RetrogeneDB ID: retro_drer_26

Retrocopy location

• Organism: Zebrafish (Danio rerio)
• Coordinates: 2:53637395..53637845(+)
• Located in intron of: ENSDARG00000039945

Retrocopy information

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

Parental gene information

• Parental gene symbol: eef1da
• Ensembl ID: ENSDARG00000008109
• Aliases: eef1da, eef1d, zgc:66406
• Description: elongation factor-1, delta, a [Source:ZFIN;Acc:ZDB-GENE-040426-2740]

Sequence

>retro_drer_26
ATGAGTGGACTTCAGGGACTCGCCCAGGAGAACATCTAGTTTGACAAGTCCAGATACAACGAGGCTGAAAGATGCTTCTA
CGAGGGCGCCAACGGCATCCCTCAGACATCTCAGAGTCAGAATGCCAGCAAGTCTTAGGATAAGAGCGAACTGCCCTCAC
GTTTGAAGAGTCTTGAACTGGACAACAAGAATCAGCACAAAGTAGTGGATGAAATGAGAGCCACACTATTCAAAGTGGAG
TTCAGAATGGCCACACTGAAGAACACCCAAGCACCAGCTACAAAAGGAGTTACTGTCACCAAGGCTGCTCCTGTCCAGAA
GCCCAAGGTGGAGGAACACAAAGGTGCAGATTATGAAGACGACGACATTAACCTGTTTGGCAGTGGTGAAGAAGACGAAG
AAGCAAAGTGCATTCAAGCAAAGCGTGTGAAGAAACACTCCCAGAGAAAA

Alignment

ORF - retro_drer_26 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.33 %
• Parental protein coverage: 61.22 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSGLQGLAQENIWFDKSRYDEAERCFYEGANGIPQTSQSQNASKSEDQSELVSRLKSLELDNKNLHRVVD
          MSGLQGLAQENI.FDKSRY.EAERCFYEGANGIPQTSQSQNASKS.D.SEL.SRLKSLELDNKN.H.VVD
Retrocopy MSGLQGLAQENI*FDKSRYNEAERCFYEGANGIPQTSQSQNASKS*DKSELPSRLKSLELDNKNQHKVVD

Parental  DLRATLSKLESRMVTLEKTQAPATKGVTVTKAAPVQKPKVEEHNGADDEDDDIDLFGSDEEDEEAERIKA
          ..RATL.K.E.RM.TL..TQAPATKGVTVTKAAPVQKPKVEEH.GAD.EDDDI.LFGS.EEDEEA..I.A
Retrocopy EMRATLFKVEFRMATLKNTQAPATKGVTVTKAAPVQKPKVEEHKGADYEDDDINLFGSGEEDEEAKCIQA

Parental  ERVKEYSQRK
          .RVK..SQRK
Retrocopy KRVKKHSQRK

Legend:

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

Expression

RNA-Seq

Danio rerio was not studied using RNA-Seq expression data.

ChIP-Seq

Danio rerio was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_drer_26 retrocopy.

TSS

Danio rerio was not studied using FANTOM5 data.

Lab

retro_drer_26 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_drer_26 has 0 orthologous retrocopies within teleost group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Danio rerio	ENSDARG00000008109	1 retrocopy	retro_drer_26 ,
Macaca mulatta	ENSMMUG00000001645	4 retrocopies	retro_mmul_1795, retro_mmul_197, retro_mmul_733, retro_mmul_747,