RetrogeneDB ID: retro_itri_1868

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH394282.1:61718..62288(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GPD1
• Ensembl ID: ENSSTOG00000004948
• Aliases: None
• Description: glycerol-3-phosphate dehydrogenase 1 (soluble) [Source:HGNC Symbol;Acc:4455]

Sequence

>retro_itri_1868
GGGTCAGCTGTTGCAAAAATAATTGGTAATAATGTCAAGAAACTACAGAAGTTTGCCTCCACAGTCAAGATGTGGGTCTT
TGAGGAAACAGTGAATGGGAGAAAACTGACAGACATCATAAATAATGACCATGAAAATGTCAAATATCTCCCTGGACACA
AGCTGCCAGAAAATGTGGACGCAGTCTCCAGTCTCAGCGAGGCTGTGCAGGATGCAGACCTGCTGGTGTTTGTCATCCCC
CACCAGTTCATTCACAAGATCTTCGATGAGATCACTGGCAGAGTACCCAAGAAAGCACTGGGGATCACCCTCATCAAGGG
CATAGACGAGGGCCCCGAGGGACTGAACCTCATTTCTGACATCATCTGGGAGAAGATGGCCATTGACATCAGTGTGCTGA
TGGGTGCTAACATTGCCAGCGAGGTGGCTGCGGAGAAGTTCTGTGAGACCACCATTGGCAGCAAAATCATGGAGAATGGC
CTTCTCTTCAAAGAACTTCTGCAAACCCCCAATTTCCGAATAACTGTGGTTGATGATGCAGACACGGTTGAACTTTGTGG
TGCTCTTAAG

Alignment

ORF - retro_itri_1868 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.21 %
• Parental protein coverage: 54.29 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GSAIAKIVGANAAQLAHFDARVTMWVFEEDVGGRKLTEIINTQHENVKYLPGHKLPPNVVAIPDVVQAAA
          GSA.AKI.G.N...L..F...V.MWVFEE.V.GRKLT.IIN..HENVKYLPGHKLP.NV.A......A..
Retrocopy GSAVAKIIGNNVKKLQKFASTVKMWVFEETVNGRKLTDIINNDHENVKYLPGHKLPENVDAVSSLSEAVQ

Parental  DADILIFVVPHQFIGKICDQLKGHLKANAIGMSLIKGVDEGPNGLKLISEVIGERLDIPMSVLMGANIAN
          DAD.L.FV.PHQFI.KI.D...G.....A.G..LIKG.DEGP.GL.LIS..I.E...I..SVLMGANIA.
Retrocopy DADLLVFVIPHQFIHKIFDEITGRVPKKALGITLIKGIDEGPEGLNLISDIIWEKMAIDISVLMGANIAS

Parental  EVADEKFCETTIGCKDPVQGQLLKELMQTPNFRITVVQEVDTVEICGALK
          EVA.EKFCETTIG.K....G.L.KEL.QTPNFRITVV...DTVE.CGALK
Retrocopy EVAAEKFCETTIGSKIMENGLLFKELLQTPNFRITVVDDADTVELCGALK

Legend:

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

Expression

RNA-Seq

Ictidomys tridecemlineatus was not studied using RNA-Seq expression data.

ChIP-Seq

Ictidomys tridecemlineatus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_itri_1868 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1868 was not experimentally validated.

Homology

Retrocopy orthology:

Ictidomys tridecemlineatus 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000020375	1 retrocopy	retro_etel_1326,
Macropus eugenii	ENSMEUG00000015143	1 retrocopy	retro_meug_346,
Ictidomys tridecemlineatus	ENSSTOG00000004948	1 retrocopy	retro_itri_1868 ,
Tursiops truncatus	ENSTTRG00000001012	1 retrocopy	retro_ttru_1295,