RetrogeneDB ID: retro_hsap_355

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 1:25620657..25621134(-)
• Located in intron of: ENSG00000187010

Retrocopy information

• Ensembl ID: ENSG00000224183
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SDHD
• Ensembl ID: ENSG00000204370
• Aliases: SDHD, CBT1, CII-4, CWS3, PGL, PGL1, QPs3, SDH4, cybS
• Description: succinate dehydrogenase complex, subunit D, integral membrane protein [Source:HGNC Symbol;Acc:10683]

Sequence

>retro_hsap_355
ATGGCGGTTCCCTGGAGGCTGAGTGCCGTTTGCGGTGCCCAAGGAGGCCGAGCTCTGTTGCTGCGAACTCCAGTGGTCAG
ACCTGCTCATATCTCAGCATTTCTTCAGGACCGACCTATCCCAGAATGGTGTGGAGTGCAGCACATACACTTGTCACCGA
GCCACCATTCTGGCTCCAAGGCTGCATCTCTCCACTGGACTAGCGAGAGGGTTGTCAGTGTTTTGCTCCCGGGTCTGCTT
CCGGCTGCTTATTTGAATCCTTGCTCTGCGACGGACTATTCCCTGGCTGCAGCCCTCACTCTTCATGGTCACTGGGGCCT
TGGACAAGTTGTTACTGATTATGTTCATGGGGATGCCTCGCAGAAAGCTGCCAAGGCAGGGCTTTTGGCATTTTCAGCTT
TAACCTTTGCTGGGCTTTGCTATTTCAACTATCACGATGTGGGCATCTGCAAAGCTGTTGCCATGCTGTGGAAGCTC

Alignment

ORF - retro_hsap_355 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.23 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAVLWRLSAVCGALGGRALLLRTPVVRPAHISAFLQDRPIPEWCGVQHIHLSPSHHSGSKAASLHWTSER
          MAV.WRLSAVCGA.GGRALLLRTPVVRPAHISAFLQDRPIPEWCGVQHIHLSPSHHSGSKAASLHWTSER
Retrocopy MAVPWRLSAVCGAQGGRALLLRTPVVRPAHISAFLQDRPIPEWCGVQHIHLSPSHHSGSKAASLHWTSER

Parental  VVSVLLLGLLPAAYLNPCSAMDYSLAAALTLHGHWGLGQVVTDYVHGDALQKAAKAGLLALSALTFAGLC
          VVSVLL.GLLPAAYLNPCSA.DYSLAAALTLHGHWGLGQVVTDYVHGDA.QKAAKAGLLA.SALTFAGLC
Retrocopy VVSVLLPGLLPAAYLNPCSATDYSLAAALTLHGHWGLGQVVTDYVHGDASQKAAKAGLLAFSALTFAGLC

Parental  YFNYHDVGICKAVAMLWKL
          YFNYHDVGICKAVAMLWKL
Retrocopy YFNYHDVGICKAVAMLWKL

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	0.14 RPM	35.34 RPM
bodymap2_adrenal	0.55 RPM	47.80 RPM
bodymap2_brain	0.07 RPM	26.49 RPM
bodymap2_breast	0.02 RPM	61.01 RPM
bodymap2_colon	0.14 RPM	89.31 RPM
bodymap2_heart	0.11 RPM	113.66 RPM
bodymap2_kidney	0.06 RPM	166.31 RPM
bodymap2_liver	0.04 RPM	93.30 RPM
bodymap2_lung	0.04 RPM	63.41 RPM
bodymap2_lymph_node	0.00 RPM	65.62 RPM
bodymap2_ovary	0.00 RPM	42.64 RPM
bodymap2_prostate	0.23 RPM	114.02 RPM
bodymap2_skeletal_muscle	0.02 RPM	55.65 RPM
bodymap2_testis	0.09 RPM	39.91 RPM
bodymap2_thyroid	0.30 RPM	75.48 RPM
bodymap2_white_blood_cells	1.34 RPM	88.20 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_355 was not detected

EST

No EST(s) were mapped for retro_hsap_355 retrocopy.

TSS

No TSS is located nearby retro_hsap_355 retrocopy 5' end.

Lab

retro_hsap_355 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_355 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 47 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000004066	3 retrocopies	retro_amel_1556, retro_amel_1588, retro_amel_998,
Callithrix jacchus	ENSCJAG00000010975	4 retrocopies	retro_cjac_1385, retro_cjac_1390, retro_cjac_1557, retro_cjac_3829,
Erinaceus europaeus	ENSEEUG00000013091	1 retrocopy	retro_eeur_336,
Echinops telfairi	ENSETEG00000008424	1 retrocopy	retro_etel_252,
Felis catus	ENSFCAG00000022580	3 retrocopies	retro_fcat_1371, retro_fcat_175, retro_fcat_492,
Homo sapiens	ENSG00000204370	8 retrocopies	retro_hsap_124, retro_hsap_1912, retro_hsap_2132, retro_hsap_2182, retro_hsap_2729, retro_hsap_2784, retro_hsap_355 , retro_hsap_3791,
Gorilla gorilla	ENSGGOG00000026496	1 retrocopy	retro_ggor_50,
Loxodonta africana	ENSLAFG00000002763	1 retrocopy	retro_lafr_432,
Myotis lucifugus	ENSMLUG00000012228	3 retrocopies	retro_mluc_2418, retro_mluc_457, retro_mluc_756,
Macaca mulatta	ENSMMUG00000015247	1 retrocopy	retro_mmul_224,
Otolemur garnettii	ENSOGAG00000008568	5 retrocopies	retro_ogar_1651, retro_ogar_1795, retro_ogar_2087, retro_ogar_3122, retro_ogar_3147,
Pongo abelii	ENSPPYG00000003876	5 retrocopies	retro_pabe_1549, retro_pabe_1924, retro_pabe_2233, retro_pabe_2999, retro_pabe_3096,
Rattus norvegicus	ENSRNOG00000022980	3 retrocopies	retro_rnor_1529, retro_rnor_1686, retro_rnor_744,
Sus scrofa	ENSSSCG00000015034	3 retrocopies	retro_sscr_1060, retro_sscr_626, retro_sscr_627,
Tursiops truncatus	ENSTTRG00000010520	5 retrocopies	retro_ttru_1554, retro_ttru_238, retro_ttru_616, retro_ttru_633, retro_ttru_885,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.13 RPM
CEU_NA11843	0.00 RPM
CEU_NA11930	0.20 RPM
CEU_NA12004	0.00 RPM
CEU_NA12400	0.32 RPM
CEU_NA12751	0.17 RPM
CEU_NA12760	0.31 RPM
CEU_NA12827	0.09 RPM
CEU_NA12872	0.19 RPM
CEU_NA12873	0.00 RPM
FIN_HG00183	0.30 RPM
FIN_HG00277	0.04 RPM
FIN_HG00315	0.17 RPM
FIN_HG00321	0.00 RPM
FIN_HG00328	0.36 RPM
FIN_HG00338	0.06 RPM
FIN_HG00349	0.06 RPM
FIN_HG00375	0.12 RPM
FIN_HG00377	0.08 RPM
FIN_HG00378	0.13 RPM
GBR_HG00099	0.12 RPM
GBR_HG00111	0.19 RPM
GBR_HG00114	0.37 RPM
GBR_HG00119	0.05 RPM
GBR_HG00131	0.00 RPM
GBR_HG00133	0.00 RPM
GBR_HG00134	0.00 RPM
GBR_HG00137	0.25 RPM
GBR_HG00142	0.06 RPM
GBR_HG00143	0.16 RPM
TSI_NA20512	0.11 RPM
TSI_NA20513	0.02 RPM
TSI_NA20518	0.08 RPM
TSI_NA20532	0.00 RPM
TSI_NA20538	0.23 RPM
TSI_NA20756	0.12 RPM
TSI_NA20765	0.02 RPM
TSI_NA20771	0.11 RPM
TSI_NA20786	0.00 RPM
TSI_NA20798	0.16 RPM
YRI_NA18870	0.20 RPM
YRI_NA18907	0.14 RPM
YRI_NA18916	0.04 RPM
YRI_NA19093	0.13 RPM
YRI_NA19099	0.00 RPM
YRI_NA19114	0.26 RPM
YRI_NA19118	0.12 RPM
YRI_NA19213	0.24 RPM
YRI_NA19214	0.00 RPM
YRI_NA19223	0.16 RPM

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Indel association:

The presence of retro_hsap_355 across human populations is associated with 2 indels. The percentage values indicate the frequencies of retro_hsap_355 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.	1:25591100..25662600	79.51	87.5	92.78	84.85	65.45	71.67	57.65	42.86	61.24	65.59	62.76	93.26	92.27	97.5
2.	1:25614200..25661700	74.59	83.52	88.66	81.82	64.55	70	58.24	32.14	60.11	63.44	62.76	93.82	89.18	97

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Indel #1, located at the genomic coordinates 1:25591100..25662600.

Indel #2, located at the genomic coordinates 1:25614200..25661700.