RetrogeneDB ID: retro_hsap_119

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 1:19934607..19935059(+)
• Located in intron of: ENSG00000173436

Retrocopy information

• Ensembl ID: ENSG00000226396
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RPS14
• Ensembl ID: ENSG00000164587
• Aliases: RPS14, EMTB, S14
• Description: ribosomal protein S14 [Source:HGNC Symbol;Acc:10387]

Sequence

>retro_hsap_119
ATGGCACCTGGAAAGGGGAAGGAAAAGAAGGAAGAACAGGTCATCAACCTCGGACCTCAGGTGGCTGAAGGGGAGAATGT
ATTTGGTGTCTGCCATATCTTTGCATCCTTCAATGACACTTTTGTCCATGTCACGGATCTTTCTGGCAAACAAACCATCT
GCCGTGTGACTGGTGGGATGAAGGTGAAGGCAGACCGAGATGAATCCTCGCCATATGCTGCTATGTTGACCACCCAGGAT
GTGGCCCAGAGGTGCAAGGAGCTGGGTATCATTGCCCTACACATCCAACTCCGGGCCACAGGAGGAAATAGGACCAAGAC
CCTTGGACCTGGGGCCCAGTCGGCCCTCAGAGCCCTTGCCTGCTCGGGTATGAAGATCGGGAGGATTGAGGACGTCACCC
CCATCCCCTCTGACAGCACTCTCAGGAAGGGGGTCACCGTGGTCGCCGTCTG

Alignment

ORF - retro_hsap_119 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.11 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAPRKGKEKKEEQVISLGPQVAEGENVFGVCHIFASFNDTFVHVTDLSGKETICRVTGGMKVKADRDESS
          MAP.KGKEKKEEQVI.LGPQVAEGENVFGVCHIFASFNDTFVHVTDLSGK.TICRVTGGMKVKADRDESS
Retrocopy MAPGKGKEKKEEQVINLGPQVAEGENVFGVCHIFASFNDTFVHVTDLSGKQTICRVTGGMKVKADRDESS

Parental  PYAAMLAAQDVAQRCKELGITALHIKLRATGGNRTKTPGPGAQSALRALARSGMKIGRIEDVTPIPSDST
          PYAAML..QDVAQRCKELGI.ALHI.LRATGGNRTKT.GPGAQSALRALA.SGMKIGRIEDVTPIPSDST
Retrocopy PYAAMLTTQDVAQRCKELGIIALHIQLRATGGNRTKTLGPGAQSALRALACSGMKIGRIEDVTPIPSDST

Parental  RRK-GGRRGRRL
          .RK.GG.RGRRL
Retrocopy LRK<GGHRGRRL

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	0.26 RPM	639.89 RPM
bodymap2_adrenal	0.70 RPM	859.94 RPM
bodymap2_brain	0.28 RPM	215.93 RPM
bodymap2_breast	0.12 RPM	544.48 RPM
bodymap2_colon	0.73 RPM	825.31 RPM
bodymap2_heart	0.13 RPM	153.10 RPM
bodymap2_kidney	0.77 RPM	313.72 RPM
bodymap2_liver	0.21 RPM	140.62 RPM
bodymap2_lung	1.74 RPM	540.54 RPM
bodymap2_lymph_node	3.03 RPM	522.77 RPM
bodymap2_ovary	0.66 RPM	754.52 RPM
bodymap2_prostate	1.07 RPM	706.05 RPM
bodymap2_skeletal_muscle	0.02 RPM	380.07 RPM
bodymap2_testis	0.81 RPM	469.12 RPM
bodymap2_thyroid	0.36 RPM	478.14 RPM
bodymap2_white_blood_cells	0.35 RPM	888.14 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_119 was not detected

EST

No EST(s) were mapped for retro_hsap_119 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_87556	30 libraries	5 libraries	155 libraries	414 libraries	1225 libraries

The graphical summary, for retro_hsap_119 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

• Experiment type: PCR amplification
• Forward primer: CGACTAGGTTTCCATATAGAG (21 nt long)
• Reverse primer: ACATGAAGGCAATTTATTAACAG (23 nt long)
• Anneling temperature: 58 °C
• (Expected) product size: 627
• Electrophoresis gel image:
• Additional comment: Red arrow indicates PCR product of retrogene in pooled cDNA from 16 human tissues (Clontech). Red number of lane indicates particular retrogene; L - GeneRuler 100 bp DNA Ladder (Thermo Fisher Scientific); N - No template control (water instead of cDNA)

Homology

Retrocopy orthology:

Retrocopy retro_hsap_119 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_130
Gorilla gorilla	retro_ggor_222
Pongo abelii	retro_pabe_494
Macaca mulatta	retro_mmul_358

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 72 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000015004	1 retrocopy	retro_acar_201,
Ailuropoda melanoleuca	ENSAMEG00000004644	2 retrocopies	retro_amel_1390, retro_amel_524,
Bos taurus	ENSBTAG00000008570	2 retrocopies	retro_btau_1109, retro_btau_213,
Canis familiaris	ENSCAFG00000018094	2 retrocopies	retro_cfam_1589, retro_cfam_301,
Callithrix jacchus	ENSCJAG00000020981	1 retrocopy	retro_cjac_89,
Cavia porcellus	ENSCPOG00000024408	2 retrocopies	retro_cpor_253, retro_cpor_284,
Echinops telfairi	ENSETEG00000002899	6 retrocopies	retro_etel_1270, retro_etel_1358, retro_etel_1851, retro_etel_1995, retro_etel_293, retro_etel_967,
Homo sapiens	ENSG00000164587	8 retrocopies	retro_hsap_119 , retro_hsap_1622, retro_hsap_268, retro_hsap_3001, retro_hsap_3113, retro_hsap_3232, retro_hsap_3495, retro_hsap_3789,
Gorilla gorilla	ENSGGOG00000024593	8 retrocopies	retro_ggor_1225, retro_ggor_2080, retro_ggor_2135, retro_ggor_2199, retro_ggor_222, retro_ggor_2362, retro_ggor_2548, retro_ggor_316,
Latimeria chalumnae	ENSLACG00000016164	1 retrocopy	retro_lcha_12,
Macaca mulatta	ENSMMUG00000002848	5 retrocopies	retro_mmul_1921, retro_mmul_1983, retro_mmul_358, retro_mmul_570, retro_mmul_90,
Mustela putorius furo	ENSMPUG00000013776	1 retrocopy	retro_mputfur_127,
Nomascus leucogenys	ENSNLEG00000010366	1 retrocopy	retro_nleu_101,
Oryctolagus cuniculus	ENSOCUG00000011509	1 retrocopy	retro_ocun_128,
Otolemur garnettii	ENSOGAG00000000721	1 retrocopy	retro_ogar_286,
Pongo abelii	ENSPPYG00000015950	7 retrocopies	retro_pabe_1340, retro_pabe_2487, retro_pabe_2571, retro_pabe_2888, retro_pabe_3204, retro_pabe_401, retro_pabe_494,
Rattus norvegicus	ENSRNOG00000018774	10 retrocopies	retro_rnor_1313, retro_rnor_1467, retro_rnor_1532, retro_rnor_1759, retro_rnor_1875, retro_rnor_1918, retro_rnor_2181, retro_rnor_228, retro_rnor_2728, retro_rnor_873,
Sarcophilus harrisii	ENSSHAG00000018052	3 retrocopies	retro_shar_380, retro_shar_381, retro_shar_503,
Tupaia belangeri	ENSTBEG00000006368	10 retrocopies	retro_tbel_1147, retro_tbel_1332, retro_tbel_1603, retro_tbel_1868, retro_tbel_202, retro_tbel_3517, retro_tbel_3619, retro_tbel_416, retro_tbel_519, retro_tbel_740,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.45 RPM
CEU_NA11843	6.60 RPM
CEU_NA11930	2.61 RPM
CEU_NA12004	4.25 RPM
CEU_NA12400	1.19 RPM
CEU_NA12751	0.44 RPM
CEU_NA12760	7.59 RPM
CEU_NA12827	4.01 RPM
CEU_NA12872	0.44 RPM
CEU_NA12873	4.15 RPM
FIN_HG00183	0.88 RPM
FIN_HG00277	0.63 RPM
FIN_HG00315	2.40 RPM
FIN_HG00321	2.30 RPM
FIN_HG00328	0.57 RPM
FIN_HG00338	0.30 RPM
FIN_HG00349	4.04 RPM
FIN_HG00375	0.59 RPM
FIN_HG00377	2.12 RPM
FIN_HG00378	3.42 RPM
GBR_HG00099	0.52 RPM
GBR_HG00111	0.92 RPM
GBR_HG00114	7.02 RPM
GBR_HG00119	2.85 RPM
GBR_HG00131	0.98 RPM
GBR_HG00133	3.55 RPM
GBR_HG00134	0.46 RPM
GBR_HG00137	0.58 RPM
GBR_HG00142	0.44 RPM
GBR_HG00143	0.41 RPM
TSI_NA20512	0.37 RPM
TSI_NA20513	0.53 RPM
TSI_NA20518	7.58 RPM
TSI_NA20532	3.67 RPM
TSI_NA20538	0.41 RPM
TSI_NA20756	0.23 RPM
TSI_NA20765	1.68 RPM
TSI_NA20771	3.32 RPM
TSI_NA20786	0.18 RPM
TSI_NA20798	0.22 RPM
YRI_NA18870	0.37 RPM
YRI_NA18907	0.10 RPM
YRI_NA18916	1.54 RPM
YRI_NA19093	0.10 RPM
YRI_NA19099	1.68 RPM
YRI_NA19114	0.16 RPM
YRI_NA19118	2.92 RPM
YRI_NA19213	0.33 RPM
YRI_NA19214	2.34 RPM
YRI_NA19223	0.46 RPM

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Indel association:

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