RetrogeneDB ID: retro_hsap_568

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 10:46914150..46914702(+)
• Located in intron of: ENSG00000165874

Retrocopy information

• Ensembl ID: ENSG00000229927
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RHEB
• Ensembl ID: ENSG00000106615
• Aliases: RHEB, RHEB2
• Description: Ras homolog enriched in brain [Source:HGNC Symbol;Acc:10011]

Sequence

>retro_hsap_568
ATGCCGCAGTCAAAGTCCCGGAAGATCGCGATCCTGGGCTACCGGTCTGTGGGGAAATCCTCATTGACGATTCAATTTGT
TGAAGGCCAATTTGTGGACTCCTACGATCCAACCATAGAAAACACTTTTACAAAGTTGATCACAGTAAATGGACAAGAAT
ATCATCTTTAACTTGTAGACACAGCCGGGCAAGATGAATATTCTATCTTTCCTCAGACATACTCCATAGATATTAATGGC
TATATTCTTGTGTATTCTGTTACATCAATCAAAAGTTTTGAAGTGATTAAAGTTATCCATGGCAAATTGTTGGATATGGT
GGGGAAAGTACAAATACCTATTATGTTGGTTGGAAATAAGAAAGACCTGCATATGGAAAGGGTGATCAGTTATGAAGAAG
GGAAAGCTTTGGCAGAATCTTGGAATGCAGCTTTTTTGGAATCTTCTGCTAAAGAAAATCAGACTGCTGTTGATGTTTTT
CGAAGGATGATTTTGGAGGCAGAAAAAATGGACGGGGCAGCTTCACAAGGCAAGTCTTCATGCTCGGTGATG

Alignment

ORF - retro_hsap_568 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.91 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MPQSKSRKIAILGYRSVGKSSLTIQFVEGQFVDSYDPTIENTFTKLITVNGQEYHLQLVDTAGQDEYSIF
          MPQSKSRKIAILGYRSVGKSSLTIQFVEGQFVDSYDPTIENTFTKLITVNGQEYHL.LVDTAGQDEYSIF
Retrocopy MPQSKSRKIAILGYRSVGKSSLTIQFVEGQFVDSYDPTIENTFTKLITVNGQEYHL*LVDTAGQDEYSIF

Parental  PQTYSIDINGYILVYSVTSIKSFEVIKVIHGKLLDMVGKVQIPIMLVGNKKDLHMERVISYEEGKALAES
          PQTYSIDINGYILVYSVTSIKSFEVIKVIHGKLLDMVGKVQIPIMLVGNKKDLHMERVISYEEGKALAES
Retrocopy PQTYSIDINGYILVYSVTSIKSFEVIKVIHGKLLDMVGKVQIPIMLVGNKKDLHMERVISYEEGKALAES

Parental  WNAAFLESSAKENQTAVDVFRRIILEAEKMDGAASQGKSSCSVM
          WNAAFLESSAKENQTAVDVFRR.ILEAEKMDGAASQGKSSCSVM
Retrocopy WNAAFLESSAKENQTAVDVFRRMILEAEKMDGAASQGKSSCSVM

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	71.54 RPM
bodymap2_adrenal	0.25 RPM	54.49 RPM
bodymap2_brain	0.28 RPM	113.97 RPM
bodymap2_breast	0.19 RPM	57.02 RPM
bodymap2_colon	0.15 RPM	120.95 RPM
bodymap2_heart	0.00 RPM	56.77 RPM
bodymap2_kidney	0.23 RPM	82.31 RPM
bodymap2_liver	1.50 RPM	41.99 RPM
bodymap2_lung	0.12 RPM	105.57 RPM
bodymap2_lymph_node	0.00 RPM	57.53 RPM
bodymap2_ovary	0.13 RPM	72.13 RPM
bodymap2_prostate	0.55 RPM	147.05 RPM
bodymap2_skeletal_muscle	0.05 RPM	106.89 RPM
bodymap2_testis	1.60 RPM	71.70 RPM
bodymap2_thyroid	0.30 RPM	111.18 RPM
bodymap2_white_blood_cells	0.10 RPM	38.92 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_568 was not detected

EST

No EST(s) were mapped for retro_hsap_568 retrocopy.

TSS

No TSS is located nearby retro_hsap_568 retrocopy 5' end.

Lab

retro_hsap_568 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_568 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_570
Pan troglodytes	retro_ptro_115

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000031861	1 retrocopy	retro_btau_373,
Cavia porcellus	ENSCPOG00000007541	2 retrocopies	retro_cpor_287, retro_cpor_787,
Dasypus novemcinctus	ENSDNOG00000016493	1 retrocopy	retro_dnov_2542,
Homo sapiens	ENSG00000106615	2 retrocopies	retro_hsap_568 , retro_hsap_570,
Gorilla gorilla	ENSGGOG00000014675	1 retrocopy	retro_ggor_149,
Loxodonta africana	ENSLAFG00000000691	1 retrocopy	retro_lafr_471,
Macropus eugenii	ENSMEUG00000011774	1 retrocopy	retro_meug_172,
Myotis lucifugus	ENSMLUG00000004309	2 retrocopies	retro_mluc_2140, retro_mluc_857,
Mus musculus	ENSMUSG00000028945	1 retrocopy	retro_mmus_1779,
Oryctolagus cuniculus	ENSOCUG00000013173	1 retrocopy	retro_ocun_1309,
Ictidomys tridecemlineatus	ENSSTOG00000004544	2 retrocopies	retro_itri_1251, retro_itri_1357,
Tarsius syrichta	ENSTSYG00000001286	2 retrocopies	retro_tsyr_1174, retro_tsyr_1848,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.06 RPM
CEU_NA11843	0.03 RPM
CEU_NA11930	0.00 RPM
CEU_NA12004	0.04 RPM
CEU_NA12400	0.04 RPM
CEU_NA12751	0.00 RPM
CEU_NA12760	0.04 RPM
CEU_NA12827	0.05 RPM
CEU_NA12872	0.03 RPM
CEU_NA12873	0.03 RPM
FIN_HG00183	0.03 RPM
FIN_HG00277	0.00 RPM
FIN_HG00315	0.00 RPM
FIN_HG00321	0.00 RPM
FIN_HG00328	0.00 RPM
FIN_HG00338	0.00 RPM
FIN_HG00349	0.03 RPM
FIN_HG00375	0.00 RPM
FIN_HG00377	0.00 RPM
FIN_HG00378	0.00 RPM
GBR_HG00099	0.06 RPM
GBR_HG00111	0.02 RPM
GBR_HG00114	0.05 RPM
GBR_HG00119	0.02 RPM
GBR_HG00131	0.00 RPM
GBR_HG00133	0.02 RPM
GBR_HG00134	0.02 RPM
GBR_HG00137	0.00 RPM
GBR_HG00142	0.03 RPM
GBR_HG00143	0.00 RPM
TSI_NA20512	0.00 RPM
TSI_NA20513	0.00 RPM
TSI_NA20518	0.03 RPM
TSI_NA20532	0.03 RPM
TSI_NA20538	0.05 RPM
TSI_NA20756	0.03 RPM
TSI_NA20765	0.04 RPM
TSI_NA20771	0.00 RPM
TSI_NA20786	0.00 RPM
TSI_NA20798	0.00 RPM
YRI_NA18870	0.07 RPM
YRI_NA18907	0.00 RPM
YRI_NA18916	0.00 RPM
YRI_NA19093	0.00 RPM
YRI_NA19099	0.00 RPM
YRI_NA19114	0.03 RPM
YRI_NA19118	0.02 RPM
YRI_NA19213	0.05 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).