RetrogeneDB ID: retro_sscr_33

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: X:105013206..105013977(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSSCG00000012578
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSSCG00000027840
• Aliases: None
• Description: None

Sequence

>retro_sscr_33
ATGGCGCCACCGGCACCCGGCCCGGCCTCCGGCGGCTCCGGGGAAGTAGACGAGTTGTTTGACGTAAAGAATGCCTTTTA
CATTGGCAGCTACCAACAGTGCATCAACGAGGCTCAGCGGGTGAAGCCATCAAGCCCCGAGAGAGATGTGGAAAGGGATG
TCTTCCTGTACAGAGCATACCTCGAACAGAGGAAGTTCGGCGTGGTCCTCGAAGAGATCAAGCCCTCCTCGTCACCTGAG
CTCCAGGCCATCCGCATGTTTGCTGAGTACCTGGCTAGCGACAGCCGGCGGGATGCGATTGTGGCCGAGCTGGACCGGGA
GATGAGCCGGAGCGTGGACGTGACCAACACCACCTTCCTGCTCATGGCTGCCTCCATCTACTTCCATGACCAGAACCCGG
ACGCCGCCCTGCGCACCCTGCACCAAGGGGACAGCCTGGAGTGCATGGCCATGACGGTGCAGATCCTGCTGAAGCTAGAC
CGCCTGGACCTCGCCCGGAAAGAGCTGAAGAAAATGCAGGACCAGGACGAGGATGCCACCCTCACCCAGCTGGCCACCGC
CTGGGTCAACCTGGCTGTGGACAGCAGCCACCCAGAGACACCGATCAACCTCATTGTCCTGTCCCAGCATCTGGGGAAGC
CTCCTGAGGTGACAAACCGCTACCTGTCCCAGCTGAAGGACGCCCACAGGACCCACCCCTTCATCAAGGAGTACCATGCC
AAGGAAAACGACTTTGACAGACTGGTGCTGCAGTATGCTCCCAGTGCCTGA

Alignment

ORF - retro_sscr_33 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.45 %
• Parental protein coverage: 62.66 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAPPAPGPASGGSGEVDELFDVKNAFYIGSYQQCINEAQRVKPSSPERDVERDVFLYRAYLAQRKFGVVL
          MAPPAPGPASGGSGEVDELFDVKNAFYIGSYQQCINEAQRVKPSSPERDVERDVFLYRAYL.QRKFGVVL
Retrocopy MAPPAPGPASGGSGEVDELFDVKNAFYIGSYQQCINEAQRVKPSSPERDVERDVFLYRAYLEQRKFGVVL

Parental  DEIKPSSAPELQAIRMFAEYLASDSRRDAIVAELDREMSRSVDVTNTTFLLMAASIYFHDQNPDAALRTL
          .EIKPSS.PELQAIRMFAEYLASDSRRDAIVAELDREMSRSVDVTNTTFLLMAASIYFHDQNPDAALRTL
Retrocopy EEIKPSSSPELQAIRMFAEYLASDSRRDAIVAELDREMSRSVDVTNTTFLLMAASIYFHDQNPDAALRTL

Parental  HQGDSLECMAMTVQILLKLDRLDLARKELKKMQDQDEDATLTQLATAWVNLAV
          HQGDSLECMAMTVQILLKLDRLDLARKELKKMQDQDEDATLTQLATAWVNLAV
Retrocopy HQGDSLECMAMTVQILLKLDRLDLARKELKKMQDQDEDATLTQLATAWVNLAV

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	1.99 RPM	171.89 RPM
SRP014902_testis	1.98 RPM	70.44 RPM
SRP018288_heart	0.31 RPM	32.38 RPM
SRP018288_kidney	0.59 RPM	65.51 RPM
SRP018288_liver	0.80 RPM	56.93 RPM
SRP018288_lung	0.10 RPM	48.57 RPM
SRP018856_adipose	0.34 RPM	70.11 RPM
SRP035408_brain	0.48 RPM	27.22 RPM
SRP035408_liver	0.76 RPM	20.99 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

1 EST(s) were mapped to retro_sscr_33 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
EB413345	105013603	105013730	99.3	126	1	125

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_33 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_33 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Mus musculus	ENSMUSG00000055681	1 retrocopy	retro_mmus_2268,
Sus scrofa	ENSSSCG00000027840	1 retrocopy	retro_sscr_33 ,