RetrogeneDB ID: retro_hsap_3026

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 4:16258001..16258178(-)
• Located in intron of: ENSG00000263327

Retrocopy information

• Ensembl ID: ENSG00000242358
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RPS21
• Ensembl ID: ENSG00000171858
• Aliases: RPS21, HLDF, S21
• Description: ribosomal protein S21 [Source:HGNC Symbol;Acc:10409]

Sequence

>retro_hsap_3026
ATGCAGAACAACGCCGGCGAGTTCGTGGACCTGTAAGTTCCGCGGAAATGCTCCGCTAGCAACCGCATCATCGGTGCCAA
GGACCACGCATCCATCCAGATGAACGTGGCCGAGGCTGACAAGGTCACGGGCAGGTTTAATGGCCAGTTTAAAACTTATG
CTATCTGCGGGGCGATA

Alignment

ORF - retro_hsap_3026 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.92 %
• Parental protein coverage: 72.84 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MQNDAGEFVDLYVPRKCSASNRIIGAKDHASIQMNVAEVDKVTGRFNGQFKTYAICGAI
          MQN.AGEFVDL.VPRKCSASNRIIGAKDHASIQMNVAE.DKVTGRFNGQFKTYAICGAI
Retrocopy MQNNAGEFVDL*VPRKCSASNRIIGAKDHASIQMNVAEADKVTGRFNGQFKTYAICGAI

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	128.53 RPM
bodymap2_adrenal	0.12 RPM	194.85 RPM
bodymap2_brain	0.09 RPM	40.65 RPM
bodymap2_breast	0.06 RPM	106.71 RPM
bodymap2_colon	0.15 RPM	138.21 RPM
bodymap2_heart	0.00 RPM	58.52 RPM
bodymap2_kidney	0.27 RPM	78.69 RPM
bodymap2_liver	0.09 RPM	83.75 RPM
bodymap2_lung	0.00 RPM	279.38 RPM
bodymap2_lymph_node	0.57 RPM	323.61 RPM
bodymap2_ovary	0.23 RPM	177.12 RPM
bodymap2_prostate	0.26 RPM	320.49 RPM
bodymap2_skeletal_muscle	0.04 RPM	240.23 RPM
bodymap2_testis	0.38 RPM	113.29 RPM
bodymap2_thyroid	0.04 RPM	118.51 RPM
bodymap2_white_blood_cells	0.22 RPM	338.08 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_3026 was not detected

EST

No EST(s) were mapped for retro_hsap_3026 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_141364	89 libraries	54 libraries	471 libraries	558 libraries	657 libraries

The graphical summary, for retro_hsap_3026 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

retro_hsap_3026 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_3026 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Gorilla gorilla	retro_ggor_2089
Pongo abelii	retro_pabe_2505

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 70 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017399	2 retrocopies	retro_amel_1783, retro_amel_87,
Bos taurus	ENSBTAG00000020795	2 retrocopies	retro_btau_174, retro_btau_1780,
Canis familiaris	ENSCAFG00000012676	4 retrocopies	retro_cfam_1055, retro_cfam_1687, retro_cfam_1896, retro_cfam_28,
Callithrix jacchus	ENSCJAG00000014195	5 retrocopies	retro_cjac_2266, retro_cjac_2572, retro_cjac_629, retro_cjac_82, retro_cjac_884,
Homo sapiens	ENSG00000171858	6 retrocopies	retro_hsap_1179, retro_hsap_1883, retro_hsap_2300, retro_hsap_2949, retro_hsap_3026 , retro_hsap_4303,
Gorilla gorilla	ENSGGOG00000023745	7 retrocopies	retro_ggor_131, retro_ggor_1380, retro_ggor_1647, retro_ggor_2043, retro_ggor_2089, retro_ggor_2875, retro_ggor_917,
Latimeria chalumnae	ENSLACG00000012753	1 retrocopy	retro_lcha_124,
Monodelphis domestica	ENSMODG00000016769	1 retrocopy	retro_mdom_464,
Mus musculus	ENSMUSG00000039001	11 retrocopies	retro_mmus_1100, retro_mmus_1324, retro_mmus_1482, retro_mmus_1510, retro_mmus_1688, retro_mmus_1837, retro_mmus_2039, retro_mmus_2071, retro_mmus_2243, retro_mmus_576, retro_mmus_992,
Ornithorhynchus anatinus	ENSOANG00000003361	2 retrocopies	retro_oana_102, retro_oana_107,
Otolemur garnettii	ENSOGAG00000016673	12 retrocopies	retro_ogar_1013, retro_ogar_1339, retro_ogar_1742, retro_ogar_2111, retro_ogar_2176, retro_ogar_2532, retro_ogar_2703, retro_ogar_2921, retro_ogar_3119, retro_ogar_3214, retro_ogar_3256, retro_ogar_719,
Pongo abelii	ENSPPYG00000011205	8 retrocopies	retro_pabe_1562, retro_pabe_157, retro_pabe_2446, retro_pabe_2505, retro_pabe_3503, retro_pabe_365, retro_pabe_710, retro_pabe_986,
Pan troglodytes	ENSPTRG00000013708	1 retrocopy	retro_ptro_42,
Rattus norvegicus	ENSRNOG00000006325	2 retrocopies	retro_rnor_128, retro_rnor_172,
Sus scrofa	ENSSSCG00000021825	1 retrocopy	retro_sscr_7,
Ictidomys tridecemlineatus	ENSSTOG00000001029	5 retrocopies	retro_itri_1027, retro_itri_1487, retro_itri_637, retro_itri_82, retro_itri_849,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.11 RPM
CEU_NA11843	0.31 RPM
CEU_NA11930	0.46 RPM
CEU_NA12004	0.15 RPM
CEU_NA12400	0.21 RPM
CEU_NA12751	0.27 RPM
CEU_NA12760	0.22 RPM
CEU_NA12827	0.14 RPM
CEU_NA12872	0.24 RPM
CEU_NA12873	0.19 RPM
FIN_HG00183	0.25 RPM
FIN_HG00277	0.07 RPM
FIN_HG00315	0.22 RPM
FIN_HG00321	0.03 RPM
FIN_HG00328	0.12 RPM
FIN_HG00338	0.06 RPM
FIN_HG00349	0.06 RPM
FIN_HG00375	0.24 RPM
FIN_HG00377	0.10 RPM
FIN_HG00378	0.04 RPM
GBR_HG00099	0.38 RPM
GBR_HG00111	0.19 RPM
GBR_HG00114	0.13 RPM
GBR_HG00119	0.14 RPM
GBR_HG00131	0.26 RPM
GBR_HG00133	0.05 RPM
GBR_HG00134	0.22 RPM
GBR_HG00137	0.27 RPM
GBR_HG00142	0.17 RPM
GBR_HG00143	0.03 RPM
TSI_NA20512	0.11 RPM
TSI_NA20513	0.31 RPM
TSI_NA20518	0.17 RPM
TSI_NA20532	0.07 RPM
TSI_NA20538	0.23 RPM
TSI_NA20756	0.06 RPM
TSI_NA20765	0.21 RPM
TSI_NA20771	0.23 RPM
TSI_NA20786	0.13 RPM
TSI_NA20798	0.12 RPM
YRI_NA18870	0.10 RPM
YRI_NA18907	0.14 RPM
YRI_NA18916	0.21 RPM
YRI_NA19093	0.10 RPM
YRI_NA19099	0.35 RPM
YRI_NA19114	0.00 RPM
YRI_NA19118	0.21 RPM
YRI_NA19213	0.14 RPM
YRI_NA19214	0.10 RPM
YRI_NA19223	0.24 RPM

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Indel association:

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