RetrogeneDB ID: retro_gacu_23

Retrocopy location

• Organism: Stickleback (Gasterosteus aculeatus)
• Coordinates: groupXVIII:6891872..6892300(-)
• Located in intron of: ENSGACG00000007942

Retrocopy information

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

Parental gene information

• Parental gene symbol: KRBA2
• Ensembl ID: ENSGACG00000003664
• Aliases: None
• Description: KRAB-A domain containing 2 [Source:HGNC Symbol;Acc:26989]

Sequence

>retro_gacu_23
CCCCTCATGATGCCGAAGAAAAAAGTTGATTCTGAAAACAGAGCCTTTCAAAACCGATGGGAGGCGGAGTATATGTTTAC
TGACATTGCTGGTGAGCCCGTTTGTCTCATCTGTGGCGCTAATGTGGCTGTATTTAAAGAGTTTAATCTAAGACGGCACT
ATGAGACAAAACATCAGGATAACCTGAAAGACCTGAATGCAGAGCAGAAGATACAGAAAGTACAAGAGTTAAAGAATAAG
CTGACACTCCAGCAGACGTTTTTTACTCGTGCAAAATCACAAAGTGAAGCTGCTGTGAAAGCAAGTTTTATCGTGGCGGA
GGAGATCGCCTAAGCAGCCGGCCATTCACAGAGGGAACATTTCTGAAGAGCTGCATGGTCAAGGTGTGCGACGTCATATG
TCCAGACAAAAAGCAGATGCTGGCAAAT

Alignment

ORF - retro_gacu_23 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.93 %
• Parental protein coverage: 53.73 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PSKMAKRKVDTENRGFQTRWESEYLFTEVAGKPVCLLCGESVAVRKEYNLRSRAHSWHADDKNKNMDMEQ
          P..M.K.KVD.ENR.FQ.RWE.EY.FT..AG.PVCL.CG..VAV.KE.NLR......H.D...K....EQ
Retrocopy PLMMPKKKVDSENRAFQNRWEAEYMFTDIAGEPVCLICGANVAVFKEFNLRRHYETKHQDNL-KDLNAEQ

Parental  RLQKAEELKRGLKSRQALFKKAKSQGQAAVKASFILAEEIA-KSARPFTEGDFIKNCMIKVCDEVCPEKR
          ..QK..ELK..L...Q..F..AKSQ..AAVKASFI.AEEIA..S.RPFTEG.F.K.CM.KVCD..CP.K.
Retrocopy KIQKVQELKNKLTLQQTFFTRAKSQSEAAVKASFIVAEEIA<LSSRPFTEGTFLKSCMVKVCDVICPDKK

Parental  QLFLN
          Q...N
Retrocopy QMLAN

Legend:

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

Expression

RNA-Seq

Gasterosteus aculeatus was not studied using RNA-Seq expression data.

ChIP-Seq

Gasterosteus aculeatus was not studied using ChIP-Seq data.

EST

Gasterosteus aculeatus was not studied using EST data.

TSS

Gasterosteus aculeatus was not studied using FANTOM5 data.

Lab

retro_gacu_23 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_gacu_23 has 0 orthologous retrocopies within teleost group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Gasterosteus aculeatus	ENSGACG00000003664	1 retrocopy	retro_gacu_23 ,
Pelodiscus sinensis	ENSPSIG00000011044	1 retrocopy	retro_psin_58,