RetrogeneDB ID: retro_itri_882

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393338.1:1799727..1800115(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HSD17B13
• Ensembl ID: ENSSTOG00000015091
• Aliases: None
• Description: hydroxysteroid (17-beta) dehydrogenase 13 [Source:HGNC Symbol;Acc:18685]

Sequence

>retro_itri_882
AAGTATGGCATAGAGGAAATGGCAGCTGAATGCAGAAAACTGGGTGCCCAGGCTCATTCCTTTGTAGTAGACTGCAGTAA
TCGATAAGATGTTTACAACTCTGCAAAGAAGGTGAAAACAGAAATTGGAGATATTAGTATTTTAGTAAATAATACTGGTA
TAGTCTACACATCAGATTTGTTTTCTACACAAGACCCTCAAATTGAAAAGACCTTTGCAGTCAATACACTTGCACATTTT
TGGATTACAAAGGCATTTCTCCCATCAATGATGAAGAATAATCATGGTCACATTGTCACTGTGGCTTCAGCAGCTGGGCT
TTGGGGTTCCCTTCTTACTGGCTTATTGTTCAAGTAAATTTGCTGCTGTTGGATTTCATGGAGCTCTG

Alignment

ORF - retro_itri_882 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.54 %
• Parental protein coverage: 56.28 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  QHGVEETATECQKSGAIVHAFVVDCSSREEIYSSVNQDKERSGDVTIVVNNAGAIYPADLLSTKDEEITK
          ..G.EE.A.EC.K.GA..H.FVVDCS.R...Y.S....K...GD..I.VNN.G..Y..DL.ST.D..I.K
Retrocopy KYGIEEMAAECRKLGAQAHSFVVDCSNR*DVYNSAKKVKTEIGDISILVNNTGIVYTSDLFSTQDPQIEK

Parental  TFEVNILGHFWIIKALLPSMIKRNYGHIVTVASVC-GHGVIPYLIPYCSSKFVAVGFHRAL
          TF.VN.L.HFWI.KA.LPSM.K.N.GHIVTVAS...G.GV.P.L..YCSSKF.AVGFH.AL
Retrocopy TFAVNTLAHFWITKAFLPSMMKNNHGHIVTVASAA>GFGV-PFLLAYCSSKFAAVGFHGAL

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_882 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_882 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Ictidomys tridecemlineatus	ENSSTOG00000015091	1 retrocopy	retro_itri_882 ,