RetrogeneDB ID: retro_drer_29

Retrocopy location

• Organism: Zebrafish (Danio rerio)
• Coordinates: 21:34862901..34863328(-)
• Located in intron of: ENSDARG00000093449

Retrocopy information

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

Parental gene information

• Parental gene symbol: si:ch211-178j18.4
• Ensembl ID: ENSDARG00000096024
• Aliases: None
• Description: si:ch211-178j18.4 [Source:ZFIN;Acc:ZDB-GENE-110914-148]

Sequence

>retro_drer_29
ATGGAGGCGGATATGGCTGAGGTCTCCCGTCGCCTCGGCCAGCGGTGCGAGCTGCCTCCCAGGACCCAGACGGATTTTCG
CAGTTTCTGCGTTGCCACTCTAATGTGGCTACACCGTCTGGGTCCTGGAAGCGTCAGGGAGCGTTAGGGTGCGGGAGTGG
CTGGGCAGGCGGCCAGAGGGAGAGGCTGTAATCTTGACGCTTCCCGGGAAAACCGTGAGCCTGAGCCGGAAAGAGGAGGA
GTGGCTGGAATGCTATTACAGGCACATCCGGCCGCTCTGCCTTAGGGCTCGGGCTTCGGGGGCAGAGGACAAAGGATGCT
TCTTCCTGGGAGCGTCAGGACTCCCCCTCACTAACCCCAGCCAGGAAGTCCTGCGCCTGAAAGCAAAGTACGTCAAGAGG
CAGCCCGCGCCGCCCGCTACCACCGCT

Alignment

ORF - retro_drer_29 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.13 %
• Parental protein coverage: 72.45 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MEADMAEVARRLSQRCELPPRTQMEFRSFCVATLVWLHRLGPGSVRE-LKEREWLGRRPEGDAVILTLPS
          MEADMAEV.RRL.QRCELPPRTQ..FRSFCVATL.WLHRLGPGSVRE....REWLGRRPEG.AVILTLP.
Retrocopy MEADMAEVSRRLGQRCELPPRTQTDFRSFCVATLMWLHRLGPGSVRE>VRVREWLGRRPEGEAVILTLPG

Parental  EAVSLSRKEKEWLECYFRHVRPLCLKAYAAGTDDKGCFFLGASGLALTNPTADIQRLKAKQVFLSAINPS
          ..VSLSRKE.EWLECY.RH.RPLCL.A.A.G..DKGCFFLGASGL.LTNP.....RLKAK.V......P.
Retrocopy KTVSLSRKEEEWLECYYRHIRPLCLRARASGAEDKGCFFLGASGLPLTNPSQEVLRLKAKYVKRQPAPPA

Parental  LTS
          .T.
Retrocopy TTA

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_29 retrocopy.

TSS

Danio rerio was not studied using FANTOM5 data.

Lab

retro_drer_29 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_drer_29 has 0 orthologous retrocopies within teleost group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Danio rerio	ENSDARG00000096024	3 retrocopies	retro_drer_27, retro_drer_29 , retro_drer_30,