RetrogeneDB ID: retro_sscr_1099

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: GL894139.2:24578..25020(-)
• Located in intron of: ENSSSCG00000028039

Retrocopy information

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

Parental gene information

• Parental gene symbol: SSBP1
• Ensembl ID: ENSSSCG00000016488
• Aliases: None
• Description: single-stranded DNA binding protein 1, mitochondrial [Source:HGNC Symbol;Acc:11317]

Sequence

>retro_sscr_1099
TTTTGAAGACGTGTATTTCAGGCGCTTCATCCGTTTGTAAGACCTGCATCCGAAGGAGCTGGCAGGTTGCTTCTTGAAAG
ATCTCTGAATCGTGTGCAATTACTTGGTCGAGTAGGTCAGGACCCTGTCATGTGGCAGGTGGAAGCGAAAAACCCCATCA
CAATAGTCTCTCCAGCAGCAAATGAGCTGCGGTGAGCAGGGGAAAATGAAGCATACCAAGTGGGGGATGTCAGTCAAAAG
CCAGCAGGGCCCTGAATTTCAGTTCTCCGGCCAGGCCTCCGAGACGTGGCATATCAGTGTGTGCAAAAAGGTCCTTGAGT
TTACAGGGAACGGACAGGAGGGCTGTGGTGACTACATGCATAAAAATAATGCGAGACGACAAGCAACAGCAGTTATAGCT
GAGAGCATTCTGTTTCTGAGCGACCAGGTGAAAGGGAAGGCA

Alignment

ORF - retro_sscr_1099 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.24 %
• Parental protein coverage: 99.32 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  FRRPVFQVLHQFVRHESEVASSLVLERSLNRVQLLGRVGQDPVMRQVEGKNPVTIFSLATNEMWRSGENE
          F.R.VFQ.LH.FVR..SE.A..L.LERSLNRVQLLGRVGQDPVM.QVE.KNP.TI.S.A.NE....GENE
Retrocopy F*RRVFQALHPFVRPASEGAGRLLLERSLNRVQLLGRVGQDPVMWQVEAKNPITIVSPAANELR*AGENE

Parental  AYQMGDVSQKTTWHRISVFRPGLRDVAYQYVKKGSRVYVE-GKVDYGEYTDKNNVRRQATTIIADNIIFL
          AYQ.GDVSQK.....ISV.RPGLRDVAYQ.V.KG..VY.E.G....G.Y..KNN.RRQAT..IA..I.FL
Retrocopy AYQVGDVSQKPAGP*ISVLRPGLRDVAYQCVQKGP*VYRE>GQEGCGDYMHKNNARRQATAVIAESILFL

Parental  SDQVKEKA
          SDQVK.KA
Retrocopy SDQVKGKA

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	6.90 RPM
SRP014902_testis	0.00 RPM	11.88 RPM
SRP018288_heart	0.00 RPM	15.38 RPM
SRP018288_kidney	0.00 RPM	21.57 RPM
SRP018288_liver	0.00 RPM	22.87 RPM
SRP018288_lung	0.00 RPM	7.54 RPM
SRP018856_adipose	0.00 RPM	16.15 RPM
SRP035408_brain	0.00 RPM	20.93 RPM
SRP035408_liver	0.00 RPM	28.30 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_1099 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_1099 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_1099 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 27 parental genes, and 99 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000015145	3 retrocopies	retro_amel_1415, retro_amel_171, retro_amel_494,
Bos taurus	ENSBTAG00000010931	2 retrocopies	retro_btau_1711, retro_btau_1838,
Canis familiaris	ENSCAFG00000003885	7 retrocopies	retro_cfam_1286, retro_cfam_2013, retro_cfam_2040, retro_cfam_303, retro_cfam_308, retro_cfam_470, retro_cfam_782,
Callithrix jacchus	ENSCJAG00000013650	3 retrocopies	retro_cjac_1951, retro_cjac_3242, retro_cjac_669,
Cavia porcellus	ENSCPOG00000003354	1 retrocopy	retro_cpor_940,
Dasypus novemcinctus	ENSDNOG00000015867	15 retrocopies	retro_dnov_1050, retro_dnov_1101, retro_dnov_1242, retro_dnov_1506, retro_dnov_1517, retro_dnov_1929, retro_dnov_1983, retro_dnov_2059, retro_dnov_2246, retro_dnov_2428, retro_dnov_2557, retro_dnov_2631, retro_dnov_480, retro_dnov_837, retro_dnov_980,
Dipodomys ordii	ENSDORG00000015161	2 retrocopies	retro_dord_367, retro_dord_40,
Equus caballus	ENSECAG00000004023	4 retrocopies	retro_ecab_764, retro_ecab_842, retro_ecab_955, retro_ecab_956,
Erinaceus europaeus	ENSEEUG00000010837	2 retrocopies	retro_eeur_155, retro_eeur_194,
Felis catus	ENSFCAG00000006568	8 retrocopies	retro_fcat_1249, retro_fcat_1565, retro_fcat_1604, retro_fcat_1640, retro_fcat_439, retro_fcat_768, retro_fcat_802, retro_fcat_805,
Homo sapiens	ENSG00000106028	1 retrocopy	retro_hsap_655,
Gorilla gorilla	ENSGGOG00000009615	3 retrocopies	retro_ggor_1762, retro_ggor_368, retro_ggor_571,
Loxodonta africana	ENSLAFG00000011526	1 retrocopy	retro_lafr_753,
Myotis lucifugus	ENSMLUG00000007133	3 retrocopies	retro_mluc_1874, retro_mluc_2297, retro_mluc_2509,
Macaca mulatta	ENSMMUG00000022442	3 retrocopies	retro_mmul_1014, retro_mmul_2437, retro_mmul_662,
Mustela putorius furo	ENSMPUG00000003257	5 retrocopies	retro_mputfur_1129, retro_mputfur_1488, retro_mputfur_538, retro_mputfur_835, retro_mputfur_893,
Mus musculus	ENSMUSG00000029911	3 retrocopies	retro_mmus_2762, retro_mmus_546, retro_mmus_703,
Nomascus leucogenys	ENSNLEG00000002361	2 retrocopies	retro_nleu_2258, retro_nleu_61,
Otolemur garnettii	ENSOGAG00000016661	9 retrocopies	retro_ogar_1021, retro_ogar_1085, retro_ogar_1729, retro_ogar_1806, retro_ogar_1958, retro_ogar_2345, retro_ogar_2572, retro_ogar_3020, retro_ogar_757,
Procavia capensis	ENSPCAG00000003383	1 retrocopy	retro_pcap_371,
Pongo abelii	ENSPPYG00000018068	4 retrocopies	retro_pabe_2103, retro_pabe_490, retro_pabe_578, retro_pabe_661,
Pan troglodytes	ENSPTRG00000019778	3 retrocopies	retro_ptro_132, retro_ptro_1695, retro_ptro_476,
Pteropus vampyrus	ENSPVAG00000006221	2 retrocopies	retro_pvam_493, retro_pvam_525,
Rattus norvegicus	ENSRNOG00000012100	4 retrocopies	retro_rnor_1758, retro_rnor_2001, retro_rnor_2631, retro_rnor_915,
Sus scrofa	ENSSSCG00000016488	3 retrocopies	retro_sscr_1099 , retro_sscr_658, retro_sscr_915,
Ictidomys tridecemlineatus	ENSSTOG00000007007	4 retrocopies	retro_itri_1307, retro_itri_1481, retro_itri_1490, retro_itri_902,
Vicugna pacos	ENSVPAG00000003679	1 retrocopy	retro_vpac_71,