RetrogeneDB ID: retro_tnig_22

Retrocopy location

• Organism: Tetraodon (Tetraodon nigroviridis)
• Coordinates: 1:6666280..6668638(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSTNIG00000005148
• Aliases: None
• Description: None

Sequence

>retro_tnig_22
GTCCTTGCTCTTATTTTCCTCGTTCTGCAGCGCGTCAATGGAGACGTGAGCTACTCTGTACCGGAGGAGATGAAACGTGG
ATCTGTAGTCGGGAATATCGGGAAGGATCTGGGACTTGATTTGGCCAGACTGTCTGCTCGGAAGGCCCGCATCGATACTG
AGGACAACAGCGTGAAATACTGCAGTCTGAACCTGAACACCGGAGAGCTGATCGTTCAAGAGAGGATCGACAGGGAAGCT
CTTTGTGAGAAGAAGGCGTCGTGCGTTCTGAAGCAGGAACTGGTGCTGGAAAATCCTTTAGAACTGCACCGTATTAGTAT
CCATGTTCAGGACATCAACGATAATTCACCGCAGTTTAAAGAGGAGTCAATTAAATTAGAGATCAGGGAATCAGCTGTTA
AAGGTGCACGTTTTCTCCTTGGAGAAGCCCACGACGCAGATATCGGACAAAATACTGTTCAAGGCTACACCCTTCAGCAG
AATGATCATTTTAAATTAAACGTAAACACGAAATCTAGTAATAGAAAATATTGTGAATTATTATTAGATAAAGAATTAGA
CAGAGAGGACAAACAAGAATTGCAGTTGTTACTCACAGCTGTAGATGGAGGCTCTCCTCAGAGATCAGGGACTGTAGTCA
TCCACGTCACTGTGCTGGATGCTAATGATAACGCCCCAGTGTTCAGCCAGTCTGTCTATAAAACCAGTCTGCCTGAGAAT
TCTCCTCTGGACACACTGGTGATCACAGTCAGTGCTGCTGATGCAGACGAAGGAGTGAATAGTGAAATTACATATGGATT
TGATCATGTTTTAGAGGATGAAAATGTATTTTTACTTGACACAAAAACAGGAGTTGTGAGAGTTAATGGAGCGATTGATT
ATGAGAAAATACCATCATATGAAATGCAAATAAGTGCAAAAGATGGTCTGGGATTAGTTGCATATGCCACATTAATTATT
GAGATTACCGATGTAAATGACAACGCTCCAGTTATTCATCTGAAATCCCTGACCAATCCCATACCTGAGAACGTGTCACC
TGGTTCAGAGGTGGGCATCATCAACGTTCAGGACAGAGACTCCGAGAATAACAGACAGGTGCGCTGCTCCATTCAGCAAA
ACGTCCCTTTCAAGTTGGTTGCGTCCATCAAAAACTATTATTCTCTGGTGACCACAGGACAACTGGACCGTGAACTAGTG
TCTGACTACAACATCACAATCAGCGCCACTGACGAGGGCTCTCCACCTCTGTCCTCCTCCAAAAGTGTCCACTTGTCTGT
AGCAGACGTCAACGACAACCCCCCTGTGTTTGAGGAGCAGTCGTACAGCGCATATGTGAGTGAGAACAACAGAGCCGGAT
CCACTTTGTGTTCCGTTAGTGCTCGAGACCCCGACTGGAGACAAAACGGTACCGTGATTTATTCTCTGTTAGCGGCTGAG
GTGAGCGGCGCTCCGGTGTCCTCGTATGTGTCTGTGAACGGAGACACGGGGGTGATCCACGCTGTCAGGTCCTTTGATTA
CGAACAGCTGAGGAGCTTCAAAGTGCACGTGATGGCCAGAGACAACGGCTCTCCTCCTCTCAGCAGTAACGTGAGCGTGA
GCGTCTTTGTGTCCGACGTCAACGACAACCCTCCTCAAATCCTGTATCCGGCCCCGGAGGGCAACTCCTTCATGACTGAG
CTGGTCCCCAAAGCTGCACACGGAGGCTCTCTGGTGTCCAAAGTGATCGCTGTGGACGCAGACTCTGGACAGAACGCCTG
GCTGTCCTACCACATAGTCCAATCCAGCGACCCGGGCCTTTTCACCATCGGTGTCCACAGTGGGGAGATCAGGACGCAGC
GGGACATTTCTGAGTCTGACAGCATGAAGCAGAACCTGATTGTGGCGGTGAAAGATAACGGACAGCCCTCTCTCTCTGCC
ACCTGCTCCATGTATTTACTCATTTCTGACAACTTGGCTGAGGTGCCAGAGCTGAAGGACATTTCCTACGAGGAGAAGAA
TTCCAAACTGACGTCCTATCTGATCATCGCGCTGGTGTGCGTGTCCACCTTCTTTCTGACCTTCATCATCATCATCCTGG
GTGTGAGGTTCTGTCGCAGGAGGAAGCCCAGGATGTTGTTTGACGGAGCAGTAACCATCCCCGGAGCTTATCTGCCTCCT
AACTACGCAGATGTTGACGGCACAGGAACCTTGCGCAGCGCTTACAACTATGACGCCTACCTGACAACAGGTTCTAGAAC
CAGTGACTTTAAGTTTGTGACGTCTTACAATGACAACACACTTCCTGCTGAGCAGACTCTGAGGAAAAGCCCCTCTGACT
TTGCTGATGTCTTTGGAGATGGTGACAGTTCTCCTGAG

Alignment

ORF - retro_tnig_22 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.8 %
• Parental protein coverage: 83.01 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LLAVFFAALDLVHGDLSYSVPEEMKRDSVIGNVAKDLGLDVRVLSSRKARVDFGGTRKRYCDMNLRTGDL
          .LA..F..L..V.GD.SYSVPEEMKR.SV.GN..KDLGLD...LS.RKAR.D.......YC..NL.TG.L
Retrocopy VLALIFLVLQRVNGDVSYSVPEEMKRGSVVGNIGKDLGLDLARLSARKARIDTEDNSVKYCSLNLNTGEL

Parental  ITSERIDRESLCGKKASCLVTVDLVLENPLELHRVSLHVQDINDNSPQFREDLIEMEIRESADKGTRFSI
          I..ERIDRE.LC.KKASC.....LVLENPLELHR.S.HVQDINDNSPQF.E..I..EIRESA.KG.RF..
Retrocopy IVQERIDREALCEKKASCVLKQELVLENPLELHRISIHVQDINDNSPQFKEESIKLEIRESAVKGARFLL

Parental  EEANDADIGQNAVQRYILQKNDNFILSVDNKKV-ELVLENKLDREKQKE----MHLLLTAVDGGSPQRSG
          .EA.DADIGQN.VQ.Y.LQ.ND.F.L.V..K.......E..LD.E...E......LLLTAVDGGSPQRSG
Retrocopy GEAHDADIGQNTVQGYTLQQNDHFKLNVNTKSSNRKYCELLLDKELDREDKQELQLLLTAVDGGSPQRSG

Parental  TVVIHVTVLDANDNAPVFSQSVYKSSLPENSPLDTLVITVSAADADEGVNSEITYGFDHVLEDDENVFLL
          TVVIHVTVLDANDNAPVFSQSVYK.SLPENSPLDTLVITVSAADADEGVNSEITYGFDHVLE.DENVFLL
Retrocopy TVVIHVTVLDANDNAPVFSQSVYKTSLPENSPLDTLVITVSAADADEGVNSEITYGFDHVLE-DENVFLL

Parental  DTKTGVVRVNGAIDYETTATFELRVTAKDGLGLTSYAKVIIDVTDVNDNAPVIHLKSLTNPIPENVSPGS
          DTKTGVVRVNGAIDYE.....E....AKDGLGL..YA..II..TDVNDNAPVIHLKSLTNPIPENVSPGS
Retrocopy DTKTGVVRVNGAIDYEKIPSYEMQISAKDGLGLVAYATLIIEITDVNDNAPVIHLKSLTNPIPENVSPGS

Parental  EVGIINVQDRDSENNRQVRCSIQQNVPFKLVASIKNYYSLVTTGQLDRELVSDYNITISATDEGSPPLSS
          EVGIINVQDRDSENNRQVRCSIQQNVPFKLVASIKNYYSLVTTGQLDRELVSDYNITISATDEGSPPLSS
Retrocopy EVGIINVQDRDSENNRQVRCSIQQNVPFKLVASIKNYYSLVTTGQLDRELVSDYNITISATDEGSPPLSS

Parental  SKSVHLSVADVNDNPPVFEEQSYSAYVSENNRAGSTLCSVSARDPDWRQNGTVIYSLLAAEVSGAPVSSY
          SKSVHLSVADVNDNPPVFEEQSYSAYVSENNRAGSTLCSVSARDPDWRQNGTVIYSLLAAEVSGAPVSSY
Retrocopy SKSVHLSVADVNDNPPVFEEQSYSAYVSENNRAGSTLCSVSARDPDWRQNGTVIYSLLAAEVSGAPVSSY

Parental  VSVNGDTGVIHAVRSFDYEQLRSFKVHVMARDNGSPPLSSNVSVSVFVSDVNDNPPQILYPAPEGNSFMT
          VSVNGDTGVIHAVRSFDYEQLRSFKVHVMARDNGSPPLSSNVSVSVFVSDVNDNPPQILYPAPEGNSFMT
Retrocopy VSVNGDTGVIHAVRSFDYEQLRSFKVHVMARDNGSPPLSSNVSVSVFVSDVNDNPPQILYPAPEGNSFMT

Parental  ELVPKAAHGGSLVSKVIAVDADSGQNAWLSYHIVQSSDPGLFTIGVHSGEIRTQRDISESDSMKQNLIVA
          ELVPKAAHGGSLVSKVIAVDADSGQNAWLSYHIVQSSDPGLFTIGVHSGEIRTQRDISESDSMKQNLIVA
Retrocopy ELVPKAAHGGSLVSKVIAVDADSGQNAWLSYHIVQSSDPGLFTIGVHSGEIRTQRDISESDSMKQNLIVA

Parental  VKDNGQPSLSATCSMYLLISDNLAEVPELKDISYEEKNSKLTSYLIIALVCVSTFFLTFIIIILGVRFCR
          VKDNGQPSLSATCSMYLLISDNLAEVPELKDISYEEKNSKLTSYLIIALVCVSTFFLTFIIIILGVRFCR
Retrocopy VKDNGQPSLSATCSMYLLISDNLAEVPELKDISYEEKNSKLTSYLIIALVCVSTFFLTFIIIILGVRFCR

Parental  RRKPRMLFDGAVTIPGAYLPPNYADVDGTGTLRSAYNYDAYLTTGSRTSDFKFVTSYNDNTLPAEQTLRK
          RRKPRMLFDGAVTIPGAYLPPNYADVDGTGTLRSAYNYDAYLTTGSRTSDFKFVTSYNDNTLPAEQTLRK
Retrocopy RRKPRMLFDGAVTIPGAYLPPNYADVDGTGTLRSAYNYDAYLTTGSRTSDFKFVTSYNDNTLPAEQTLRK

Parental  SPSDFADVFGDGDSSPE
          SPSDFADVFGDGDSSPE
Retrocopy SPSDFADVFGDGDSSPE

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_22 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_tnig_22 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	ENSTNIG00000005148	1 retrocopy	retro_tnig_22 ,
Takifugu rubripes	ENSTRUG00000002066	1 retrocopy	retro_trub_40,