RetrogeneDB ID: retro_hsap_586

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 10:70184316..70184751(+)
• Located in intron of: ENSG00000138346

Retrocopy information

• Ensembl ID: ENSG00000234806
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RPL26L1
• Ensembl ID: ENSG00000037241
• Aliases: RPL26L1, RPL26P1
• Description: ribosomal protein L26-like 1 [Source:HGNC Symbol;Acc:17050]

Sequence

>retro_hsap_586
ATGAAGTTCAATCCCTTCGTGAACTTGGACCGCAGCAAAAACCGCAAACGTCACTTCCATGCCCCCTTGCACGTGCACCG
GAAGATCATGTCATCCCCGCTCTCCAAGGAGCTGCGGCAGAAGTACAATGTCCGCTCCACACCCATCCGCAAGGACGACG
AGGTCCAGGTAGTTCAAGGACACTACAAAGGTCAGCAAATTGGCAAGGTAGTCCAGGTGTACAGAAAGAAAGATGTCATC
TACACTGAGCAGGTGCAGCGTGAGTAGGCCAACAGCACAACCGTCCACGTGGGTACTCACCCAAACAAGGTGGTTATCAC
CAGGCTAAATCTCAACAAGGATCGGAAAAAAATTATTGAACACAAAGCCAAGTCTCGACAAGTCAGAAAAGAGAAAGGCA
AATATAAGGAGGAACTTATTGAGAAAATGCAGGAA

Alignment

ORF - retro_hsap_586 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.9 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MKFNPFVTSDRSKNRKRHFNAPSHVRRKIMSSPLSKELRQKYNVRSMPIRKDDEVQVVRGHYKGQQIGKV
          MKFNPFV..DRSKNRKRHF.AP.HV.RKIMSSPLSKELRQKYNVRS.PIRKDDEVQVV.GHYKGQQIGKV
Retrocopy MKFNPFVNLDRSKNRKRHFHAPLHVHRKIMSSPLSKELRQKYNVRSTPIRKDDEVQVVQGHYKGQQIGKV

Parental  VQVYRKKYVIYIERVQREKANGTTVHVGIHPSKVVITRLKLDKDRKKILERKAKSRQVGKEKGKYKEELI
          VQVYRKK.VIY.E.VQRE.AN.TTVHVG.HP.KVVITRL.L.KDRKKI.E.KAKSRQV.KEKGKYKEELI
Retrocopy VQVYRKKDVIYTEQVQRE*ANSTTVHVGTHPNKVVITRLNLNKDRKKIIEHKAKSRQVRKEKGKYKEELI

Parental  EKMQE
          EKMQE
Retrocopy EKMQE

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	4.75 RPM
bodymap2_adrenal	0.06 RPM	9.03 RPM
bodymap2_brain	0.02 RPM	5.72 RPM
bodymap2_breast	0.08 RPM	6.21 RPM
bodymap2_colon	0.00 RPM	4.47 RPM
bodymap2_heart	0.04 RPM	6.61 RPM
bodymap2_kidney	0.00 RPM	11.29 RPM
bodymap2_liver	0.00 RPM	12.13 RPM
bodymap2_lung	0.00 RPM	5.92 RPM
bodymap2_lymph_node	0.00 RPM	6.49 RPM
bodymap2_ovary	0.00 RPM	7.98 RPM
bodymap2_prostate	0.00 RPM	9.92 RPM
bodymap2_skeletal_muscle	0.00 RPM	8.46 RPM
bodymap2_testis	0.00 RPM	28.94 RPM
bodymap2_thyroid	0.00 RPM	7.53 RPM
bodymap2_white_blood_cells	0.00 RPM	9.98 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_586 was not detected

EST

No EST(s) were mapped for retro_hsap_586 retrocopy.

TSS

No TSS is located nearby retro_hsap_586 retrocopy 5' end.

Lab

retro_hsap_586 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_586 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 112 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000002289	35 retrocopies	retro_dnov_1106, retro_dnov_1147, retro_dnov_1171, retro_dnov_1258, retro_dnov_1304, retro_dnov_1319, retro_dnov_1344, retro_dnov_1381, retro_dnov_1501, retro_dnov_1676, retro_dnov_1819, retro_dnov_1959, retro_dnov_2039, retro_dnov_2041, retro_dnov_2061, retro_dnov_2078, retro_dnov_2103, retro_dnov_2116, retro_dnov_2121, retro_dnov_2287, retro_dnov_2297, retro_dnov_2438, retro_dnov_2545, retro_dnov_2580, retro_dnov_2632, retro_dnov_300, retro_dnov_306, retro_dnov_467, retro_dnov_646, retro_dnov_666, retro_dnov_681, retro_dnov_760, retro_dnov_850, retro_dnov_970, retro_dnov_985,
Felis catus	ENSFCAG00000026949	1 retrocopy	retro_fcat_524,
Homo sapiens	ENSG00000037241	2 retrocopies	retro_hsap_586 , retro_hsap_837,
Homo sapiens	ENSG00000161970	27 retrocopies	retro_hsap_1137, retro_hsap_1309, retro_hsap_1376, retro_hsap_1394, retro_hsap_191, retro_hsap_2108, retro_hsap_2165, retro_hsap_2253, retro_hsap_253, retro_hsap_267, retro_hsap_2946, retro_hsap_3118, retro_hsap_3260, retro_hsap_3324, retro_hsap_3490, retro_hsap_3700, retro_hsap_3803, retro_hsap_3813, retro_hsap_3914, retro_hsap_4043, retro_hsap_4061, retro_hsap_4874, retro_hsap_4932, retro_hsap_642, retro_hsap_691, retro_hsap_915, retro_hsap_998,
Latimeria chalumnae	ENSLACG00000007599	2 retrocopies	retro_lcha_5, retro_lcha_8,
Microcebus murinus	ENSMICG00000011312	10 retrocopies	retro_mmur_1020, retro_mmur_1144, retro_mmur_313, retro_mmur_327, retro_mmur_346, retro_mmur_412, retro_mmur_471, retro_mmur_623, retro_mmur_72, retro_mmur_75,
Macaca mulatta	ENSMMUG00000003070	1 retrocopy	retro_mmul_676,
Oryctolagus cuniculus	ENSOCUG00000006172	4 retrocopies	retro_ocun_1015, retro_ocun_1224, retro_ocun_354, retro_ocun_845,
Procavia capensis	ENSPCAG00000002246	10 retrocopies	retro_pcap_137, retro_pcap_157, retro_pcap_188, retro_pcap_204, retro_pcap_337, retro_pcap_404, retro_pcap_419, retro_pcap_42, retro_pcap_422, retro_pcap_448,
Pteropus vampyrus	ENSPVAG00000003253	8 retrocopies	retro_pvam_1062, retro_pvam_1208, retro_pvam_122, retro_pvam_353, retro_pvam_688, retro_pvam_71, retro_pvam_769, retro_pvam_877,
Sus scrofa	ENSSSCG00000016989	3 retrocopies	retro_sscr_1104, retro_sscr_462, retro_sscr_685,
Ictidomys tridecemlineatus	ENSSTOG00000026876	1 retrocopy	retro_itri_1141,
Tursiops truncatus	ENSTTRG00000010624	8 retrocopies	retro_ttru_1070, retro_ttru_1124, retro_ttru_1694, retro_ttru_1818, retro_ttru_364, retro_ttru_386, retro_ttru_474, retro_ttru_646,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.11 RPM
CEU_NA11843	0.17 RPM
CEU_NA11930	0.07 RPM
CEU_NA12004	0.00 RPM
CEU_NA12400	0.04 RPM
CEU_NA12751	0.00 RPM
CEU_NA12760	0.04 RPM
CEU_NA12827	0.05 RPM
CEU_NA12872	0.08 RPM
CEU_NA12873	0.03 RPM
FIN_HG00183	0.14 RPM
FIN_HG00277	0.15 RPM
FIN_HG00315	0.03 RPM
FIN_HG00321	0.09 RPM
FIN_HG00328	0.07 RPM
FIN_HG00338	0.11 RPM
FIN_HG00349	0.00 RPM
FIN_HG00375	0.05 RPM
FIN_HG00377	0.05 RPM
FIN_HG00378	0.04 RPM
GBR_HG00099	0.06 RPM
GBR_HG00111	0.00 RPM
GBR_HG00114	0.05 RPM
GBR_HG00119	0.17 RPM
GBR_HG00131	0.00 RPM
GBR_HG00133	0.10 RPM
GBR_HG00134	0.17 RPM
GBR_HG00137	0.03 RPM
GBR_HG00142	0.11 RPM
GBR_HG00143	0.03 RPM
TSI_NA20512	0.03 RPM
TSI_NA20513	0.10 RPM
TSI_NA20518	0.06 RPM
TSI_NA20532	0.27 RPM
TSI_NA20538	0.05 RPM
TSI_NA20756	0.00 RPM
TSI_NA20765	0.29 RPM
TSI_NA20771	0.03 RPM
TSI_NA20786	0.03 RPM
TSI_NA20798	0.16 RPM
YRI_NA18870	0.00 RPM
YRI_NA18907	0.03 RPM
YRI_NA18916	0.04 RPM
YRI_NA19093	0.08 RPM
YRI_NA19099	0.08 RPM
YRI_NA19114	0.03 RPM
YRI_NA19118	0.06 RPM
YRI_NA19213	0.02 RPM
YRI_NA19214	0.05 RPM
YRI_NA19223	0.26 RPM

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Indel association:

The presence of retro_hsap_586 across human populations is associated with 1 indel. The percentage values indicate the frequencies of retro_hsap_586 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.	10:70182372..70187700	100	100	99.48	100	100	100	100	100	100	100	100	100	100	100

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Indel #1, located at the genomic coordinates 10:70182372..70187700.