RetrogeneDB ID: retro_sscr_1031

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 9:78846957..78847448(+)
• Located in intron of: ENSSSCG00000029092

Retrocopy information

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

Parental gene information

• Parental gene symbol: CBX3
• Ensembl ID: ENSSSCG00000016711
• Aliases: None
• Description: chromobox homolog 3 [Source:HGNC Symbol;Acc:1553]

Sequence

>retro_sscr_1031
ATGGCCTCCAATAAAACTACATTTCAAAAAATGGGAAAGAAACAGAATGGAAAAAGTAAAACAGTTGAAGAGGCAGAGCC
TGAAGAATTTACTGTAGAAAAGGTACTGGACTGACGTGTAGTGAATGGGAAAATGGAATATTTCCTGAAGTAGAAGGGGT
TTACAGATGCAGACAATACTTGGGAATCTGAAGAGAATTTGGATTGTCCAGAGTTAATTGAAGCATTTCTTTACCAAAAA
GCTGGTAAAGAAAAAGATGGAGCAAAGAGAAAGTCATTGTCTGACAGTGAATCTGATGATAGCAAATCAAAGAAAAGAGA
TGCTGCTGATAAACCAAGAGGTTTTGCCAGAGGTCTTGATCTGGAAAGAATAACTGATGCCATAGACAGCAGTGGAGAAT
TAATGTTTCTCATGAAATGGAAAGATGCAGATGAGGCAGACTTGGTGCTGGCAAAAAGGCAAATATGAAGTTTCCTCAAA
TTATAATTGCC

Alignment

ORF - retro_sscr_1031 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.62 %
• Parental protein coverage: 90.71 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MASNKTTLQKMGKKQNGKSKKVEEAEPEEFVVEKVLDRRVVNGKVEYFLKWKGFTDADNTWEPEENLDCP
          MASNKTT.QKMGKKQNGKSK.VEEAEPEEF.VEKVLD.RVVNGK.EYFLK.KGFTDADNTWE.EENLDCP
Retrocopy MASNKTTFQKMGKKQNGKSKTVEEAEPEEFTVEKVLD*RVVNGKMEYFLK*KGFTDADNTWESEENLDCP

Parental  ELIEAFLNSQKAGKEKDGAKRKSLSDSESDDSKSKKKRDAADKPRGFARGLDPERIIGATDSSGELMFLM
          ELIEAFL..QKAGKEKDGAKRKSLSDSESDDSKS.KKRDAADKPRGFARGLD.ERI..A.DSSGELMFLM
Retrocopy ELIEAFL-YQKAGKEKDGAKRKSLSDSESDDSKS-KKRDAADKPRGFARGLDLERITDAIDSSGELMFLM

Parental  KWKDSDEADLVLA-KEANMKCPQIVIA
          KWKD.DEADLVLA.K.ANMK.PQI.IA
Retrocopy KWKDADEADLVLA<KKANMKFPQIIIA

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	7.43 RPM
SRP014902_testis	0.00 RPM	47.81 RPM
SRP018288_heart	0.05 RPM	55.35 RPM
SRP018288_kidney	0.00 RPM	64.62 RPM
SRP018288_liver	0.00 RPM	47.33 RPM
SRP018288_lung	0.20 RPM	96.23 RPM
SRP018856_adipose	0.00 RPM	16.27 RPM
SRP035408_brain	0.19 RPM	80.67 RPM
SRP035408_liver	0.09 RPM	52.75 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_1031 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_1031 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_1031 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 30 parental genes, and 182 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000005969	1 retrocopy	retro_amel_1184,
Canis familiaris	ENSCAFG00000002897	11 retrocopies	retro_cfam_1157, retro_cfam_161, retro_cfam_1811, retro_cfam_1823, retro_cfam_1849, retro_cfam_2083, retro_cfam_502, retro_cfam_594, retro_cfam_739, retro_cfam_931, retro_cfam_948,
Choloepus hoffmanni	ENSCHOG00000013843	22 retrocopies	retro_chof_1128, retro_chof_1147, retro_chof_1156, retro_chof_1178, retro_chof_1210, retro_chof_1223, retro_chof_132, retro_chof_1569, retro_chof_1672, retro_chof_1779, retro_chof_1863, retro_chof_1962, retro_chof_222, retro_chof_2269, retro_chof_2347, retro_chof_2379, retro_chof_2435, retro_chof_2695, retro_chof_411, retro_chof_676, retro_chof_87, retro_chof_936,
Callithrix jacchus	ENSCJAG00000007952	8 retrocopies	retro_cjac_1100, retro_cjac_1414, retro_cjac_1612, retro_cjac_2405, retro_cjac_2623, retro_cjac_2728, retro_cjac_3322, retro_cjac_869,
Cavia porcellus	ENSCPOG00000015168	1 retrocopy	retro_cpor_66,
Dasypus novemcinctus	ENSDNOG00000006250	19 retrocopies	retro_dnov_1136, retro_dnov_1174, retro_dnov_1208, retro_dnov_1270, retro_dnov_1605, retro_dnov_2306, retro_dnov_2307, retro_dnov_2397, retro_dnov_2543, retro_dnov_2605, retro_dnov_2633, retro_dnov_321, retro_dnov_359, retro_dnov_385, retro_dnov_445, retro_dnov_772, retro_dnov_794, retro_dnov_833, retro_dnov_844,
Dipodomys ordii	ENSDORG00000005487	11 retrocopies	retro_dord_309, retro_dord_405, retro_dord_437, retro_dord_440, retro_dord_456, retro_dord_502, retro_dord_629, retro_dord_630, retro_dord_655, retro_dord_700, retro_dord_780,
Equus caballus	ENSECAG00000012780	1 retrocopy	retro_ecab_784,
Felis catus	ENSFCAG00000015224	6 retrocopies	retro_fcat_1005, retro_fcat_1103, retro_fcat_1485, retro_fcat_1519, retro_fcat_336, retro_fcat_473,
Homo sapiens	ENSG00000122565	9 retrocopies	retro_hsap_1071, retro_hsap_1145, retro_hsap_1902, retro_hsap_2332, retro_hsap_2771, retro_hsap_3368, retro_hsap_3650, retro_hsap_766, retro_hsap_910,
Gorilla gorilla	ENSGGOG00000025853	6 retrocopies	retro_ggor_1928, retro_ggor_2281, retro_ggor_2466, retro_ggor_2467, retro_ggor_635, retro_ggor_845,
Loxodonta africana	ENSLAFG00000006907	3 retrocopies	retro_lafr_661, retro_lafr_687, retro_lafr_776,
Microcebus murinus	ENSMICG00000006998	11 retrocopies	retro_mmur_1015, retro_mmur_1030, retro_mmur_1076, retro_mmur_1178, retro_mmur_1497, retro_mmur_1500, retro_mmur_1548, retro_mmur_386, retro_mmur_421, retro_mmur_68, retro_mmur_685,
Myotis lucifugus	ENSMLUG00000007591	2 retrocopies	retro_mluc_2486, retro_mluc_813,
Mus musculus	ENSMUSG00000029836	1 retrocopy	retro_mmus_77,
Nomascus leucogenys	ENSNLEG00000014931	9 retrocopies	retro_nleu_141, retro_nleu_1685, retro_nleu_2462, retro_nleu_373, retro_nleu_397, retro_nleu_511, retro_nleu_676, retro_nleu_944, retro_nleu_964,
Otolemur garnettii	ENSOGAG00000016583	1 retrocopy	retro_ogar_136,
Ochotona princeps	ENSOPRG00000011713	9 retrocopies	retro_opri_103, retro_opri_159, retro_opri_209, retro_opri_300, retro_opri_429, retro_opri_569, retro_opri_598, retro_opri_728, retro_opri_733,
Procavia capensis	ENSPCAG00000004904	2 retrocopies	retro_pcap_108, retro_pcap_166,
Pongo abelii	ENSPPYG00000017714	10 retrocopies	retro_pabe_2112, retro_pabe_2243, retro_pabe_2724, retro_pabe_2770, retro_pabe_2997, retro_pabe_3608, retro_pabe_758, retro_pabe_786, retro_pabe_892, retro_pabe_951,
Pan troglodytes	ENSPTRG00000019003	10 retrocopies	retro_ptro_17, retro_ptro_1706, retro_ptro_1875, retro_ptro_2289, retro_ptro_2475, retro_ptro_395, retro_ptro_537, retro_ptro_630, retro_ptro_729, retro_ptro_780,
Pteropus vampyrus	ENSPVAG00000006297	2 retrocopies	retro_pvam_294, retro_pvam_786,
Rattus norvegicus	ENSRNOG00000011814	2 retrocopies	retro_rnor_120, retro_rnor_301,
Sorex araneus	ENSSARG00000008011	2 retrocopies	retro_sara_496, retro_sara_709,
Sarcophilus harrisii	ENSSHAG00000017913	1 retrocopy	retro_shar_153,
Sus scrofa	ENSSSCG00000016711	4 retrocopies	retro_sscr_1031 , retro_sscr_204, retro_sscr_420, retro_sscr_755,
Sus scrofa	ENSSSCG00000017529	1 retrocopy	retro_sscr_635,
Ictidomys tridecemlineatus	ENSSTOG00000006223	4 retrocopies	retro_itri_1093, retro_itri_1682, retro_itri_1764, retro_itri_912,
Tarsius syrichta	ENSTSYG00000008159	6 retrocopies	retro_tsyr_1459, retro_tsyr_1545, retro_tsyr_1552, retro_tsyr_1645, retro_tsyr_203, retro_tsyr_583,
Tursiops truncatus	ENSTTRG00000000711	7 retrocopies	retro_ttru_1238, retro_ttru_1247, retro_ttru_1851, retro_ttru_294, retro_ttru_52, retro_ttru_591, retro_ttru_644,