RetrogeneDB ID: retro_sscr_1064

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 9:78866590..78867021(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSSCG00000003042
• Aliases: None
• Description: None

Sequence

>retro_sscr_1064
ATGCCTGGAGTTACCATAAAAGATGTGAACTAGCAGGAGTTGGTCAGAGCTCTGGCAGTCTTCCTTAAACAGTCTGGAGA
GCTGAAGGTTCCTGAAGTGGTGAACACTGTCAAGCTCGCCAAGCATAAAGAGGTCGCTCCCTTTGATGAGAACTGCCTCT
ATATACGAGGTGCTTCCACAGCACAAAACTTGTACCTCCGAGGCAGCACTGGTGTTGGCTTCATGACAAGATCTATGGGG
GCACCAGAGAAAGGGTGCCACACCCAGCCACTTCAGCAGAGGCTCCAAGAGTGTGGCTGACCACATCTCCAAGCTCTGGA
GGGGCTAAAAATGGAGGAGAAGGACCAAGATGTGGGCACAAATTGATACCTCAGGGATAGAGAGATCTGAACAGAATCGC
TGGACAGGTGGAAGCTGCCAACAAGAAGCAT

Alignment

ORF - retro_sscr_1064 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.17 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MPGVTVKDVNQQEFVRALAAFLKKSGKLKVPEWVDTVKLAKHKELAPYDENWFYTRAASTARHLYLRGGA
          MPGVT.KDVN.QE.VRALA.FLK.SG.LKVPE.V.TVKLAKHKE.AP.DEN..Y.R.ASTA..LYLRG..
Retrocopy MPGVTIKDVN*QELVRALAVFLKQSGELKVPEVVNTVKLAKHKEVAPFDENCLYIRGASTAQNLYLRGST

Parental  GVGSMT-KIYG-GRQRNGVMPSHFSRGSKSVARRV-LQALEGLKMVEKDQD-GGRKLTPQGQRDLDRIAG
          GVG.MT.KIYG.G.QR.G..PSHFSRGSKSVA....LQALEGLKM.EKDQD..G.KL.PQG.RDL.RIAG
Retrocopy GVGFMT<KIYG<GHQRKGATPSHFSRGSKSVADHI<LQALEGLKMEEKDQD<CGHKLIPQG*RDLNRIAG

Parental  QVAAANKKH
          QV.AANKKH
Retrocopy QVEAANKKH

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	138.97 RPM
SRP014902_testis	0.00 RPM	476.67 RPM
SRP018288_heart	0.05 RPM	150.77 RPM
SRP018288_kidney	0.20 RPM	211.29 RPM
SRP018288_liver	0.00 RPM	161.67 RPM
SRP018288_lung	0.20 RPM	408.22 RPM
SRP018856_adipose	0.00 RPM	1115.01 RPM
SRP035408_brain	0.06 RPM	330.12 RPM
SRP035408_liver	0.06 RPM	217.44 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_1064 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_1064 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_1064 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 27 parental genes, and 136 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000004456	4 retrocopies	retro_amel_1418, retro_amel_1816, retro_amel_193, retro_amel_550,
Bos taurus	ENSBTAG00000011963	2 retrocopies	retro_btau_722, retro_btau_77,
Canis familiaris	ENSCAFG00000028485	10 retrocopies	retro_cfam_1017, retro_cfam_1074, retro_cfam_1155, retro_cfam_1251, retro_cfam_1377, retro_cfam_149, retro_cfam_1998, retro_cfam_2212, retro_cfam_249, retro_cfam_499,
Callithrix jacchus	ENSCJAG00000020243	5 retrocopies	retro_cjac_1968, retro_cjac_2004, retro_cjac_2094, retro_cjac_2324, retro_cjac_3,
Cavia porcellus	ENSCPOG00000025140	1 retrocopy	retro_cpor_1018,
Dasypus novemcinctus	ENSDNOG00000002376	4 retrocopies	retro_dnov_1084, retro_dnov_1124, retro_dnov_1838, retro_dnov_2456,
Equus caballus	ENSECAG00000009738	2 retrocopies	retro_ecab_263, retro_ecab_815,
Erinaceus europaeus	ENSEEUG00000013614	4 retrocopies	retro_eeur_252, retro_eeur_259, retro_eeur_318, retro_eeur_385,
Felis catus	ENSFCAG00000008125	3 retrocopies	retro_fcat_2026, retro_fcat_543, retro_fcat_816,
Homo sapiens	ENSG00000105372	5 retrocopies	retro_hsap_1400, retro_hsap_2417, retro_hsap_3174, retro_hsap_3642, retro_hsap_667,
Gorilla gorilla	ENSGGOG00000015279	4 retrocopies	retro_ggor_1085, retro_ggor_1503, retro_ggor_2458, retro_ggor_578,
Microcebus murinus	ENSMICG00000004554	1 retrocopy	retro_mmur_1480,
Myotis lucifugus	ENSMLUG00000006143	5 retrocopies	retro_mluc_1316, retro_mluc_2247, retro_mluc_2426, retro_mluc_980, retro_mluc_987,
Macaca mulatta	ENSMMUG00000013429	8 retrocopies	retro_mmul_1201, retro_mmul_1358, retro_mmul_1807, retro_mmul_2007, retro_mmul_2443, retro_mmul_404, retro_mmul_607, retro_mmul_691,
Monodelphis domestica	ENSMODG00000010067	3 retrocopies	retro_mdom_1531, retro_mdom_1888, retro_mdom_883,
Mustela putorius furo	ENSMPUG00000007164	4 retrocopies	retro_mputfur_1071, retro_mputfur_1148, retro_mputfur_1470, retro_mputfur_1503,
Mus musculus	ENSMUSG00000040952	15 retrocopies	retro_mmus_1206, retro_mmus_1207, retro_mmus_1528, retro_mmus_1711, retro_mmus_1713, retro_mmus_2095, retro_mmus_2295, retro_mmus_2535, retro_mmus_2850, retro_mmus_3337, retro_mmus_3499, retro_mmus_639, retro_mmus_643, retro_mmus_684, retro_mmus_899,
Otolemur garnettii	ENSOGAG00000026255	3 retrocopies	retro_ogar_1315, retro_ogar_1663, retro_ogar_2305,
Pongo abelii	ENSPPYG00000010029	7 retrocopies	retro_pabe_1158, retro_pabe_1754, retro_pabe_1781, retro_pabe_2636, retro_pabe_430, retro_pabe_585, retro_pabe_586,
Pan troglodytes	ENSPTRG00000011037	6 retrocopies	retro_ptro_1392, retro_ptro_2269, retro_ptro_2467, retro_ptro_485, retro_ptro_612, retro_ptro_961,
Pteropus vampyrus	ENSPVAG00000008980	4 retrocopies	retro_pvam_1032, retro_pvam_1171, retro_pvam_137, retro_pvam_895,
Rattus norvegicus	ENSRNOG00000048199	3 retrocopies	retro_rnor_221, retro_rnor_299, retro_rnor_51,
Sarcophilus harrisii	ENSSHAG00000006831	1 retrocopy	retro_shar_731,
Sus scrofa	ENSSSCG00000003042	3 retrocopies	retro_sscr_1064 , retro_sscr_308, retro_sscr_58,
Ictidomys tridecemlineatus	ENSSTOG00000003502	3 retrocopies	retro_itri_256, retro_itri_751, retro_itri_872,
Tupaia belangeri	ENSTBEG00000003457	21 retrocopies	retro_tbel_103, retro_tbel_1275, retro_tbel_1575, retro_tbel_1748, retro_tbel_1803, retro_tbel_1888, retro_tbel_2104, retro_tbel_2521, retro_tbel_2554, retro_tbel_2971, retro_tbel_3008, retro_tbel_3339, retro_tbel_3388, retro_tbel_345, retro_tbel_3607, retro_tbel_3860, retro_tbel_4425, retro_tbel_673, retro_tbel_875, retro_tbel_913, retro_tbel_945,
Tursiops truncatus	ENSTTRG00000008278	5 retrocopies	retro_ttru_1308, retro_ttru_1608, retro_ttru_1686, retro_ttru_336, retro_ttru_593,