrenal	0.04 RPM	26.16 RPM
bodymap2_brain	0.21 RPM	28.69 RPM
bodymap2_breast	0.10 RPM	26.77 RPM
bodymap2_colon	0.06 RPM	32.35 RPM
bodymap2_heart	0.00 RPM	34.04 RPM
bodymap2_kidney	0.04 RPM	25.91 RPM
bodymap2_liver	0.00 RPM	17.19 RPM
bodymap2_lung	0.00 RPM	48.29 RPM
bodymap2_lymph_node	0.00 RPM	28.67 RPM
bodymap2_ovary	0.00 RPM	35.43 RPM
bodymap2_prostate	0.00 RPM	49.86 RPM
bodymap2_skeletal_muscle	0.00 RPM	32.37 RPM
bodymap2_testis	0.04 RPM	11.14 RPM
bodymap2_thyroid	0.00 RPM	23.86 RPM
bodymap2_white_blood_cells	0.08 RPM	12.44 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_379 was not detected

EST

No EST(s) were mapped for retro_hsap_379 retrocopy.

TSS

No TSS is located nearby retro_hsap_379 retrocopy 5' end.

Lab

retro_hsap_379 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_379 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_295
Pongo abelii	retro_pabe_328
Macaca mulatta	retro_mmul_490
Bos taurus	retro_btau_1238

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001341	1 retrocopy	retro_amel_836,
Bos taurus	ENSBTAG00000000759	1 retrocopy	retro_btau_1238,
Dasypus novemcinctus	ENSDNOG00000003399	1 retrocopy	retro_dnov_1256,
Felis catus	ENSFCAG00000031796	1 retrocopy	retro_fcat_1171,
Homo sapiens	ENSG00000117691	2 retrocopies	retro_hsap_3288, retro_hsap_379 ,
Gorilla gorilla	ENSGGOG00000025197	1 retrocopy	retro_ggor_830,
Macaca mulatta	ENSMMUG00000002142	2 retrocopies	retro_mmul_2064, retro_mmul_490,
Mus musculus	ENSMUSG00000037499	1 retrocopy	retro_mmus_3309,
Nomascus leucogenys	ENSNLEG00000002893	1 retrocopy	retro_nleu_1354,
Ochotona princeps	ENSOPRG00000014204	2 retrocopies	retro_opri_127, retro_opri_775,
Pongo abelii	ENSPPYG00000000236	2 retrocopies	retro_pabe_2717, retro_pabe_328,
Pan troglodytes	ENSPTRG00000001961	2 retrocopies	retro_ptro_2224, retro_ptro_295,
Sus scrofa	ENSSSCG00000015597	1 retrocopy	retro_sscr_393,
Ictidomys tridecemlineatus	ENSSTOG00000022293	2 retrocopies	retro_itri_1876, retro_itri_340,
Tarsius syrichta	ENSTSYG00000001880	3 retrocopies	retro_tsyr_1189, retro_tsyr_411, retro_tsyr_549,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.02 RPM
CEU_NA11843	0.06 RPM
CEU_NA11930	0.03 RPM
CEU_NA12004	0.00 RPM
CEU_NA12400	0.00 RPM
CEU_NA12751	0.02 RPM
CEU_NA12760	0.00 RPM
CEU_NA12827	0.14 RPM
CEU_NA12872	0.00 RPM
CEU_NA12873	0.00 RPM
FIN_HG00183	0.05 RPM
FIN_HG00277	0.07 RPM
FIN_HG00315	0.06 RPM
FIN_HG00321	0.00 RPM
FIN_HG00328	0.02 RPM
FIN_HG00338	0.02 RPM
FIN_HG00349	0.03 RPM
FIN_HG00375	0.02 RPM
FIN_HG00377	0.05 RPM
FIN_HG00378	0.00 RPM
GBR_HG00099	0.03 RPM
GBR_HG00111	0.02 RPM
GBR_HG00114	0.08 RPM
GBR_HG00119	0.02 RPM
GBR_HG00131	0.00 RPM
GBR_HG00133	0.05 RPM
GBR_HG00134	0.02 RPM
GBR_HG00137	0.03 RPM
GBR_HG00142	0.00 RPM
GBR_HG00143	0.06 RPM
TSI_NA20512	0.03 RPM
TSI_NA20513	0.02 RPM
TSI_NA20518	0.00 RPM
TSI_NA20532	0.03 RPM
TSI_NA20538	0.00 RPM
TSI_NA20756	0.03 RPM
TSI_NA20765	0.02 RPM
TSI_NA20771	0.03 RPM
TSI_NA20786	0.00 RPM
TSI_NA20798	0.06 RPM
YRI_NA18870	0.03 RPM
YRI_NA18907	0.00 RPM
YRI_NA18916	0.02 RPM
YRI_NA19093	0.00 RPM
YRI_NA19099	0.03 RPM
YRI_NA19114	0.00 RPM
YRI_NA19118	0.00 RPM
YRI_NA19213	0.07 RPM
YRI_NA19214	0.00 RPM
YRI_NA19223	0.02 RPM

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Indel association:

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