RetrogeneDB ID: retro_sscr_402

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 14:4482997..4483327(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSSCG00000009599
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: EIF1
• Ensembl ID: ENSSSCG00000017430
• Aliases: None
• Description: eukaryotic translation initiation factor 1 [Source:HGNC Symbol;Acc:3249]

Sequence

>retro_sscr_402
TCCGCGATCCAGAACCTCCACTCTCACCATCCCTTTGCTGGTGTAGGTAGGGATGGTGATCTGATCCCTGCTGGCACTTA
GGGATCATATAAAAATTCAACAGAAAAACGGCAGGAAGATCTTAACACTGTCCAAGGGATCGCTGAGGATTACGATAAAA
AGAAACTAGTGAAGGCGTTTAAGAAGAAATTTGCCTGCAATGGTACCGTAATTGAGCATCCAGACTATGGAGAAGTCATT
CATCTACAGGGTGACCAGCGCAAGAACATATGGCAGTTCCTTGCAGTGACTGGACTGGCTAAGGACGACCAGCTGAAGGT
TCATGGGTTT

Alignment

ORF - retro_sscr_402 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.07 %
• Parental protein coverage: 99.12 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SAIQNLHSFDPFADASKGDDLLPAGT-EDYIHIRIQQRNGRKTLT-TVQGIADDYDKKKLVKAFKKKFAC
          SAIQNLHS..PFA......DL.PAGT..D.I...IQQ.NGRK.LT.TVQGIA.DYDKKKLVKAFKKKFAC
Retrocopy SAIQNLHSHHPFAGVGRDGDLIPAGT>RDHI--KIQQKNGRKILT<TVQGIAEDYDKKKLVKAFKKKFAC

Parental  NGTVIEHPEYGEVIQLQGDQRKNICQFLVEIGLAKDDQLKVHGF
          NGTVIEHP.YGEVI.LQGDQRKNI.QFL...GLAKDDQLKVHGF
Retrocopy NGTVIEHPDYGEVIHLQGDQRKNIWQFLAVTGLAKDDQLKVHGF

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	660.07 RPM
SRP014902_testis	0.00 RPM	240.74 RPM
SRP018288_heart	0.00 RPM	396.68 RPM
SRP018288_kidney	0.00 RPM	339.55 RPM
SRP018288_liver	0.16 RPM	294.55 RPM
SRP018288_lung	0.00 RPM	138.89 RPM
SRP018856_adipose	0.00 RPM	379.54 RPM
SRP035408_brain	0.00 RPM	170.46 RPM
SRP035408_liver	0.00 RPM	109.23 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_402 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_402 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_402 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 83 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000005620	9 retrocopies	retro_amel_1335, retro_amel_335, retro_amel_567, retro_amel_575, retro_amel_587, retro_amel_666, retro_amel_782, retro_amel_798, retro_amel_823,
Canis familiaris	ENSCAFG00000029584	4 retrocopies	retro_cfam_1465, retro_cfam_1479, retro_cfam_359, retro_cfam_655,
Callithrix jacchus	ENSCJAG00000012120	6 retrocopies	retro_cjac_1237, retro_cjac_2089, retro_cjac_346, retro_cjac_3815, retro_cjac_600, retro_cjac_84,
Cavia porcellus	ENSCPOG00000014350	3 retrocopies	retro_cpor_42, retro_cpor_613, retro_cpor_643,
Dasypus novemcinctus	ENSDNOG00000007856	11 retrocopies	retro_dnov_1098, retro_dnov_1110, retro_dnov_1368, retro_dnov_148, retro_dnov_1516, retro_dnov_1668, retro_dnov_1807, retro_dnov_2062, retro_dnov_2209, retro_dnov_402, retro_dnov_421,
Dipodomys ordii	ENSDORG00000013853	4 retrocopies	retro_dord_349, retro_dord_350, retro_dord_663, retro_dord_753,
Homo sapiens	ENSG00000173812	2 retrocopies	retro_hsap_1659, retro_hsap_271,
Gorilla gorilla	ENSGGOG00000027201	2 retrocopies	retro_ggor_1251, retro_ggor_318,
Macropus eugenii	ENSMEUG00000015360	6 retrocopies	retro_meug_1513, retro_meug_1635, retro_meug_2189, retro_meug_315, retro_meug_749, retro_meug_821,
Myotis lucifugus	ENSMLUG00000005077	3 retrocopies	retro_mluc_233, retro_mluc_305, retro_mluc_330,
Otolemur garnettii	ENSOGAG00000031577	6 retrocopies	retro_ogar_1349, retro_ogar_1701, retro_ogar_1940, retro_ogar_2645, retro_ogar_2899, retro_ogar_856,
Pongo abelii	ENSPPYG00000029667	1 retrocopy	retro_pabe_127,
Rattus norvegicus	ENSRNOG00000033765	15 retrocopies	retro_rnor_1088, retro_rnor_1347, retro_rnor_1518, retro_rnor_1744, retro_rnor_1971, retro_rnor_2067, retro_rnor_2171, retro_rnor_2203, retro_rnor_2532, retro_rnor_2548, retro_rnor_2579, retro_rnor_45, retro_rnor_532, retro_rnor_571, retro_rnor_65,
Sorex araneus	ENSSARG00000006287	1 retrocopy	retro_sara_36,
Sarcophilus harrisii	ENSSHAG00000005729	1 retrocopy	retro_shar_42,
Sus scrofa	ENSSSCG00000017430	6 retrocopies	retro_sscr_1114, retro_sscr_1126, retro_sscr_1192, retro_sscr_394, retro_sscr_402 , retro_sscr_922,
Tursiops truncatus	ENSTTRG00000017135	3 retrocopies	retro_ttru_1664, retro_ttru_224, retro_ttru_315,