RetrogeneDB ID: retro_sscr_406

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 14:16895338..16895536(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSSCG00000000374
• Aliases: None
• Description: 40S ribosomal protein S26 [Source:RefSeq peptide;Acc:NP_001090950]

Sequence

>retro_sscr_406
GTCAGGGACATTTCCGAAGCGAGCATTTTCGATGCCTATGGGCTTCCCAAGCTGTATGTGAAACTACACTGTGGCGTGAG
TTGTGCCATTCACAGCAAGGTAGTCAGGAGTCGTTCTGGGGAAGCCCAAAAGGGTAGAGCACCTCCACTCCGATTTAGAC
CTGCGGGTGCGTCCCCATGACCTCCACCAAAGTCCATG

Alignment

ORF - retro_sscr_406 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.3 %
• Parental protein coverage: 56.9 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VRDISEASVFDAYVLPKLYVKLHYCVSCAIHSKVVRNRSREARKDRTPPPRFRPAGAAPRPPPKPM
          VRDISEAS.FDAY.LPKLYVKLH..VSCAIHSKVVR.RS.EA.K.R.PP.RFRPAGA.P.PPPK.M
Retrocopy VRDISEASIFDAYGLPKLYVKLHCGVSCAIHSKVVRSRSGEAQKGRAPPLRFRPAGASP*PPPKSM

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	0.13 RPM	304.62 RPM
SRP014902_testis	0.00 RPM	504.40 RPM
SRP018288_heart	0.00 RPM	163.08 RPM
SRP018288_kidney	0.00 RPM	223.12 RPM
SRP018288_liver	0.00 RPM	207.56 RPM
SRP018288_lung	0.00 RPM	153.04 RPM
SRP018856_adipose	0.00 RPM	475.71 RPM
SRP035408_brain	0.00 RPM	323.29 RPM
SRP035408_liver	0.00 RPM	328.52 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_406 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_406 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_406 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 21 parental genes, and 184 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000003260	7 retrocopies	retro_amel_1037, retro_amel_1240, retro_amel_303, retro_amel_777, retro_amel_926, retro_amel_927, retro_amel_928,
Bos taurus	ENSBTAG00000038896	3 retrocopies	retro_btau_191, retro_btau_25, retro_btau_724,
Choloepus hoffmanni	ENSCHOG00000001489	10 retrocopies	retro_chof_1367, retro_chof_1423, retro_chof_1793, retro_chof_1825, retro_chof_2156, retro_chof_2255, retro_chof_2482, retro_chof_382, retro_chof_611, retro_chof_756,
Cavia porcellus	ENSCPOG00000023630	6 retrocopies	retro_cpor_115, retro_cpor_1231, retro_cpor_134, retro_cpor_173, retro_cpor_48, retro_cpor_992,
Dipodomys ordii	ENSDORG00000001151	2 retrocopies	retro_dord_239, retro_dord_279,
Echinops telfairi	ENSETEG00000004510	35 retrocopies	retro_etel_1072, retro_etel_1145, retro_etel_1149, retro_etel_1175, retro_etel_1321, retro_etel_1357, retro_etel_1407, retro_etel_1423, retro_etel_1469, retro_etel_1498, retro_etel_155, retro_etel_162, retro_etel_1647, retro_etel_1691, retro_etel_1703, retro_etel_1734, retro_etel_1801, retro_etel_181, retro_etel_1859, retro_etel_1913, retro_etel_1963, retro_etel_2006, retro_etel_2043, retro_etel_2138, retro_etel_2146, retro_etel_2175, retro_etel_269, retro_etel_354, retro_etel_38, retro_etel_424, retro_etel_462, retro_etel_741, retro_etel_77, retro_etel_894, retro_etel_898,
Felis catus	ENSFCAG00000013977	10 retrocopies	retro_fcat_1211, retro_fcat_1332, retro_fcat_1460, retro_fcat_1728, retro_fcat_1851, retro_fcat_1948, retro_fcat_1949, retro_fcat_428, retro_fcat_508, retro_fcat_949,
Homo sapiens	ENSG00000197728	13 retrocopies	retro_hsap_1000, retro_hsap_1665, retro_hsap_2289, retro_hsap_2301, retro_hsap_2691, retro_hsap_2977, retro_hsap_3978, retro_hsap_4120, retro_hsap_481, retro_hsap_4853, retro_hsap_498, retro_hsap_605, retro_hsap_946,
Gorilla gorilla	ENSGGOG00000011566	6 retrocopies	retro_ggor_106, retro_ggor_121, retro_ggor_19, retro_ggor_55, retro_ggor_56, retro_ggor_63,
Loxodonta africana	ENSLAFG00000013329	8 retrocopies	retro_lafr_180, retro_lafr_240, retro_lafr_40, retro_lafr_464, retro_lafr_513, retro_lafr_768, retro_lafr_835, retro_lafr_962,
Myotis lucifugus	ENSMLUG00000029968	10 retrocopies	retro_mluc_1153, retro_mluc_149, retro_mluc_1925, retro_mluc_2065, retro_mluc_2163, retro_mluc_2462, retro_mluc_266, retro_mluc_309, retro_mluc_332, retro_mluc_477,
Macaca mulatta	ENSMMUG00000017042	7 retrocopies	retro_mmul_1009, retro_mmul_1017, retro_mmul_1676, retro_mmul_1944, retro_mmul_2092, retro_mmul_294, retro_mmul_646,
Mus musculus	ENSMUSG00000025362	1 retrocopy	retro_mmus_115,
Ochotona princeps	ENSOPRG00000005721	3 retrocopies	retro_opri_437, retro_opri_497, retro_opri_860,
Pongo abelii	ENSPPYG00000004642	16 retrocopies	retro_pabe_1234, retro_pabe_1372, retro_pabe_140, retro_pabe_1405, retro_pabe_1431, retro_pabe_155, retro_pabe_1613, retro_pabe_237, retro_pabe_25, retro_pabe_2835, retro_pabe_3068, retro_pabe_3399, retro_pabe_3432, retro_pabe_809, retro_pabe_903, retro_pabe_924,
Pan troglodytes	ENSPTRG00000005075	1 retrocopy	retro_ptro_74,
Pteropus vampyrus	ENSPVAG00000007559	15 retrocopies	retro_pvam_1008, retro_pvam_1033, retro_pvam_1115, retro_pvam_1167, retro_pvam_1184, retro_pvam_1435, retro_pvam_251, retro_pvam_259, retro_pvam_298, retro_pvam_496, retro_pvam_644, retro_pvam_735, retro_pvam_871, retro_pvam_970, retro_pvam_984,
Rattus norvegicus	ENSRNOG00000005517	1 retrocopy	retro_rnor_196,
Sus scrofa	ENSSSCG00000000374	2 retrocopies	retro_sscr_406 , retro_sscr_650,
Ictidomys tridecemlineatus	ENSSTOG00000010559	12 retrocopies	retro_itri_1300, retro_itri_1446, retro_itri_1477, retro_itri_1488, retro_itri_289, retro_itri_418, retro_itri_469, retro_itri_470, retro_itri_643, retro_itri_652, retro_itri_729, retro_itri_871,
Tursiops truncatus	ENSTTRG00000015012	16 retrocopies	retro_ttru_1169, retro_ttru_1300, retro_ttru_131, retro_ttru_1319, retro_ttru_1329, retro_ttru_1412, retro_ttru_1514, retro_ttru_1635, retro_ttru_17, retro_ttru_1734, retro_ttru_1795, retro_ttru_1897, retro_ttru_428, retro_ttru_47, retro_ttru_651, retro_ttru_893,