RetrogeneDB ID: retro_sscr_3

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 1:212536678..212537005(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSSCG00000005101
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: HMGA2
• Ensembl ID: ENSSSCG00000000471
• Aliases: None
• Description: None

Sequence

>retro_sscr_3
ATGAGCACACGCAGTAAAGGCGCTGAGCAGAAGTCCACCTCAGCCCAGGGAAAACCAGCAGCCCCAGCTCCTCAGAAGAG
AGGACCCGGCCGACCCAGGAAGCAGCAACAAGAGCCAACCAGTGAGCCTTCTTCTAAGAGACCAAGGGGCAGACCCAAAG
GCAGCAAAAACAAGAGTCCCTCCAAAGCAGCTCAAAAGAAACCAGAAGCCACTGGACAAAGACGGCCAAGAGGCAGACCT
AGGAAATGGCCACAACAAGTCGTTCAGAAGACGTCTGCTCAGGAGACTGAAGAGACATCCTCACAGAAGTCTGCAGAAGA
GGATTAG

Alignment

ORF - retro_sscr_3 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.19 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSARGEGAGQPSTSAQGQPAAPVPQKRGRGRPRKQQQEPTGEPSPKRPRGRPKGSKNKSPSKAAQKKAEA
          MS.R..GA.Q.STSAQG.PAAP.PQKRG.GRPRKQQQEPT.EPS.KRPRGRPKGSKNKSPSKAAQKK.EA
Retrocopy MSTRSKGAEQKSTSAQGKPAAPAPQKRGPGRPRKQQQEPTSEPSSKRPRGRPKGSKNKSPSKAAQKKPEA

Parental  TGEKRPRGRPRKWPQQVVQKKPAQETEETSSQESAEED
          TG..RPRGRPRKWPQQVVQK..AQETEETSSQ.SAEED
Retrocopy TGQRRPRGRPRKWPQQVVQKTSAQETEETSSQKSAEED

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	0.18 RPM
SRP018288_kidney	0.00 RPM	0.00 RPM
SRP018288_liver	0.00 RPM	0.00 RPM
SRP018288_lung	0.00 RPM	0.41 RPM
SRP018856_adipose	0.00 RPM	0.17 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_3 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_3 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_3 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Mus musculus	ENSMUSG00000056758	1 retrocopy	retro_mmus_391,
Otolemur garnettii	ENSOGAG00000031502	1 retrocopy	retro_ogar_1596,
Sus scrofa	ENSSSCG00000000471	1 retrocopy	retro_sscr_3 ,