RetrogeneDB ID: retro_sscr_358

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 13:194632958..194633434(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LIN28
• Ensembl ID: ENSSSCG00000003557
• Aliases: LIN28A, LIN28, lin-28
• Description: Sus scrofa lin-28 homolog A (C. elegans) (LIN28A), mRNA. [Source:RefSeq mRNA;Acc:NM_001123133]

Sequence

>retro_sscr_358
ATGCATTCTGTGTCAAACCAGCAGCTTGCAGGTGGCTGCGCCAAGGCACCAGAAGAGGTGCCAGTGGAAGTGGCCCTGGG
CAGCCAAGGAACCAAGCTGCTCCACGGTCCTGGCATCTGTAATTGGCTCAGCGTGTGCAAGGGGTTCGGCTTCCTCTCCA
TGACCACCTGCTTTTGGGTGGCAATGGACCTCCGGTGGATGTCTTTTAGCACCAGTGTAAGCTGCACATGGAGGTCTTCT
GGAACCTGAAGGAGGGTGAGGCTGTGGAATTCACCTTTATGAAATCTGCCAAGGGCTTGGAATCCATCCGAGTCACCAGC
CTTGGTGGGTTGTTCTGTATTGGGAGCAAGAGGCGGCCTAAATGGAAGAATATGCAGAAACGCAGATTCAAGGGAGACAG
GTGCTACAACTGAGGATGTCTACACCATCATGCCAAGGAATGCAAATGGCCACCCCATCCCAAGAAGTGCCACTTC

Alignment

ORF - retro_sscr_358 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.75 %
• Parental protein coverage: 77.56 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MGSVSNQQFAGGCAKAPEEAPEDAARAAEEPQLLHGAGICKWFNVRMGFGFLSMTARAGVALD-PPVDVF
          M.SVSNQQ.AGGCAKAPEE.P...A.......LLHG.GIC.W..V..GFGFLSMT....VA.D.PPVDVF
Retrocopy MHSVSNQQLAGGCAKAPEEVPVEVALGSQGTKLLHGPGICNWLSVCKGFGFLSMTTCFWVAMD<PPVDVF

Parental  VHQSKLHMEGFRSLKEGEAVEFTFKKSAKGLESIRVTGPGGVFCIGSERRPKGKNMQKRRSKGDRCYNCG
          .HQ.KLHME.F..LKEGEAVEFTF.KSAKGLESIRVT..GG.FCIGS.RRPK.KNMQKRR.KGDRCYN.G
Retrocopy *HQCKLHMEVFWNLKEGEAVEFTFMKSAKGLESIRVTSLGGLFCIGSKRRPKWKNMQKRRFKGDRCYN*G

Parental  GLDHHAKECKLPPQPKKCHF
          .L.HHAKECK.PP.PKKCHF
Retrocopy CLHHHAKECKWPPHPKKCHF

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	0.00 RPM
SRP014902_testis	0.00 RPM	0.00 RPM
SRP018288_heart	0.00 RPM	0.00 RPM
SRP018288_kidney	0.00 RPM	0.00 RPM
SRP018288_liver	0.00 RPM	0.00 RPM
SRP018288_lung	0.00 RPM	0.00 RPM
SRP018856_adipose	0.00 RPM	0.00 RPM
SRP035408_brain	0.00 RPM	0.00 RPM
SRP035408_liver	0.00 RPM	0.00 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_358 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_358 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_358 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 40 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000010582	2 retrocopies	retro_amel_396, retro_amel_649,
Bos taurus	ENSBTAG00000040497	3 retrocopies	retro_btau_1150, retro_btau_1594, retro_btau_199,
Canis familiaris	ENSCAFG00000012488	2 retrocopies	retro_cfam_2049, retro_cfam_767,
Callithrix jacchus	ENSCJAG00000009796	5 retrocopies	retro_cjac_1468, retro_cjac_1784, retro_cjac_186, retro_cjac_2597, retro_cjac_33,
Cavia porcellus	ENSCPOG00000019646	1 retrocopy	retro_cpor_120,
Dasypus novemcinctus	ENSDNOG00000010710	5 retrocopies	retro_dnov_102, retro_dnov_1112, retro_dnov_2300, retro_dnov_690, retro_dnov_853,
Equus caballus	ENSECAG00000020267	1 retrocopy	retro_ecab_258,
Homo sapiens	ENSG00000131914	2 retrocopies	retro_hsap_2187, retro_hsap_2450,
Gorilla gorilla	ENSGGOG00000024918	2 retrocopies	retro_ggor_1526, retro_ggor_1732,
Myotis lucifugus	ENSMLUG00000010158	1 retrocopy	retro_mluc_1023,
Nomascus leucogenys	ENSNLEG00000009294	4 retrocopies	retro_nleu_204, retro_nleu_2300, retro_nleu_2896, retro_nleu_316,
Oryctolagus cuniculus	ENSOCUG00000000299	1 retrocopy	retro_ocun_19,
Otolemur garnettii	ENSOGAG00000003971	1 retrocopy	retro_ogar_481,
Pongo abelii	ENSPPYG00000001684	3 retrocopies	retro_pabe_1801, retro_pabe_2067, retro_pabe_2849,
Pan troglodytes	ENSPTRG00000000384	2 retrocopies	retro_ptro_1415, retro_ptro_1665,
Pteropus vampyrus	ENSPVAG00000017267	1 retrocopy	retro_pvam_110,
Rattus norvegicus	ENSRNOG00000038409	2 retrocopies	retro_rnor_2076, retro_rnor_2077,
Sus scrofa	ENSSSCG00000003557	1 retrocopy	retro_sscr_358 ,
Ictidomys tridecemlineatus	ENSSTOG00000004329	1 retrocopy	retro_itri_1647,