RetrogeneDB ID: retro_tnig_18

Retrocopy location

• Organism: Tetraodon (Tetraodon nigroviridis)
• Coordinates: 4:7946222..7946834(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSTNIG00000018739
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: zgc:66286
• Ensembl ID: ENSTNIG00000008476
• Aliases: None
• Description: zgc:66286 [Source:ZFIN;Acc:ZDB-GENE-040426-1593]

Sequence

>retro_tnig_18
CAATATGCCACCAAAGAAGCTCGAGCCCAAAAAACCAGAGCCCAAAAAACCCGAGCCGAAGAAGGATGCGCTCCGCTGGC
TAAGGCGGCCCCTCCTCCTGAGCCGCTGCCCGAGCAGCCCAAGGAGCCTGACTTTGACCCCAAAAGCATCACCCTGGAGT
TTACCTCCGATCAGATTGAGGAGTTCAAGGAGGCTTTTACTCTGTTTGACCGCACTCCCACCGGGGAGATGAAGATCACC
TACGCCCAGTGCGGGGACGTCATGCGTGCCCTGGGCCAGAACCCGACCAATGCAGACGTGCTGAAAGTGCTTGGAAAGCC
ACGGCCAGAGGACATGAGCACCAAAATGGTGGACTTTGAGACCTTTTTGCCCATGCTGCAGCACATCTCCCGCAAAAAAG
ACCAAGGCAATTTTGAGGATTTTGTGGAGGGGCTCAGAGTATTCGACAAGGAAGGCAACGGCACCATCATGGGGGCAGAG
CTGCGTCACGTTCTGGCCACTCTGGGAGAGAGGATGACAGAAGATGAGGTGGACAGACTGATGGCGGGACAGGAGGATGC
CAACGGATGCATCAACTACGCCTCCTTTGTCAAACACATTCTCTCTGGATGA

Alignment

ORF - retro_tnig_18 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.72 %
• Parental protein coverage: 98.95 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  APKKKEEPKPAPAPAPAPAKPPEPEVPKIPEFDPASVTLEFTAEQIEDFKDAFQLFDRTPANEMKIAYGQ
          A.K...E...AP....AP...P.PE.PK.P.FDP.S.TLEFT..QIE.FK.AF.LFDRTP..EMKI.Y.Q
Retrocopy AQKTRAEEGCAPLAKAAPPPEPLPEQPKEPDFDPKSITLEFTSDQIEEFKEAFTLFDRTPTGEMKITYAQ

Parental  CGDLIRALGQNPTQSEIMHVLGKPKAEDMQAKMLDFEQFLPIHQHICRAKDRGTYEDFVEGLRVFDKEGN
          CGD..RALGQNPT......VLGKP..EDM..KM.DFE.FLP..QHI.R.KD.G..EDFVEGLRVFDKEGN
Retrocopy CGDVMRALGQNPTNADVLKVLGKPRPEDMSTKMVDFETFLPMLQHISRKKDQGNFEDFVEGLRVFDKEGN

Parental  GTVMGAELRHVLATLGEKMSEDEVEQLMQNQEDANGCINYEAFVKYIMS
          GT.MGAELRHVLATLGE.M.EDEV..LM..QEDANGCINY..FVK.I.S
Retrocopy GTIMGAELRHVLATLGERMTEDEVDRLMAGQEDANGCINYASFVKHILS

Legend:

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

Expression

RNA-Seq

Tetraodon nigroviridis was not studied using RNA-Seq expression data.

ChIP-Seq

Tetraodon nigroviridis was not studied using ChIP-Seq data.

EST

Tetraodon nigroviridis was not studied using EST data.

TSS

Tetraodon nigroviridis was not studied using FANTOM5 data.

Lab

retro_tnig_18 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_tnig_18 has 0 orthologous retrocopies within teleost group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000013199	1 retrocopy	retro_chof_2215,
Danio rerio	ENSDARG00000011519	1 retrocopy	retro_drer_3,
Pteropus vampyrus	ENSPVAG00000004194	1 retrocopy	retro_pvam_841,
Tetraodon nigroviridis	ENSTNIG00000008476	1 retrocopy	retro_tnig_18 ,