RetrogeneDB ID: retro_sscr_1223

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: Y:1212881..1213110(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSSCG00000030295
• Aliases: None
• Description: None

Sequence

>retro_sscr_1223
ATTGATATGTCATGCCTTATTGGGAAGGACAACAATTCCAGGGTAAAATTGTCCCATTTTTGACAAAATTATATAGTCTT
CAATTCCAAAAATTCCAGCATAGTATCATGACCAGGACCATCAGCACATACCAGAAAGTAGCATCATCACCATGGCTGTG
GACCAGCTCAAGACTGATGAATACCCCATCTTGGGATTCCACCAGATGTTCTAATTAAAGAATATCAAC

Alignment

ORF - retro_sscr_1223 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.09 %
• Parental protein coverage: 59.84 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  IDASCLT-WEGQQFQGKTA-IVEKLSSLPFQKIQHSITA-QDHQPTPDSCIISMVVGQLKADEDPIMGFH
          ID.SCL..WEGQQFQGK......KL.SL.FQK.QHSI...QDHQ..P.S.II.M.V.QLK.DE.PI.GFH
Retrocopy IDMSCLI<WEGQQFQGKIVPFLTKLYSLQFQKFQHSIMT<QDHQHIPESSIITMAVDQLKTDEYPILGFH

Parental  QMFLLKNIN
          QMF.LKNIN
Retrocopy QMF*LKNIN

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	43.40 RPM
SRP014902_testis	0.00 RPM	20.09 RPM
SRP018288_heart	0.00 RPM	27.92 RPM
SRP018288_kidney	0.00 RPM	27.68 RPM
SRP018288_liver	0.00 RPM	17.91 RPM
SRP018288_lung	0.00 RPM	67.51 RPM
SRP018856_adipose	0.00 RPM	17.94 RPM
SRP035408_brain	0.00 RPM	20.52 RPM
SRP035408_liver	0.00 RPM	12.62 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_1223 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_1223 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_1223 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 35 parental genes, and 131 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017548	5 retrocopies	retro_amel_1225, retro_amel_134, retro_amel_1485, retro_amel_415, retro_amel_445,
Bos taurus	ENSBTAG00000006414	2 retrocopies	retro_btau_1573, retro_btau_881,
Choloepus hoffmanni	ENSCHOG00000003059	3 retrocopies	retro_chof_1386, retro_chof_1619, retro_chof_2488,
Callithrix jacchus	ENSCJAG00000016015	14 retrocopies	retro_cjac_1328, retro_cjac_2247, retro_cjac_2562, retro_cjac_2864, retro_cjac_2913, retro_cjac_2953, retro_cjac_2978, retro_cjac_3126, retro_cjac_3299, retro_cjac_4044, retro_cjac_4173, retro_cjac_587, retro_cjac_777, retro_cjac_924,
Cavia porcellus	ENSCPOG00000003521	1 retrocopy	retro_cpor_1368,
Equus caballus	ENSECAG00000021530	1 retrocopy	retro_ecab_151,
Erinaceus europaeus	ENSEEUG00000003470	2 retrocopies	retro_eeur_149, retro_eeur_571,
Echinops telfairi	ENSETEG00000016354	9 retrocopies	retro_etel_1700, retro_etel_1737, retro_etel_1909, retro_etel_1925, retro_etel_245, retro_etel_281, retro_etel_301, retro_etel_399, retro_etel_746,
Felis catus	ENSFCAG00000008167	3 retrocopies	retro_fcat_154, retro_fcat_743, retro_fcat_845,
Homo sapiens	ENSG00000102898	7 retrocopies	retro_hsap_1322, retro_hsap_1480, retro_hsap_1858, retro_hsap_207, retro_hsap_4181, retro_hsap_4854, retro_hsap_544,
Gorilla gorilla	ENSGGOG00000023925	5 retrocopies	retro_ggor_1032, retro_ggor_2152, retro_ggor_279, retro_ggor_2806, retro_ggor_3028,
Loxodonta africana	ENSLAFG00000031037	1 retrocopy	retro_lafr_623,
Macropus eugenii	ENSMEUG00000009874	11 retrocopies	retro_meug_1023, retro_meug_136, retro_meug_1539, retro_meug_1585, retro_meug_1778, retro_meug_2140, retro_meug_253, retro_meug_282, retro_meug_352, retro_meug_676, retro_meug_748,
Myotis lucifugus	ENSMLUG00000025175	3 retrocopies	retro_mluc_1265, retro_mluc_2194, retro_mluc_911,
Macaca mulatta	ENSMMUG00000012038	6 retrocopies	retro_mmul_1160, retro_mmul_1270, retro_mmul_2127, retro_mmul_2169, retro_mmul_2593, retro_mmul_27,
Monodelphis domestica	ENSMODG00000005517	6 retrocopies	retro_mdom_1031, retro_mdom_1291, retro_mdom_1488, retro_mdom_1489, retro_mdom_1903, retro_mdom_37,
Mustela putorius furo	ENSMPUG00000006737	4 retrocopies	retro_mputfur_229, retro_mputfur_614, retro_mputfur_714, retro_mputfur_962,
Mus musculus	ENSMUSG00000008450	1 retrocopy	retro_mmus_232,
Nomascus leucogenys	ENSNLEG00000004889	7 retrocopies	retro_nleu_1295, retro_nleu_1791, retro_nleu_1855, retro_nleu_2374, retro_nleu_2384, retro_nleu_2953, retro_nleu_731,
Oryctolagus cuniculus	ENSOCUG00000006322	1 retrocopy	retro_ocun_115,
Otolemur garnettii	ENSOGAG00000015568	2 retrocopies	retro_ogar_2713, retro_ogar_2811,
Ochotona princeps	ENSOPRG00000013727	4 retrocopies	retro_opri_1089, retro_opri_1102, retro_opri_1170, retro_opri_229,
Procavia capensis	ENSPCAG00000015344	1 retrocopy	retro_pcap_56,
Pongo abelii	ENSPPYG00000007472	7 retrocopies	retro_pabe_1101, retro_pabe_1229, retro_pabe_1515, retro_pabe_3421, retro_pabe_3772, retro_pabe_433, retro_pabe_502,
Pan troglodytes	ENSPTRG00000008248	7 retrocopies	retro_ptro_1001, retro_ptro_1239, retro_ptro_2835, retro_ptro_3230, retro_ptro_338, retro_ptro_409, retro_ptro_903,
Pteropus vampyrus	ENSPVAG00000016605	1 retrocopy	retro_pvam_843,
Rattus norvegicus	ENSRNOG00000018945	4 retrocopies	retro_rnor_1149, retro_rnor_1616, retro_rnor_2427, retro_rnor_545,
Sorex araneus	ENSSARG00000007472	1 retrocopy	retro_sara_333,
Sarcophilus harrisii	ENSSHAG00000006100	1 retrocopy	retro_shar_274,
Sus scrofa	ENSSSCG00000030295	3 retrocopies	retro_sscr_1223 , retro_sscr_710, retro_sscr_740,
Ictidomys tridecemlineatus	ENSSTOG00000002878	1 retrocopy	retro_itri_800,
Tupaia belangeri	ENSTBEG00000011016	1 retrocopy	retro_tbel_7,
Tarsius syrichta	ENSTSYG00000010702	3 retrocopies	retro_tsyr_1689, retro_tsyr_380, retro_tsyr_745,
Tursiops truncatus	ENSTTRG00000009251	2 retrocopies	retro_ttru_1534, retro_ttru_433,
Drosophila melanogaster	FBgn0031145	1 retrocopy	retro_dmel_27,