RetrogeneDB ID: retro_hsap_146

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 1:46246948..46247629(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000236111
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RPL6
• Ensembl ID: ENSG00000089009
• Aliases: RPL6, L6, SHUJUN-2, TAXREB107, TXREB1
• Description: ribosomal protein L6 [Source:HGNC Symbol;Acc:10362]

Sequence

>retro_hsap_146
ATGGTGGGTGAAAAAGTTGAGAAGCCAGATGCTAAAGAGAAGAAACCCAAAGCCAAGAAGGCTGATGTTGGTGGCAAGGT
GAAAAAGGGTAACCTCAAGGCTAAAAAGCCCAAGAAGGGAAAGCCCCATTGCAGCCGCAACCCTGTCCTTGTCAGAGGAA
TTGGCAGGTATTGCCGATCTGCCATGTATTCCAGAAAGGCCATGTACAAGAGGAAGTACTCAGCCGCTAAATCTAAGGTT
GAAAAGAAAAAGAAGGAGAAGGTTCTTGCAACTGTTACAAAACCAGTTGGTTGTGACAAGAATGGCGGTGCCCGGGTGGT
TAAACTTCGCAAAATGCCTAGATATTATCCTACTGAAGATGTGCCTCGAAAGCTGTTGAGCCATGGCAAAAAATCCTTCA
GTCAGCACGTGAGAAAACTGCGAGCCAGCATCACTCCCGGGACCATTCTCATCATCCTCGCTGGATGCCATAGGGGCAAG
AAGGTGGTTTTCCTGAAGCAGCTGGCTAGTGGTTTGTTACTTGTGACTGGACCTCTGGTCCTCAATCGAATTCCTCTACG
AAGAACATACCAGAAATTTGTCATTGCCACCTCAACCAAAATTGATATCGGCAATGTAAAAATCCCCAAACATCTTATTG
ATACTTACTTCAAGAAGAAGAAGCTGTGGAAGCCCAGACAC

Alignment

ORF - retro_hsap_146 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.07 %
• Parental protein coverage: 78.82 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAGEKVEKPDTKEKKPEAKKVDAGGKVKKGNLKAKKPKKGKPHCSRNPVLVRGIGRYSRSAMYSRKAMYK
          M.GEKVEKPD.KEKKP.AKK.D.GGKVKKGNLKAKKPKKGKPHCSRNPVLVRGIGRY.RSAMYSRKAMYK
Retrocopy MVGEKVEKPDAKEKKPKAKKADVGGKVKKGNLKAKKPKKGKPHCSRNPVLVRGIGRYCRSAMYSRKAMYK

Parental  RKYSAAKSKVEKKKKEKVLATVTKPVGGDKNGGTRVVKLRKMPRYYPTEDVPRKLLSHGKKPFSQHVRKL
          RKYSAAKSKVEKKKKEKVLATVTKPVG.DKNGG.RVVKLRKMPRYYPTEDVPRKLLSHGKK.FSQHVRKL
Retrocopy RKYSAAKSKVEKKKKEKVLATVTKPVGCDKNGGARVVKLRKMPRYYPTEDVPRKLLSHGKKSFSQHVRKL

Parental  RASITPGTILIILTGRHRGKRVVFLKQLASGLLLVTGPLVLNRVPLRRTHQKFVIATSTKIDISNVKIPK
          RASITPGTILIIL.G.HRGK.VVFLKQLASGLLLVTGPLVLNR.PLRRT.QKFVIATSTKIDI.NVKIPK
Retrocopy RASITPGTILIILAGCHRGKKVVFLKQLASGLLLVTGPLVLNRIPLRRTYQKFVIATSTKIDIGNVKIPK

Parental  HLTDAYFKKKKLRKPRH
          HL.D.YFKKKKL.KPRH
Retrocopy HLIDTYFKKKKLWKPRH

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	476.10 RPM
bodymap2_adrenal	0.02 RPM	699.56 RPM
bodymap2_brain	0.00 RPM	206.53 RPM
bodymap2_breast	0.00 RPM	440.47 RPM
bodymap2_colon	0.04 RPM	761.83 RPM
bodymap2_heart	0.00 RPM	153.63 RPM
bodymap2_kidney	0.00 RPM	364.93 RPM
bodymap2_liver	0.00 RPM	285.99 RPM
bodymap2_lung	0.00 RPM	494.64 RPM
bodymap2_lymph_node	0.02 RPM	800.90 RPM
bodymap2_ovary	0.06 RPM	879.55 RPM
bodymap2_prostate	0.00 RPM	824.70 RPM
bodymap2_skeletal_muscle	0.00 RPM	237.75 RPM
bodymap2_testis	0.00 RPM	394.46 RPM
bodymap2_thyroid	0.00 RPM	557.99 RPM
bodymap2_white_blood_cells	0.04 RPM	915.35 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_146 was not detected

EST

No EST(s) were mapped for retro_hsap_146 retrocopy.

TSS

No TSS is located nearby retro_hsap_146 retrocopy 5' end.

Lab

retro_hsap_146 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_146 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pongo abelii	retro_pabe_472

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Parental genes homology:

Parental genes homology involve 22 parental genes, and 157 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000003060	1 retrocopy	retro_acar_171,
Bos taurus	ENSBTAG00000031723	6 retrocopies	retro_btau_1038, retro_btau_1117, retro_btau_1305, retro_btau_16, retro_btau_424, retro_btau_809,
Canis familiaris	ENSCAFG00000008873	1 retrocopy	retro_cfam_36,
Callithrix jacchus	ENSCJAG00000012450	7 retrocopies	retro_cjac_1362, retro_cjac_1620, retro_cjac_1949, retro_cjac_2723, retro_cjac_328, retro_cjac_349, retro_cjac_497,
Cavia porcellus	ENSCPOG00000013526	8 retrocopies	retro_cpor_1105, retro_cpor_1149, retro_cpor_1486, retro_cpor_382, retro_cpor_412, retro_cpor_651, retro_cpor_731, retro_cpor_982,
Dipodomys ordii	ENSDORG00000005793	1 retrocopy	retro_dord_166,
Equus caballus	ENSECAG00000017514	1 retrocopy	retro_ecab_811,
Erinaceus europaeus	ENSEEUG00000000281	3 retrocopies	retro_eeur_503, retro_eeur_553, retro_eeur_595,
Felis catus	ENSFCAG00000006858	12 retrocopies	retro_fcat_1264, retro_fcat_1370, retro_fcat_1844, retro_fcat_232, retro_fcat_398, retro_fcat_500, retro_fcat_625, retro_fcat_637, retro_fcat_643, retro_fcat_690, retro_fcat_926, retro_fcat_935,
Homo sapiens	ENSG00000089009	26 retrocopies	retro_hsap_1035, retro_hsap_146 , retro_hsap_1905, retro_hsap_2074, retro_hsap_2164, retro_hsap_2206, retro_hsap_227, retro_hsap_2566, retro_hsap_2720, retro_hsap_2725, retro_hsap_2939, retro_hsap_2955, retro_hsap_3009, retro_hsap_3014, retro_hsap_3070, retro_hsap_333, retro_hsap_3431, retro_hsap_3559, retro_hsap_3795, retro_hsap_3818, retro_hsap_3856, retro_hsap_4039, retro_hsap_440, retro_hsap_4729, retro_hsap_4788, retro_hsap_648,
Gorilla gorilla	ENSGGOG00000003372	16 retrocopies	retro_ggor_1602, retro_ggor_1893, retro_ggor_1898, retro_ggor_2047, retro_ggor_2138, retro_ggor_236, retro_ggor_2569, retro_ggor_2597, retro_ggor_2709, retro_ggor_2745, retro_ggor_290, retro_ggor_2938, retro_ggor_356, retro_ggor_426, retro_ggor_566, retro_ggor_816,
Macaca mulatta	ENSMMUG00000007433	1 retrocopy	retro_mmul_171,
Monodelphis domestica	ENSMODG00000003096	4 retrocopies	retro_mdom_1556, retro_mdom_1624, retro_mdom_1784, retro_mdom_615,
Mustela putorius furo	ENSMPUG00000002526	9 retrocopies	retro_mputfur_1116, retro_mputfur_1279, retro_mputfur_1320, retro_mputfur_1367, retro_mputfur_1407, retro_mputfur_1445, retro_mputfur_1489, retro_mputfur_401, retro_mputfur_571,
Mus musculus	ENSMUSG00000029614	13 retrocopies	retro_mmus_1264, retro_mmus_1336, retro_mmus_1898, retro_mmus_2684, retro_mmus_276, retro_mmus_3065, retro_mmus_3579, retro_mmus_3611, retro_mmus_3622, retro_mmus_3719, retro_mmus_445, retro_mmus_465, retro_mmus_730,
Nomascus leucogenys	ENSNLEG00000027093	2 retrocopies	retro_nleu_1813, retro_nleu_43,
Oryctolagus cuniculus	ENSOCUG00000003802	5 retrocopies	retro_ocun_129, retro_ocun_17, retro_ocun_189, retro_ocun_229, retro_ocun_245,
Pongo abelii	ENSPPYG00000025855	13 retrocopies	retro_pabe_1764, retro_pabe_1891, retro_pabe_2451, retro_pabe_2493, retro_pabe_2573, retro_pabe_2897, retro_pabe_3314, retro_pabe_358, retro_pabe_3677, retro_pabe_3725, retro_pabe_43, retro_pabe_472, retro_pabe_868,
Rattus norvegicus	ENSRNOG00000025936	1 retrocopy	retro_rnor_129,
Sarcophilus harrisii	ENSSHAG00000007096	2 retrocopies	retro_shar_506, retro_shar_536,
Ictidomys tridecemlineatus	ENSSTOG00000009409	3 retrocopies	retro_itri_1024, retro_itri_1125, retro_itri_684,
Tarsius syrichta	ENSTSYG00000009492	22 retrocopies	retro_tsyr_1046, retro_tsyr_1254, retro_tsyr_1600, retro_tsyr_1615, retro_tsyr_2052, retro_tsyr_2080, retro_tsyr_2123, retro_tsyr_2126, retro_tsyr_291, retro_tsyr_362, retro_tsyr_364, retro_tsyr_438, retro_tsyr_477, retro_tsyr_490, retro_tsyr_566, retro_tsyr_586, retro_tsyr_626, retro_tsyr_637, retro_tsyr_774, retro_tsyr_833, retro_tsyr_894, retro_tsyr_923,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.02 RPM
CEU_NA11843	0.03 RPM
CEU_NA11930	0.03 RPM
CEU_NA12004	0.08 RPM
CEU_NA12400	0.04 RPM
CEU_NA12751	0.00 RPM
CEU_NA12760	0.04 RPM
CEU_NA12827	0.05 RPM
CEU_NA12872	0.00 RPM
CEU_NA12873	0.00 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	0.02 RPM
FIN_HG00349	0.00 RPM
FIN_HG00375	0.02 RPM
FIN_HG00377	0.00 RPM
FIN_HG00378	0.02 RPM
GBR_HG00099	0.00 RPM
GBR_HG00111	0.00 RPM
GBR_HG00114	0.00 RPM
GBR_HG00119	0.00 RPM
GBR_HG00131	0.03 RPM
GBR_HG00133	0.00 RPM
GBR_HG00134	0.00 RPM
GBR_HG00137	0.00 RPM
GBR_HG00142	0.00 RPM
GBR_HG00143	0.00 RPM
TSI_NA20512	0.00 RPM
TSI_NA20513	0.00 RPM
TSI_NA20518	0.00 RPM
TSI_NA20532	0.03 RPM
TSI_NA20538	0.00 RPM
TSI_NA20756	0.00 RPM
TSI_NA20765	0.00 RPM
TSI_NA20771	0.00 RPM
TSI_NA20786	0.03 RPM
TSI_NA20798	0.00 RPM
YRI_NA18870	0.00 RPM
YRI_NA18907	0.00 RPM
YRI_NA18916	0.00 RPM
YRI_NA19093	0.03 RPM
YRI_NA19099	0.00 RPM
YRI_NA19114	0.00 RPM
YRI_NA19118	0.02 RPM
YRI_NA19213	0.00 RPM
YRI_NA19214	0.00 RPM
YRI_NA19223	0.02 RPM

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Indel association:

The presence of retro_hsap_146 across human populations is associated with 1 indel. The percentage values indicate the frequencies of retro_hsap_146 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.	1:46243510..46251900	100	97.73	99.48	100	100	100	100	100	100	100	100	100	100	100

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Indel #1, located at the genomic coordinates 1:46243510..46251900.