RetrogeneDB ID: retro_stub_12

Retrocopy location

• Organism: Potato (Solanum tuberosum)
• Coordinates: 4:16702367..16703240(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: PGSC0003DMG400002221
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: PGSC0003DMG400026532
• Aliases: None
• Description: None

Sequence

>retro_stub_12
ATGGAGTTTTGGGGTGTTGAAGTGAAAGCAGGACAAACACTAAAGGTTAAGCCTGAGCTTTTCAAGCTCATTCATGTTTC
CCAGGCTGCCATCGGTGAAGTGAAGGATGTCAAAGAAGCCAAATATGTTCCACTACGCCTAACTGTTGGAGATAACAGTT
ATGTCATTGGAACTCTATCCGCTGAGGATAGACCTCAGTTGATGTTTGACTTGGTCTTTGAAAAGGAGTTTGAACTTTCA
CATGGATGGAAGAATGGGAGTGTGCACTTCATTGGATACACTGCTGATGATCCTTGCGGTGATGAAATAGACTCTGGAGA
TGATGTTTTTTCGGCTGAAGAGAATGTTTTGGAGGCACTGAATGGGAAACTTGAGGCTGATGTGAAGGATGTAAAGCCTG
ATGCAAAGAAGTCTGCACCTGTTAAGGATGAGAAAAATGCTAAGGTAGCTGAATCAAAGAAAGAGGCGGAGTCTGATGAA
GATGACTCTGATGATTCTGATGATGTGCCTCTAGGCATGGAAGGGATGGATTTTTCTGGTGATTCTGAGGATGATGATGA
TTCCGAGGAAGATGATGATTCAGAAGAAGAGACACCTAAAAAGGTTGAGCAGAAGAAGAGACCAGCTCCATCTCCTAAAG
TAGCTCCTGGCTCTGGCAAAAAAGCTAAACAAGCAACACTCGACAACAAATCAGGCGGTAAGAAAGGTCCAGCCACCCCT
TTTGCTAAGCAAAATGGTAAACCTGCATTCAATGGTAACAACAAACCAAAACCTCAGTCCCCAAAATCTGGTGGTCAGTT
CTCTGGCAACAAGTCTAACAGCAAGAACTTCAGTGGCCAAAAGAATTTCAAGGGCAAGCAAGGAAGGAAGTAG

Alignment

ORF - retro_stub_12 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.16 %
• Parental protein coverage: 80.9 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VEVKAGQTLKVKPELFKLIHVSQAAIGEVKDVKEAKYVPLRLTVGENSYVIGTLSAEDRPQLMFDLVFEK
          VEVKAGQTLKVKPELFKLIHVSQAAIGEVKDVKEAKYVPLRLTVG.NSYVIGTLSAEDRPQLMFDLVFEK
Retrocopy VEVKAGQTLKVKPELFKLIHVSQAAIGEVKDVKEAKYVPLRLTVGDNSYVIGTLSAEDRPQLMFDLVFEK

Parental  EFELSHGWKNGSVHFIGYTADDPSGDEIDSGDDVFSDEENVLEALNGKLEADVKDVKPDAKKSAPVKDAK
          EFELSHGWKNGSVHFIGYTADDP.GDEIDSGDDVFS.EENVLEALNGKLEA...DVK.D.K..A..K...
Retrocopy EFELSHGWKNGSVHFIGYTADDPCGDEIDSGDDVFSAEENVLEALNGKLEA---DVK-DVKPDA--KKSA

Parental  NAKVAESKKEAESDEDDSDDEDDSEDDSDVPL---GMDGPEGMDFSGDSEDDDDSEEETPKKVEQKKRPA
          ..K.....K.AES......DEDDS.D..DVPL...GMD.........DSE.DDDSEEETPKKVEQKKRPA
Retrocopy PVKDEKNAKVAESKKEAESDEDDSDDSDDVPLGMEGMDFSGDSEDDDDSEEDDDSEEETPKKVEQKKRPA

Parental  PSPQVAPGSGKKAKQATPDNKSGGKKGPATPFAKQNGKPAFNGNNKPKTQSPKSGGQFSGNKSNNKNFSG
          PSP.VAPGSGKKAKQAT.DNKSGGKKGPATPFAKQNGKPAFNGNNKPK.QSPKSGGQFSGNKSN.KNFSG
Retrocopy PSPKVAPGSGKKAKQATLDNKSGGKKGPATPFAKQNGKPAFNGNNKPKPQSPKSGGQFSGNKSNSKNFSG

Parental  QKNFKGKQGRK
          QKNFKGKQGRK
Retrocopy QKNFKGKQGRK

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Solanum tuberosum was not studied using RNA-Seq expression data.

ChIP-Seq

Solanum tuberosum was not studied using ChIP-Seq data.

EST

Solanum tuberosum was not studied using EST data.

TSS

Solanum tuberosum was not studied using FANTOM5 data.

Lab

retro_stub_12 was not experimentally validated.

Homology

Retrocopy orthology:

Solanum tuberosum does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Solanum tuberosum	PGSC0003DMG400026532	1 retrocopy	retro_stub_12 ,