RetrogeneDB ID: retro_tnig_23

Retrocopy location

• Organism: Tetraodon (Tetraodon nigroviridis)
• Coordinates: 1:19188369..19189278(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: si:rp71-39b20.4
• Ensembl ID: ENSTNIG00000011060
• Aliases: None
• Description: si:rp71-39b20.4 [Source:ZFIN;Acc:ZDB-GENE-070912-704]

Sequence

>retro_tnig_23
GACAGAGACCCCGCGGTCTTCCACCACATCTTCCATTTCTACAAAAGCGGCGTTCTATGGATCGTACGGGAGATGTGCCC
CATCCACTTGGAGGAGGAGATCGATTACTGGGGCCTGAGCCTGAAGGACACGCCGTTCTGCTGCTGGACGGTGTTCCAGG
AGAAAGTGGACGAGATTAAAGACAACCTGAAAGTGGATCTGGAGCTGAGGGCTGAGGTGGAGGTAAAGTACGATAACGAG
GGTTTCAAAAACATGCTCTTCGGGAACGTCCGGAACAGCCTGTGGGATATAGTGGAGAATCCATATTCGTCCACTCTAGC
AAAGGCCTTTAGTGTTCTTTCCAGCCTTCTGGTGCTCTTCTCCATTGTTGCAATGGCTCTCAACACTGTGAAGGAGCTTC
AGAAATACAATATTTACGGCAGAACGCACATGGAATGGGTGGAGATAATAACCATTGTTTTTTTCACCTTTGAGTATTTC
ATCCGCTTGGTCACCACTCCGAACATCAAGATGTTTCTTAAAAGTGGACTTAACTTTGTGGACATGGTGGCTGTTGTTCC
CTACTTTGTTCAGATTGTGTTTGAGGCCGTTACTGGAGTCAAGGACTTGAACCAGCAGGAAGAACGGAGGACAATGGTTC
GGATGAGCAGGGTCGGCCACGTTCTCAAAGTCGTCAAGCTGATGCGGATCTTTCGGATTCTGAAGCTGGCGCGACACTCA
ACCGGCATGAGAGCCTTCGGGTTCACCCTGCGGCAATGCTACCACCAGAGCAGCTGCATTCTTCTTTTCATCGCCATGGG
AATCTCCACGTTCTCTGCTCTCCTTTACTCAGCCGAGAGAGAAACGGAAGGATCGCCAATAAGCAGTATCCCGGACGCCT
GGTGGTGGGCTGCAGTGAGTATTAGTACC

Alignment

ORF - retro_tnig_23 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.83 %
• Parental protein coverage: 68.16 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DRDPMFFHYIFHFYCSKVMWVMDNLCPLSFEEEMAFWGLSLKDSPRCCRILFEEKLDDIRDQLKVNRELI
          DRDP..FH.IFHFY.S.V.W.....CP...EEE...WGLSLKD.P.CC...F.EK.D.I.D.LKV..EL.
Retrocopy DRDPAVFHHIFHFYKSGVLWIVREMCPIHLEEEIDYWGLSLKDTPFCCWTVFQEKVDEIKDNLKVDLELR

Parental  DEIKPHQDEEVYKSMVLGDVRRALWNLMENPYSSLSAKAFAVFSSLFVLISIVAMTMNTVEETRTYSVGG
          .E.....D.E..K.M..G.VR..LW...ENPYSS..AKAF.V.SSL.VL.SIVAM..NTV.E...Y...G
Retrocopy AEVEVKYDNEGFKNMLFGNVRNSLWDIVENPYSSTLAKAFSVLSSLLVLFSIVAMALNTVKELQKYNIYG

Parental  RTYMEWIEVASILFFTLEYFLRLMTTSNITNFIKSALNFVDMVAVMPYFIQILFEAFVIDSEDVSAQEDL
          RT.MEW.E...I.FFT.EYF.RL.TT.NI..F.KS.LNFVDMVAV.PYF.QI.FEA.V....D...QE..
Retrocopy RTHMEWVEIITIVFFTFEYFIRLVTTPNIKMFLKSGLNFVDMVAVVPYFVQIVFEA-VTGVKDLNQQEER

Parental  KTMARVSKVSKVLKVVKLMRIFRILKLARHSTGMRAFGFTIRQCSEQVCCLFLFIAMGIFTFSALMHSVE
          .TM.R.S.V..VLKVVKLMRIFRILKLARHSTGMRAFGFT.RQC..Q..C..LFIAMGI.TFSAL..S.E
Retrocopy RTMVRMSRVGHVLKVVKLMRIFRILKLARHSTGMRAFGFTLRQCYHQSSCILLFIAMGISTFSALLYSAE

Parental  VDQPGTPFSSIPDAWWWAAVSIST
          ....G.P.SSIPDAWWWAAVSIST
Retrocopy RETEGSPISSIPDAWWWAAVSIST

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_23 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_tnig_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
Tetraodon nigroviridis	ENSTNIG00000005219	1 retrocopy	retro_tnig_1,
Tetraodon nigroviridis	ENSTNIG00000011060	1 retrocopy	retro_tnig_23 ,