RetrogeneDB ID: retro_itri_1256

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393416.1:460514..460838(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TSPAN31
• Ensembl ID: ENSSTOG00000001138
• Aliases: None
• Description: tetraspanin 31 [Source:HGNC Symbol;Acc:10539]

Sequence

>retro_itri_1256
CTCAACATGGTCTACATGACAGATGTCATCAGTGCTTCTTGTGGGTCAGGAGTAACAACAACCAGGCATGAACTGGAAAG
AAGTTTTGACTCTTGTGGCTTGTTGAATTTACTTTAAACCCTGTACCAAGACGACCCTTTCTGCAATGCAATCTATAAGA
AGAAGGGATCTACATGCCAGATATGCAGAGAAAAATTTCTTAAGCATTCAAGTGAAGCCCTGAAAATCCTAGCGAGTGTT
GGATTATTCCTTAGTTTGACTTGGTGTTTGGGATGGCAATGAAATTTCAGAATCAGAAAGATCCTCACACCAACCCCAGT
GCCT

Alignment

ORF - retro_itri_1256 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.91 %
• Parental protein coverage: 51.2 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  INRSKQTDVINASW-WVMSNS-TRHELERSFDCCGLFNLT-TVYQDDPSCNAICKNRSSTCQMCGEKFLK
          .N....TDVI.AS..WV.SN..TRHELERSFD.CGL.NL..T.YQDDP.CNAI.K...STCQ.C.EKFLK
Retrocopy LNMVYMTDVISASC<WVRSNN>TRHELERSFDSCGLLNLL*TLYQDDPFCNAIYKKKGSTCQICREKFLK

Parental  HSDEALKILGGVGLFFSFTEILGVWLAMRFRNQKDPRANP
          HS.EALKIL..VGLF.S.T..LG.....R.R....P...P
Retrocopy HSSEALKILASVGLFLSLTWCLGWQ*NFRIRKILTPTPVP

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_1256 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1256 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
Erinaceus europaeus	ENSEEUG00000006647	1 retrocopy	retro_eeur_342,
Ictidomys tridecemlineatus	ENSSTOG00000001138	1 retrocopy	retro_itri_1256 ,
Ictidomys tridecemlineatus	ENSSTOG00000008833	1 retrocopy	retro_itri_1367,