RetrogeneDB ID: retro_itri_1673

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393623.1:965052..965413(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMEM47
• Ensembl ID: ENSSTOG00000019440
• Aliases: None
• Description: transmembrane protein 47 [Source:HGNC Symbol;Acc:18515]

Sequence

>retro_itri_1673
CAGAAACCTGCTAGCTTAGACATTTGGCATTTCAAGTCCACATTCAGCAGTGTTTGGCAGATTGCTACTCTGGCTCTGCT
CTTGGGAGGCATTGCCATCACTCACTGCATTCTTGGTGGGTTTGATTTATATCTATGTGGGATATTGAAGGTGCTTCTAC
AGACTTGTTGCTGTCATGCTTTTTGAAGCAGTTGTTTTATAGGTTTGAGACCTGGTCTTTTACTGAATCAAGTTGATTGA
AATTGTAAGCTTGAAATTTTATCATGAGTTCAAATCGGTTATGGTGTGTGGGGTGCAACTATTTTCATTTGAGGGTGCCA
TCTTTTATTGCCTGAACCTTAAGAACTATGAAGACTACTAC

Alignment

ORF - retro_itri_1673 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.52 %
• Parental protein coverage: 68.33 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RKPASLDSWHCEGCLSCNWQIATLALLLGGAAII-LIAFLVGLISICVGSRRRFYRPVAVMLFAAVVLQV
          .KPASLD.WH.....S..WQIATLALLL.G...I.L.AFLVGLI.I.VG..R.FYR.VAVMLF.AVVL.V
Retrocopy QKPASLDIWHFKSTFSSVWQIATLALLL-GGIAI>LTAFLVGLIYIYVGY*RCFYRLVAVMLFEAVVL*V

Parental  CSLVLYPIKFIETVSLKIYHEFNWGYGLAWGATIFSFGGAILYCLNPKNYEDYY
          ..LV.Y.IK.IE.VSLK.YHEF........G...FSF.GAI.YCLN.KNYEDYY
Retrocopy *DLVFY*IKLIEIVSLKFYHEFK--SVMVCGVQLFSFEGAIFYCLNLKNYEDYY

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_1673 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1673 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000006509	1 retrocopy	retro_dnov_1659,
Macaca mulatta	ENSMMUG00000004530	1 retrocopy	retro_mmul_1399,
Ictidomys tridecemlineatus	ENSSTOG00000019440	1 retrocopy	retro_itri_1673 ,