RetrogeneDB ID: retro_hsap_1794

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 17:1761335..1761740(-)
• Located in intron of: ENSG00000132383

Retrocopy information

• Ensembl ID: ENSG00000108958
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SDHC
• Ensembl ID: ENSG00000143252
• Aliases: None
• Description: succinate dehydrogenase complex, subunit C, integral membrane protein, 15kDa [Source:HGNC Symbol;Acc:10682]

Sequence

>retro_hsap_1794
ATGGCTGCGCTGTTGCTGAGACACGTTGGTCGTCATTGCCTCCGAGCCCACTTTAGCCCTCAGCTCTGTATCAGAAATTG
GTCTCTTCCCATGGCGATGTCCATCTGCCACCGTGGCACTGGTATTGCTTTGAGTGCAGGGGTCTCTCTTTTTGGCATGT
CGGCCGTGTTACTCCCTGGGAACTTTGAGTCTTATTTGGAACTTGTGAAGTCCCTGTGTCTGGGGCCAGCACTGATCCAC
ACAGCTAAGTTTGCACTCGTCTTCCCTCTCATGTATCATACCTGGAATGGGATCCGACACTTGATGTGGAACCTAGGAAA
AGGCCTGAAGATTCCCCAGCTATACCAGTCTGGAGTGGTTGTCCTGGTTCTTACTGTGTTGTCCTCTATGGGGCTGGCAG
CCATG

Alignment

ORF - retro_hsap_1794 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.52 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAALLLRHVGRHCLRAHFSPQLCIRNWSLPMAMSICHRGTGIALSAGVSLFGMSALLLPGNFESYLELVK
          MAALLLRHVGRHCLRAHFSPQLCIRNWSLPMAMSICHRGTGIALSAGVSLFGMSA.LLPGNFESYLELVK
Retrocopy MAALLLRHVGRHCLRAHFSPQLCIRNWSLPMAMSICHRGTGIALSAGVSLFGMSAVLLPGNFESYLELVK

Parental  SLCLGPALIHTAKFALVFPLMYHTWNGIRHLMWDLGKGLKIPQLYQSGVVVLVLTVLSSMGLAAM
          SLCLGPALIHTAKFALVFPLMYHTWNGIRHLMW.LGKGLKIPQLYQSGVVVLVLTVLSSMGLAAM
Retrocopy SLCLGPALIHTAKFALVFPLMYHTWNGIRHLMWNLGKGLKIPQLYQSGVVVLVLTVLSSMGLAAM

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	0.10 RPM	29.62 RPM
bodymap2_adrenal	0.37 RPM	28.39 RPM
bodymap2_brain	0.05 RPM	27.35 RPM
bodymap2_breast	0.16 RPM	49.86 RPM
bodymap2_colon	0.00 RPM	28.17 RPM
bodymap2_heart	0.09 RPM	59.78 RPM
bodymap2_kidney	0.33 RPM	67.92 RPM
bodymap2_liver	0.06 RPM	53.21 RPM
bodymap2_lung	0.05 RPM	36.64 RPM
bodymap2_lymph_node	0.16 RPM	33.50 RPM
bodymap2_ovary	0.19 RPM	28.72 RPM
bodymap2_prostate	0.10 RPM	40.25 RPM
bodymap2_skeletal_muscle	0.36 RPM	32.85 RPM
bodymap2_testis	0.04 RPM	26.92 RPM
bodymap2_thyroid	0.26 RPM	43.61 RPM
bodymap2_white_blood_cells	0.02 RPM	47.80 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_1794 was not detected

EST

No EST(s) were mapped for retro_hsap_1794 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_55989	32 libraries	2 libraries	107 libraries	301 libraries	1387 libraries

The graphical summary, for retro_hsap_1794 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_1794 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_1794 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 41 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000015351	2 retrocopies	retro_amel_468, retro_amel_803,
Bos taurus	ENSBTAG00000015853	1 retrocopy	retro_btau_835,
Canis familiaris	ENSCAFG00000012992	2 retrocopies	retro_cfam_1529, retro_cfam_275,
Callithrix jacchus	ENSCJAG00000004757	3 retrocopies	retro_cjac_1119, retro_cjac_2455, retro_cjac_988,
Echinops telfairi	ENSETEG00000015767	1 retrocopy	retro_etel_675,
Felis catus	ENSFCAG00000000499	1 retrocopy	retro_fcat_1609,
Homo sapiens	ENSG00000143252	4 retrocopies	retro_hsap_1794 , retro_hsap_1896, retro_hsap_609, retro_hsap_854,
Gorilla gorilla	ENSGGOG00000008017	3 retrocopies	retro_ggor_1390, retro_ggor_536, retro_ggor_697,
Macaca mulatta	ENSMMUG00000012411	11 retrocopies	retro_mmul_1063, retro_mmul_1323, retro_mmul_1338, retro_mmul_1686, retro_mmul_1845, retro_mmul_2002, retro_mmul_2087, retro_mmul_239, retro_mmul_2416, retro_mmul_369, retro_mmul_672,
Mustela putorius furo	ENSMPUG00000014439	1 retrocopy	retro_mputfur_1201,
Nomascus leucogenys	ENSNLEG00000014367	3 retrocopies	retro_nleu_1476, retro_nleu_420, retro_nleu_439,
Pteropus vampyrus	ENSPVAG00000005544	2 retrocopies	retro_pvam_879, retro_pvam_974,
Rattus norvegicus	ENSRNOG00000003163	2 retrocopies	retro_rnor_1486, retro_rnor_1487,
Sarcophilus harrisii	ENSSHAG00000016835	1 retrocopy	retro_shar_205,
Sus scrofa	ENSSSCG00000030318	2 retrocopies	retro_sscr_1050, retro_sscr_1061,
Takifugu rubripes	ENSTRUG00000001873	1 retrocopy	retro_trub_41,
Tursiops truncatus	ENSTTRG00000009234	1 retrocopy	retro_ttru_196,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.11 RPM
CEU_NA11843	0.09 RPM
CEU_NA11930	0.23 RPM
CEU_NA12004	0.15 RPM
CEU_NA12400	0.04 RPM
CEU_NA12751	0.10 RPM
CEU_NA12760	0.04 RPM
CEU_NA12827	0.19 RPM
CEU_NA12872	0.14 RPM
CEU_NA12873	0.13 RPM
FIN_HG00183	0.08 RPM
FIN_HG00277	0.15 RPM
FIN_HG00315	0.22 RPM
FIN_HG00321	0.06 RPM
FIN_HG00328	0.14 RPM
FIN_HG00338	0.09 RPM
FIN_HG00349	0.20 RPM
FIN_HG00375	0.02 RPM
FIN_HG00377	0.28 RPM
FIN_HG00378	0.15 RPM
GBR_HG00099	0.06 RPM
GBR_HG00111	0.11 RPM
GBR_HG00114	0.11 RPM
GBR_HG00119	0.07 RPM
GBR_HG00131	0.03 RPM
GBR_HG00133	0.12 RPM
GBR_HG00134	0.07 RPM
GBR_HG00137	0.05 RPM
GBR_HG00142	0.11 RPM
GBR_HG00143	0.10 RPM
TSI_NA20512	0.06 RPM
TSI_NA20513	0.19 RPM
TSI_NA20518	0.36 RPM
TSI_NA20532	0.24 RPM
TSI_NA20538	0.14 RPM
TSI_NA20756	0.15 RPM
TSI_NA20765	0.27 RPM
TSI_NA20771	0.17 RPM
TSI_NA20786	0.18 RPM
TSI_NA20798	0.09 RPM
YRI_NA18870	0.17 RPM
YRI_NA18907	0.00 RPM
YRI_NA18916	0.13 RPM
YRI_NA19093	0.13 RPM
YRI_NA19099	0.24 RPM
YRI_NA19114	0.08 RPM
YRI_NA19118	0.10 RPM
YRI_NA19213	0.14 RPM
YRI_NA19214	0.05 RPM
YRI_NA19223	0.14 RPM

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Indel association:

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