RetrogeneDB ID: retro_sscr_232

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 10:76770866..76771610(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCNE1
• Ensembl ID: ENSSSCG00000002855
• Aliases: None
• Description: cyclin E1 [Source:HGNC Symbol;Acc:1589]

Sequence

>retro_sscr_232
AGAGAGACATTTTACTTGGCACAGGATTTCTTCGATCAGTGTATGGCAACACAACAAAACGTTGTAAAAACGCTTTTACA
GCTTATTGGGATTTCATCTTTATTTATTGCTGCCAAACTTGAGGAAATCTATCCTCCAAAGTTGCACCAGTTTGCTTATG
TGACAGATGGGGCTTGATCAGGAGATGAAATTCTTACCATGGAATTAATCATTATGAAGGCCCTTAATGGCATTTAAGTC
CCCTGACCATTGTGTCCTGGCTGAATGTATACATGCAGGTTGTATATCTAAATGATTTTTAGGAAGTGCTCCTGCCACAG
TATCCCCAGCAAATCTTCATACAGATCGCAGAGCTTTTAGATCTCTGTATCCTGGATGTTGGCTGCTTAGAATTTTCCTA
TGATGTACCTGCTGCTTCTGCCTTGTATCATTCCTCTTCATCCGAATTGATGAAGAAGGTTTCAGGGTATCAGTGGTGTG
ATATAGAGAAGTGTGTCAAGTGGATGGTTCCATTTGCCATGGTTATAAGGGAGACAGGAAGCTCAAAACTTAAGCACCTC
AGAGGGGTTCCTGCTGAAGATATCCATAACATCCAGATCCATATAAACAGCTTGGATTTGCTGGACAAAGCCCAAGCAAA
GAAAGCCATATTGTCTGAAGAAAATAGGATTTCTCCTCTCCCCACTGGAGTCCTCACCCCCCCAGCAGAGCAGTAAGAAG
CAGAGCAGTGGGCAGGGAACAGCA

Alignment

ORF - retro_sscr_232 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.8 %
• Parental protein coverage: 60.49 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  RETFYLAQDFFDRYMATQQNVVKTLLQLIGISSLFIAAKLEEIYPPKLHQFAYVTDGACSGDEILTMELI
          RETFYLAQDFFD..MATQQNVVKTLLQLIGISSLFIAAKLEEIYPPKLHQFAYVTDGA.SGDEILTMELI
Retrocopy RETFYLAQDFFDQCMATQQNVVKTLLQLIGISSLFIAAKLEEIYPPKLHQFAYVTDGA*SGDEILTMELI

Parental  IMKALK-WHLSPLTIVSWLNVYMQVAYLNDFYEVLLPQYPQQIFIQIAELLDLCVLDVGCLEFPYGVLAA
          IMKAL..WHLSPLTIVSWLNVYMQV.YLNDF.EVLLPQYPQQIFIQIAELLDLC.LDVGCLEF.Y.V.AA
Retrocopy IMKALN<WHLSPLTIVSWLNVYMQVVYLNDF*EVLLPQYPQQIFIQIAELLDLCILDVGCLEFSYDVPAA

Parental  SALYHFSSSELMQKVSGYQWCDIEKCVKWMVPFAMVIRETGSSKLKHFRGVPAEDAHNIQTHINSLDLLD
          SALYH.SSSELM.KVSGYQWCDIEKCVKWMVPFAMVIRETGSSKLKH.RGVPAED.HNIQ.HINSLDLLD
Retrocopy SALYHSSSSELMKKVSGYQWCDIEKCVKWMVPFAMVIRETGSSKLKHLRGVPAEDIHNIQIHINSLDLLD

Parental  KAQAKKAILSEENRISPLPTGVLTPP-PSSKKQSSGQGTA
          KAQAKKAILSEENRISPLPTGVLTPP..SSKKQSSGQGTA
Retrocopy KAQAKKAILSEENRISPLPTGVLTPP>QSSKKQSSGQGTA

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	4.91 RPM
SRP014902_testis	0.00 RPM	1.41 RPM
SRP018288_heart	0.37 RPM	0.73 RPM
SRP018288_kidney	0.10 RPM	1.77 RPM
SRP018288_liver	0.16 RPM	2.40 RPM
SRP018288_lung	0.10 RPM	3.77 RPM
SRP018856_adipose	0.00 RPM	3.45 RPM
SRP035408_brain	0.16 RPM	9.12 RPM
SRP035408_liver	0.12 RPM	3.64 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_232 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_232 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_232 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000001857	2 retrocopies	retro_cjac_3786, retro_cjac_3996,
Oryctolagus cuniculus	ENSOCUG00000009143	1 retrocopy	retro_ocun_676,
Otolemur garnettii	ENSOGAG00000006217	2 retrocopies	retro_ogar_3309, retro_ogar_930,
Sus scrofa	ENSSSCG00000002855	1 retrocopy	retro_sscr_232 ,
Vicugna pacos	ENSVPAG00000001390	1 retrocopy	retro_vpac_219,