RetrogeneDB ID: retro_sscr_271

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 11:74072935..74073316(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: RPS15
• Ensembl ID: ENSSSCG00000023248
• Aliases: None
• Description: Sus scrofa ribosomal protein S15 (RPS15), mRNA. [Source:RefSeq mRNA;Acc:NM_214334]

Sequence

>retro_sscr_271
ATGGCAGAAGTAGAGCAGAAGATGAAGCAGACCTTCCACAAGTTCACCTGCTGTGGTGTGGACCTCAACCAGCTGCTGGA
CACTTCCTTCAAGCAGCTGACGCAGCTGTATAGCCCGTGGCAGCAGTGGAGCCTGAAGCAAGGCCTGCAGAGGAAGCAGC
ACTCACTGTTGAAGTACCTGTGCAGAGCCAAGAAGGAGGTGCCACCCTTGGTGAAGCCCGAGGTAGGGAAGATGGACCTG
CATGACGTGATCATCCTGCCGGAAATGGTGGGCACCATGGTGGGCATCTGTAAGGGCAAGACCTTCAGCCAGGGGGAGAT
GGAGCCTGAGATGATCTGACACCACCTGGGAGAGTTCTCCATCACCTACAAGCCCGTGAAG

Alignment

ORF - retro_sscr_271 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.29 %
• Parental protein coverage: 87.59 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAEVEQKKKRTFRKFTYRGVDLDQLLDMSYEQLMQLYSARQRRRLNRGLRRKQHSLLKRLRKAKKEAPPM
          MAEVEQK.K.TF.KFT..GVDL.QLLD.S..QL.QLYS..Q...L..GL.RKQHSLLK.L..AKKE.PP.
Retrocopy MAEVEQKMKQTFHKFTCCGVDLNQLLDTSFKQLTQLYSPWQQWSLKQGLQRKQHSLLKYLCRAKKEVPPL

Parental  EKPEVVKTHLRDMIILPEMVGSMVGVYNGKTFNQVEIKPEMIGHYLGEFSITYKPVK
          .KPEV.K..L.D.IILPEMVG.MVG...GKTF.Q.E..PEMI.H.LGEFSITYKPVK
Retrocopy VKPEVGKMDLHDVIILPEMVGTMVGICKGKTFSQGEMEPEMI*HHLGEFSITYKPVK

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
SRP014902_placenta	0.00 RPM	1184.23 RPM
SRP014902_testis	0.00 RPM	1324.36 RPM
SRP018288_heart	0.00 RPM	275.79 RPM
SRP018288_kidney	0.00 RPM	352.16 RPM
SRP018288_liver	0.00 RPM	268.81 RPM
SRP018288_lung	0.00 RPM	474.51 RPM
SRP018856_adipose	0.00 RPM	1183.84 RPM
SRP035408_brain	0.00 RPM	307.38 RPM
SRP035408_liver	0.00 RPM	365.57 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_271 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_271 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_271 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 58 retrocopies.

Species	Parental gene accession	Retrocopies number
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,
Dasypus novemcinctus	ENSDNOG00000000706	2 retrocopies	retro_dnov_173, retro_dnov_85,
Echinops telfairi	ENSETEG00000008645	1 retrocopy	retro_etel_2,
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,
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,
Sus scrofa	ENSSSCG00000023248	1 retrocopy	retro_sscr_271 ,
Ictidomys tridecemlineatus	ENSSTOG00000006423	2 retrocopies	retro_itri_722, retro_itri_939,