RetrogeneDB ID: retro_dord_487

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: scaffold_22646:18663..19212(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Tyw3
• Ensembl ID: ENSDORG00000002718
• Aliases: None
• Description: tRNA-yW synthesizing protein 3 homolog (S. cerevisiae) [Source:MGI Symbol;Acc:MGI:2445040]

Sequence

>retro_dord_487
CTACTGGTTTCACACAAACCTTGTGTGATGGTAGCTCTGAAGAAAGCGAATGCTGATGCCATCTTAAAATTTGAACCATT
AGTCCTTCATGTGCAGTGCTGGCAGTTGGAAGATGCACAGATTCTGCATTCAGTGGCAATTGACTCTGGTTTCAGGAACT
CTGGCATCACAGTGGGAAAAAGAGGAAAAACTATGTTGGCTGTCCAGAGTACACATGGCTTAGAGGTTCCATTAAGCCAT
AAGGGAAATCTGATGGTGACAGAAGAATACATTGACTTCCTATTAAAGATAGCAAATCAAAAAATGGAAGAAAACAAGAA
CAGAATTGAAAGGTTTTACAACTGCCTACAGCATGCTTTGGAAAAAGAAACAATTATTGATTCACATCCTAAGGTCAAAG
AGAAAAACAAGTCATCTTATACTCACAAGAAAAAGAAACCGGAAAAAACAAATGGCCAATGTATTCCTGAGGAAAATGAT
GAAAAAGTTAAAAGTGACAATGATGATGATGAACCCAAAATCAATTCTACCATTTTCCCTGAAGATTAC

Alignment

ORF - retro_dord_487 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.58 %
• Parental protein coverage: 72.2 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LLVSHKPCVKDDVMVALKKANGDAILKFEPLVLHVQCRQLEDAQILHSVAIDSGFRNSGITVGKRGKTML
          LLVSHKPC....VMVALKKAN.DAILKFEPLVLHVQC.QLEDAQILHSVAIDSGFRNSGITVGKRGKTML
Retrocopy LLVSHKPC----VMVALKKANADAILKFEPLVLHVQCWQLEDAQILHSVAIDSGFRNSGITVGKRGKTML

Parental  AVRSTHGLEVPLSHKGNLMVTEEYIEFLLKIANQKMEENKKRIDRFYNCLQHALEKETIIDSHPKVKEKN
          AV.STHGLEVPLSHKGNLMVTEEYI.FLLKIANQKMEENK.RI.RFYNCLQHALEKETIIDSHPKVKEKN
Retrocopy AVQSTHGLEVPLSHKGNLMVTEEYIDFLLKIANQKMEENKNRIERFYNCLQHALEKETIIDSHPKVKEKN

Parental  KSSYTHKKKKPEKTNGQCIPEENDEKVKSDNDDEDPKINSTIFPEDY
          KSSYTHKKKKPEKTNGQCIPEENDEKVKSDNDD..PKINSTIFPEDY
Retrocopy KSSYTHKKKKPEKTNGQCIPEENDEKVKSDNDDDEPKINSTIFPEDY

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Dipodomys ordii was not studied using RNA-Seq expression data.

ChIP-Seq

Dipodomys ordii was not studied using ChIP-Seq data.

EST

Dipodomys ordii was not studied using EST data.

TSS

Dipodomys ordii was not studied using FANTOM5 data.

Lab

retro_dord_487 was not experimentally validated.

Homology

Retrocopy orthology:

Dipodomys ordii 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
Dipodomys ordii	ENSDORG00000002718	1 retrocopy	retro_dord_487 ,
Echinops telfairi	ENSETEG00000012572	1 retrocopy	retro_etel_845,
Tursiops truncatus	ENSTTRG00000010464	1 retrocopy	retro_ttru_1604,