RetrogeneDB ID: retro_hsap_667

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 10:45568665..45569004(-)
• Located in intron of: ENSG00000226937

Retrocopy information

• Ensembl ID: ENSG00000228462
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RPS19
• Ensembl ID: ENSG00000105372
• Aliases: RPS19, DBA, DBA1, S19
• Description: ribosomal protein S19 [Source:HGNC Symbol;Acc:10402]

Sequence

>retro_hsap_667
ATAAAAGACGTGAACCAGCAGGAGTTCATCAGAGCTCTGGCAGCCTTTCTCAAAAAGTCTGGGAAGCTGAAAGTCACCGA
ATGGGTGGACACCATCAAGCCGGCCAAGCACAGAGAGCTTGCTGCCTACGATAAGAACTGGTTCTACACGTGAGCTGCTT
CTACAGCGCGGCACCTGTACCTCTTGGGTGGTGCTGGGGTTGGCTCTATGACCAAGATCTACAAGGGCCGTCAGAGAAAC
AGCGTCATGCCCAGCCACTTCAGCTAAGGCTCCAAGAGTGTGGCCCGCCAGGTCCTGCAAGCCCTGGAGGGGCTGAAAAT
GGTGGAAAAGGACCAAGAT

Alignment

ORF - retro_hsap_667 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.61 %
• Parental protein coverage: 77.93 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VKDVNQQEFVRALAAFLKKSGKLKVPEWVDTVKLAKHKELAPYDENWFYTRAASTARHLYLRGGAGVGSM
          .KDVNQQEF.RALAAFLKKSGKLKV.EWVDT.K.AKH.ELA.YD.NWFYT.AASTARHLYL.GGAGVGSM
Retrocopy IKDVNQQEFIRALAAFLKKSGKLKVTEWVDTIKPAKHRELAAYDKNWFYT*AASTARHLYLLGGAGVGSM

Parental  TKIYGGRQRNGVMPSHFSRGSKSVARRVLQALEGLKMVEKDQD
          TKIY.GRQRN.VMPSHFS.GSKSVAR.VLQALEGLKMVEKDQD
Retrocopy TKIYKGRQRNSVMPSHFS*GSKSVARQVLQALEGLKMVEKDQD

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	0.02 RPM	154.11 RPM
bodymap2_adrenal	0.00 RPM	341.66 RPM
bodymap2_brain	0.00 RPM	49.34 RPM
bodymap2_breast	0.00 RPM	110.68 RPM
bodymap2_colon	0.02 RPM	346.85 RPM
bodymap2_heart	0.00 RPM	51.67 RPM
bodymap2_kidney	0.00 RPM	108.97 RPM
bodymap2_liver	0.00 RPM	107.63 RPM
bodymap2_lung	0.00 RPM	344.60 RPM
bodymap2_lymph_node	0.00 RPM	514.62 RPM
bodymap2_ovary	0.00 RPM	208.21 RPM
bodymap2_prostate	0.00 RPM	323.76 RPM
bodymap2_skeletal_muscle	0.00 RPM	151.41 RPM
bodymap2_testis	0.23 RPM	155.29 RPM
bodymap2_thyroid	0.02 RPM	130.26 RPM
bodymap2_white_blood_cells	0.00 RPM	469.73 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_667 was not detected

EST

No EST(s) were mapped for retro_hsap_667 retrocopy.

TSS

No TSS is located nearby retro_hsap_667 retrocopy 5' end.

Lab

retro_hsap_667 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_667 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_485
Gorilla gorilla	retro_ggor_578
Pongo abelii	retro_pabe_586

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 53 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000028485	10 retrocopies	retro_cfam_1017, retro_cfam_1074, retro_cfam_1155, retro_cfam_1251, retro_cfam_1377, retro_cfam_149, retro_cfam_1998, retro_cfam_2212, retro_cfam_249, retro_cfam_499,
Callithrix jacchus	ENSCJAG00000020243	5 retrocopies	retro_cjac_1968, retro_cjac_2004, retro_cjac_2094, retro_cjac_2324, retro_cjac_3,
Dasypus novemcinctus	ENSDNOG00000002376	4 retrocopies	retro_dnov_1084, retro_dnov_1124, retro_dnov_1838, retro_dnov_2456,
Equus caballus	ENSECAG00000009738	2 retrocopies	retro_ecab_263, retro_ecab_815,
Homo sapiens	ENSG00000105372	5 retrocopies	retro_hsap_1400, retro_hsap_2417, retro_hsap_3174, retro_hsap_3642, retro_hsap_667 ,
Macaca mulatta	ENSMMUG00000013429	8 retrocopies	retro_mmul_1201, retro_mmul_1358, retro_mmul_1807, retro_mmul_2007, retro_mmul_2443, retro_mmul_404, retro_mmul_607, retro_mmul_691,
Monodelphis domestica	ENSMODG00000010067	3 retrocopies	retro_mdom_1531, retro_mdom_1888, retro_mdom_883,
Mustela putorius furo	ENSMPUG00000007164	4 retrocopies	retro_mputfur_1071, retro_mputfur_1148, retro_mputfur_1470, retro_mputfur_1503,
Otolemur garnettii	ENSOGAG00000026255	3 retrocopies	retro_ogar_1315, retro_ogar_1663, retro_ogar_2305,
Rattus norvegicus	ENSRNOG00000048199	3 retrocopies	retro_rnor_221, retro_rnor_299, retro_rnor_51,
Sus scrofa	ENSSSCG00000003042	3 retrocopies	retro_sscr_1064, retro_sscr_308, retro_sscr_58,
Ictidomys tridecemlineatus	ENSSTOG00000003502	3 retrocopies	retro_itri_256, retro_itri_751, retro_itri_872,

Population studies

Expression level across human populations :

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

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Indel association:

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