RetrogeneDB ID: retro_sscr_760

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 4:103235324..103235814(+)
• Located in intron of: ENSSSCG00000006508

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCNC
• Ensembl ID: ENSSSCG00000004353
• Aliases: None
• Description: cyclin C [Source:HGNC Symbol;Acc:1581]

Sequence

>retro_sscr_760
ATGGCCGGGAACTTTTGGCAGAGCTCCCGTTATTTGCAGTGGGTTTCGGAAAAACAAGATCTGTTGAAGGAACGCCGAAA
GGACTTAAGGTTTCTTTCAGAAGAAGAGTATTGGAAATTACAGGTATTTTTTACAAATGTTATCCAAGCATTAGGTCACC
ATCTTAAATTAAGTCAAGTTATTGCCACTGCTATGGTCTATTTCAAGAGATTCTATGCCAGGTATTCTCTGAAAAGTATA
GATCCTGTATTTATGGTTACTACATGTGTGGTTTTGGCATCCAAAGTAGAGGAATTTGGAGTAGTCTCAAATACAGTATT
GATTTCTGCTACTACTTCTATATTAAAAACTAGATTTTCATATGCCGTCAAGTGAATTTCCTTATAGGTTGGACCATATA
TTAGAATGTGAATTCTGTCTTTTGGAATTAATGGATTGTTGCTTGATAGTGTATCATCCTTGTAGACTTTTGCTCCAGTA
TGTGCAGGAG

Alignment

ORF - retro_sscr_760 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.42 %
• Parental protein coverage: 58.16 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAGNFWQSSHYLQWILDKQDLLKERQKDLKFLSEEEYWKLQIFFTNVIQALGEHLKLRQQVIATATVYFK
          MAGNFWQSS.YLQW...KQDLLKER.KDL.FLSEEEYWKLQ.FFTNVIQALG.HLKL..QVIATA.VYFK
Retrocopy MAGNFWQSSRYLQWVSEKQDLLKERRKDLRFLSEEEYWKLQVFFTNVIQALGHHLKL-SQVIATAMVYFK

Parental  RFYARYSLKSIDPVLMAPTCVFLASKVEEFGVVSNTRLISAATSVSKTRFSYAF-PRFPYRMNHILECEF
          RFYARYSLKSIDPV.M..TCV.LASKVEEFGVVSNT.LISA.TS..KTRFSYA....FPYR..HILECEF
Retrocopy RFYARYSLKSIDPVFMVTTCVVLASKVEEFGVVSNTVLISATTSILKTRFSYAV>SEFPYRLDHILECEF

Parental  YLLELMDCCLIVYHPYRPLLQYVQD
          .LLELMDCCLIVYHP.R.LLQYVQ.
Retrocopy CLLELMDCCLIVYHPCRLLLQYVQE

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	5.04 RPM
SRP014902_testis	0.14 RPM	11.46 RPM
SRP018288_heart	0.05 RPM	17.71 RPM
SRP018288_kidney	0.30 RPM	57.63 RPM
SRP018288_liver	0.16 RPM	46.53 RPM
SRP018288_lung	0.00 RPM	28.51 RPM
SRP018856_adipose	0.00 RPM	12.56 RPM
SRP035408_brain	0.03 RPM	25.92 RPM
SRP035408_liver	0.06 RPM	38.16 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_760 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_760 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_760 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000008954	1 retrocopy	retro_amel_1828,
Canis familiaris	ENSCAFG00000003525	1 retrocopy	retro_cfam_1774,
Dasypus novemcinctus	ENSDNOG00000011999	3 retrocopies	retro_dnov_1153, retro_dnov_216, retro_dnov_2243,
Dipodomys ordii	ENSDORG00000008393	2 retrocopies	retro_dord_230, retro_dord_75,
Myotis lucifugus	ENSMLUG00000012815	1 retrocopy	retro_mluc_1582,
Oryctolagus cuniculus	ENSOCUG00000003309	2 retrocopies	retro_ocun_1753, retro_ocun_888,
Ochotona princeps	ENSOPRG00000012972	2 retrocopies	retro_opri_1026, retro_opri_151,
Sus scrofa	ENSSSCG00000004353	1 retrocopy	retro_sscr_760 ,
Tupaia belangeri	ENSTBEG00000017525	1 retrocopy	retro_tbel_677,