RetrogeneDB ID: retro_itri_504

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393297.1:728678..729108(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DTD2
• Ensembl ID: ENSSTOG00000025562
• Aliases: None
• Description: D-tyrosyl-tRNA deacylase 2 (putative) [Source:HGNC Symbol;Acc:20277]

Sequence

>retro_itri_504
CCACCTAAGGGGGACGCTGCGGCCCAGTGGGTGGAGGTTCAGAGAGGATCAGTGATCTATGTGTGCTTCTTCAAGGGAGC
TGATAAAGAACTACTTCCAAAAATGGTTAATACACTATTAAATGTGAAATTCAGTGAGACAGATAATGGCAAGCACGTCT
CTGTACTGGATCTACCTGGAGATATTCTTATCATCCCTCAAGCCACCCTTGGTGGTAGAGTAAAAGGAAGAAATATGCAG
TTATCACTCCAACTGTGGAAAAGAAGAAGGGTTAGAACTTCATTCCCTATTTGTATCTCTCTGTGAAAAAGAATTAGCTG
CAAACAGTAAGTGCACTGAAGCTGGGGTTGTAGTGGAACATGGCACTTATGGGAACAGGCAGGTTTTAAAGCTGGATTCC
CATGGACCATACACACACCTAATTGAGTTT

Alignment

ORF - retro_itri_504 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.36 %
• Parental protein coverage: 85.12 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PAEGDAAAQWVEIQRGLVIYVCFFKGADKELLPKMVNTLLNVKLSETENGKHVSVLDLPGDILIIPQATL
          P..GDAAAQWVE.QRG.VIYVCFFKGADKELLPKMVNTLLNVK.SET.NGKHVSVLDLPGDILIIPQATL
Retrocopy PPKGDAAAQWVEVQRGSVIYVCFFKGADKELLPKMVNTLLNVKFSETDNGKHVSVLDLPGDILIIPQATL

Parental  GGRVKGRNMQ-YHSNCGKEEGLELYSLFVSLCEKELATNSKCTEAGVVVEHGTYGNRQVLKLDTNGPYTH
          GGRVKGRNMQ.YHSNCGKEEGLEL.SLFVSLCEKELA.NSKCTEAGVVVEHGTYGNRQVLKLD..GPYTH
Retrocopy GGRVKGRNMQ>YHSNCGKEEGLELHSLFVSLCEKELAANSKCTEAGVVVEHGTYGNRQVLKLDSHGPYTH

Parental  LIEF
          LIEF
Retrocopy LIEF

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_504 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_504 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 5 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000015731	1 retrocopy	retro_amel_696,
Bos taurus	ENSBTAG00000038020	1 retrocopy	retro_btau_23,
Mustela putorius furo	ENSMPUG00000001065	1 retrocopy	retro_mputfur_1052,
Ictidomys tridecemlineatus	ENSSTOG00000025562	1 retrocopy	retro_itri_504 ,
Tursiops truncatus	ENSTTRG00000003788	3 retrocopies	retro_ttru_1617, retro_ttru_1832, retro_ttru_718,