RetrogeneDB ID: retro_hsap_1484

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 15:37782891..37783304(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000243122
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RPS15
• Ensembl ID: ENSG00000115268
• Aliases: RPS15, RIG, S15
• Description: ribosomal protein S15 [Source:HGNC Symbol;Acc:10388]

Sequence

>retro_hsap_1484
ATGACAGACGTAGAGCAGAAGAAGCGGACCTTCCGCAAGTTCACTTACCGCGGTGTGGGCCTGGACCAGATGCTGGACGT
GCCCTACGAGCAGCTTATGCAGCTATACAGTGCGCGTCGGCAGCAGCGTTTGAACCGGGTCTGGGGCGGAAACAGCACTC
GCCGCTGAAGCGCCTGCGCAAGGCCAAGAAGGAGGTACCGCCCATGGAGAAGCCGGAAGTGGTGAAGACGCACCTGTAGG
ACATGATCATCTTGCCTGAGATGATGGGCAGCATGGTGGGCGTCTACAACGGCAAAACCTTCAGCCAGGTGGAGATCAAG
CCGGAGATGATCGGCCACTACCTGGGCGAGTTGTCCATCACCTACAAGCCCGTGAAGCACTGCTGGCCCCGCATTGGGGC
CACCCCTTCTTCA

Alignment

ORF - retro_hsap_1484 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.29 %
• Parental protein coverage: 95.86 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAEVEQKKKRTFRKFTYRGVDLDQLLDMSYEQLMQLYSARQRRRLNR-GLRRKQHSLLKRLRKAKKEAPP
          M..VEQKK.RTFRKFTYRGV.LDQ.LD..YEQLMQLYSAR...RLNR.GL.RKQHS.LKRLRKAKKE.PP
Retrocopy MTDVEQKK-RTFRKFTYRGVGLDQMLDVPYEQLMQLYSARRQQRLNR<GLGRKQHSPLKRLRKAKKEVPP

Parental  MEKPEVVKTHLRDMIILPEMVGSMVGVYNGKTFNQVEIKPEMIGHYLGEFSITYKPVKHGRPGIGATHSS
          MEKPEVVKTHL.DMIILPEM.GSMVGVYNGKTF.QVEIKPEMIGHYLGE.SITYKPVKH..P.IGAT.SS
Retrocopy MEKPEVVKTHL*DMIILPEMMGSMVGVYNGKTFSQVEIKPEMIGHYLGELSITYKPVKHCWPRIGATPSS

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	173.38 RPM
bodymap2_adrenal	0.00 RPM	221.60 RPM
bodymap2_brain	0.00 RPM	38.11 RPM
bodymap2_breast	0.00 RPM	124.73 RPM
bodymap2_colon	0.00 RPM	180.93 RPM
bodymap2_heart	0.00 RPM	53.11 RPM
bodymap2_kidney	0.00 RPM	59.50 RPM
bodymap2_liver	0.00 RPM	54.58 RPM
bodymap2_lung	0.00 RPM	210.71 RPM
bodymap2_lymph_node	0.00 RPM	225.44 RPM
bodymap2_ovary	0.00 RPM	191.59 RPM
bodymap2_prostate	0.00 RPM	191.46 RPM
bodymap2_skeletal_muscle	0.00 RPM	190.21 RPM
bodymap2_testis	0.09 RPM	123.47 RPM
bodymap2_thyroid	0.00 RPM	109.65 RPM
bodymap2_white_blood_cells	0.00 RPM	204.44 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_hsap_1484 was not detected

EST

No EST(s) were mapped for retro_hsap_1484 retrocopy.

TSS

No TSS is located nearby retro_hsap_1484 retrocopy 5' end.

Lab

retro_hsap_1484 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_1484 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Gorilla gorilla	retro_ggor_1136
Pongo abelii	retro_pabe_1233

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 63 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000019718	1 retrocopy	retro_btau_1856,
Callithrix jacchus	ENSCJAG00000005632	13 retrocopies	retro_cjac_143, retro_cjac_151, retro_cjac_1517, retro_cjac_1607, retro_cjac_1672, retro_cjac_1714, retro_cjac_2069, retro_cjac_2236, retro_cjac_2596, retro_cjac_2656, retro_cjac_48, retro_cjac_756, retro_cjac_86,
Cavia porcellus	ENSCPOG00000003968	1 retrocopy	retro_cpor_495,
Echinops telfairi	ENSETEG00000008645	1 retrocopy	retro_etel_2,
Felis catus	ENSFCAG00000010769	1 retrocopy	retro_fcat_1570,
Homo sapiens	ENSG00000115268	4 retrocopies	retro_hsap_1484 , retro_hsap_2341, retro_hsap_2650, retro_hsap_530,
Gorilla gorilla	ENSGGOG00000002818	4 retrocopies	retro_ggor_1136, retro_ggor_116, retro_ggor_141, retro_ggor_1851,
Monodelphis domestica	ENSMODG00000005119	1 retrocopy	retro_mdom_1335,
Mus musculus	ENSMUSG00000063457	8 retrocopies	retro_mmus_1270, retro_mmus_208, retro_mmus_2734, retro_mmus_2786, retro_mmus_3166, retro_mmus_3642, retro_mmus_520, retro_mmus_917,
Nomascus leucogenys	ENSNLEG00000001651	8 retrocopies	retro_nleu_105, retro_nleu_1858, retro_nleu_1922, retro_nleu_2390, retro_nleu_2465, retro_nleu_2559, retro_nleu_461, retro_nleu_544,
Otolemur garnettii	ENSOGAG00000015776	4 retrocopies	retro_ogar_194, retro_ogar_210, retro_ogar_2237, retro_ogar_96,
Pongo abelii	ENSPPYG00000009317	4 retrocopies	retro_pabe_1233, retro_pabe_2321, retro_pabe_67, retro_pabe_893,
Pan troglodytes	ENSPTRG00000010200	1 retrocopy	retro_ptro_122,
Pteropus vampyrus	ENSPVAG00000003168	2 retrocopies	retro_pvam_382, retro_pvam_926,
Rattus norvegicus	ENSRNOG00000024603	8 retrocopies	retro_rnor_1384, retro_rnor_1711, retro_rnor_1712, retro_rnor_178, retro_rnor_2086, retro_rnor_2114, retro_rnor_2642, retro_rnor_700,
Ictidomys tridecemlineatus	ENSSTOG00000006423	2 retrocopies	retro_itri_722, retro_itri_939,