RetrogeneDB ID: retro_itri_406

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393289.1:12248602..12248940(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMEM164
• Ensembl ID: ENSSTOG00000024954
• Aliases: None
• Description: transmembrane protein 164 [Source:HGNC Symbol;Acc:26217]

Sequence

>retro_itri_406
ATGTTCTATGTGGTGCCCATCTACCAACTTTGGAAAGGAGGTACTTACACCCCACAGCCCCTCATCAGTTTCCGGTGGGC
TCTTCTCTCAACTGGCCTCATGTTTTTTTGTCACTTCAGCATTCTACAGATCCTTAGCCTGGTTACCAAAGTGAATTTGA
ACAACATGCTGTGTCCAGCCACCTCAGACACATTCTACGCCCTTGGTATTGCATGTGGGCCTCCAGACACCAGAATCTCA
TGACCATGACCCACGGGAAGCTGGTCATCCTGTTCTCATACATGGCTGGGCCCTTGTGTAAATATCTGCTGGATTTGCTC
TGGCCTCCAGCCAAGAAA

Alignment

ORF - retro_itri_406 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.58 %
• Parental protein coverage: 96.58 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MLYVVPIYLLWKGGAYTPEPLSSFRWALLSTGLMFFYHFSILQILGLVTEVNLNNMLCPAISDPFYG-PW
          M.YVVPIY.LWKGG.YTP.PL.SFRWALLSTGLMFF.HFSILQIL.LVT.VNLNNMLCPA.SD.FY..PW
Retrocopy MFYVVPIYQLWKGGTYTPQPLISFRWALLSTGLMFFCHFSILQILSLVTKVNLNNMLCPATSDTFYA<PW

Parental  YRIWASGHQTLMTMTHGKLVILFSYMAGPLCKYLLDLLRLPENR
          Y..WAS.HQ.LMTMTHGKLVILFSYMAGPLCKYLLDLL..P...
Retrocopy YCMWASRHQNLMTMTHGKLVILFSYMAGPLCKYLLDLLWPPAKK

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_406 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_406 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	ENSSTOG00000024954	1 retrocopy	retro_itri_406 ,