RetrogeneDB ID: retro_trub_40

Retrocopy location

• Organism: Fugu rubripes (Takifugu rubripes)
• Coordinates: scaffold_480:9869..11707(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSTRUG00000002066
• Aliases: None
• Description: None

Sequence

>retro_trub_40
AACAAGAAGGTTGAACTGGTGTTAGAGAACAGACTTGATCGAGAGAAACAAAAGGAAATGAATTTGCTGCTCACAGCTTT
AGATGGAGGCTCTCCTCAGAGATCAGGTACTGTAGTCATACACGTCACTGTGCTGGATGCTAATGATAACGCCCCAGTGT
TCAGTCAGGCCGTTTATAAAGCCAGTCTGCCTGAAAACTCTCCTCTAGACACTGTAGTGATGCAGGTTAGTGCCACTGAT
GCAGATGAAGGAGTGAATGGAGAAGTGACTTATCAATTCAGCCACGTTTCTGATGACGATATGAATATATTCTCAATTGA
CCCTAAAACTGGAGAAATCCGAGTGTCTGGTTTAATTGACTTTGAAGAAAAAAGATCTTTTGAAATGAGAGTCAAGGCTA
AAGACGGGTTAGGTCTAACATCTTATGCCAATATTATAATAGACGTGATTGATAAAAATGATAATGCCCCCCAGGTTTAT
GTAAAATCACTGATCAGTCCTATCCCAGAAAATATCTCACCTGGTTCAGAAGTGGGCATCATTAATGTGCAAGATGGAGA
TTCACTCAAAAATGGACAAGTTCGTTGCTCCATTCAGCAAAACGTCCCTTTTAAGCTGGTTCCTTCTATTAAAAACTATT
ATTCTCTGGTGACCACAGGACAACTGGACCGTGAACTAGTGTCTGATTACAACATTACAATCAGTGCCACTGACGAGGGC
TCTCCACCTCTGTCCTCCTCTAAAACGCTTCACTTGTCTGTAGCAGACATCAACGACAACCCCCCTGTGTTTGAGGAAGA
GTCCTACAGCGCATATGTGAGTGAAAATAACAGAGCCGGGTCCACTTTGTGTTCCGTTAGTGCTGGAGACCCCGACTGGA
GACAAAACGGTACCGTGATTTATTCTCTGTTAGCCGCTGAGGTGAACGGTGCTCCGGTGTCCTCTTATGTGTCTGTTAAT
GGAGACACGGGGCTGATCCACGCTGTCAGGTCCTTTGATTATGAACAGCTGAGGAGCTTTAAAGTGCACGTGATGGCCAG
AGACAACGGTCTCCTCCTCTCAGCAGTAACGTGACCGTCAGTGTGTTCATATCAGACGTTAATGACAACTCTCCTCAAAT
ACTGTATCCAGCCCCGGAGGGCAACTCCTTCATGACCGAGCTGGTCCCCAAAGCTGCACACGGAGGCTCTCTGGTGTCCA
AAGTGATCGCTGTGGACGCCGACTCTGGACAGAATGCCTGGCTGTCGTACCATATAGTCAAATCCAGCGATCCGGGACTC
TTCTCTATCGGTGTCCACAGTGGAGAGATCAGGACGCAGCGGGACATTTCTGAGTCTGACAGCATGAAACAGAACCTGAT
TGTGGCAGTGAAAGATAACGGACAGCCCTCTCTCTCTGCCACCTGCTCCATGTATTTACTCATTTCTGATAACTTGGCTG
AGGTGCCAGAGCTGAAGGACATTTCTTATGATGAGAAGAATTCCAAACTGACCTCCTATCTGATCATCGCGCTGGTGTCT
GTGTCCACCTTCTTCCTGACCTTCATCATCATCATCCTGGGTGTGAGGTTCTGTCGCAGGAGAAAGCCCAGAATGTTGTT
TGACGGAGCAGTAACCATCCCCGGCGCTTATCTCCCTCCTAATTACGCTGATGTTGACGGCACAGGAACTTTACGCAGCG
CTTACAATTATGACGCCTACCTGACAACAGGGTCTAGAACCAGTGACTTTAAGTTTGTGACATCTTACAATGACAACACA
CTTCCTGCTGAGCAGACTCTGAGGAAAAGCTCCACTGACTTTGATGAGCCATTTGAAGACTTTCACACACCTGCAGAG

Alignment

ORF - retro_trub_40 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.0 %
• Parental protein coverage: 77.14 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SKSVELVLDKELDREKEQNVNLVMVAVDGGNPQRSGTATIQITVLDANDNAPVFEQAVYKADLPENAALG
          .K.VELVL...LDREK....NL...A.DGG.PQRSGT..I..TVLDANDNAPVF.QAVYKA.LPEN..L.
Retrocopy NKKVELVLENRLDREKQKEMNLLLTALDGGSPQRSGTVVIHVTVLDANDNAPVFSQAVYKASLPENSPLD

Parental  TVVLTVSASDADEGVNGEVTYEFSRISDKAKKVFTLNSKTGEIKVSGPLDFESNPNYEMRIDAKDGFGLS
          TVV..VSA.DADEGVNGEVTY.FS..SD.....F....KTGEI.VSG..DFE.....EMR..AKDG.GL.
Retrocopy TVVMQVSATDADEGVNGEVTYQFSHVSDDDMNIFSIDPKTGEIRVSGLIDFEEKRSFEMRVKAKDGLGLT

Parental  SDCKLMIKITDINDNAPVIHVKSLTDPVPEDVSPGSEVGIINVQDRDSENNRQVRCSIQQNVPFKLVPSI
          S.....I...D.NDNAP...VKSL..P.PE..SPGSEVGIINVQD.DS..N.QVRCSIQQNVPFKLVPSI
Retrocopy SYANIIIDVIDKNDNAPQVYVKSLISPIPENISPGSEVGIINVQDGDSLKNGQVRCSIQQNVPFKLVPSI

Parental  KNYYSLVTTGQLDRELVSDYNITISATDEGSPPLSSSKTLHLSVADINDNPPVFEEESYSAYVSENNRAG
          KNYYSLVTTGQLDRELVSDYNITISATDEGSPPLSSSKTLHLSVADINDNPPVFEEESYSAYVSENNRAG
Retrocopy KNYYSLVTTGQLDRELVSDYNITISATDEGSPPLSSSKTLHLSVADINDNPPVFEEESYSAYVSENNRAG

Parental  STLCSVSAGDPDWRQNGTVIYSLLAAEVNGAPVSSYVSVNGDTGLIHAVRSFDYEQLRSFKVHVMARDNG
          STLCSVSAGDPDWRQNGTVIYSLLAAEVNGAPVSSYVSVNGDTGLIHAVRSFDYEQLRSFKVHVMARDNG
Retrocopy STLCSVSAGDPDWRQNGTVIYSLLAAEVNGAPVSSYVSVNGDTGLIHAVRSFDYEQLRSFKVHVMARDNG

Parental  -SPPLSSNVTVSVFISDVNDNSPQILYPAPEGNSFMTELIRYCSHTHTVVMQVSATDADEGVNKEITYGF
          .SPPLSSNVTVSVFISDVNDNSPQILYPAPEGNSFMTEL.....H....V..V.A.DAD.G.N....Y..
Retrocopy <SPPLSSNVTVSVFISDVNDNSPQILYPAPEGNSFMTELVPKAAHGGSLVSKVIAVDADSGQNAWLSYHI

Parental  DHVSDANQAFALNPKTGEVTTKRNTAESDSMKQNLIVAVKDNGQPSLSATCSMYLLISDNLAEVPELKDI
          ...SD....F......GE..T.R...ESDSMKQNLIVAVKDNGQPSLSATCSMYLLISDNLAEVPELKDI
Retrocopy VKSSDPG-LFSIGVHSGEIRTQRDISESDSMKQNLIVAVKDNGQPSLSATCSMYLLISDNLAEVPELKDI

Parental  SYDEKNSKLTSYLIIALVSVSTFFLTFIIIILGVRFCRRRKPRMLFDGAVTIPGAYLPPNYADVDGTGTL
          SYDEKNSKLTSYLIIALVSVSTFFLTFIIIILGVRFCRRRKPRMLFDGAVTIPGAYLPPNYADVDGTGTL
Retrocopy SYDEKNSKLTSYLIIALVSVSTFFLTFIIIILGVRFCRRRKPRMLFDGAVTIPGAYLPPNYADVDGTGTL

Parental  RSAYNYDAYLTTGSRTSDFKFVTSYNDNTLPAEQTLRKSPTDFADVFGESDSSPE
          RSAYNYDAYLTTGSRTSDFKFVTSYNDNTLPAEQTLRKS.TDF...F.......E
Retrocopy RSAYNYDAYLTTGSRTSDFKFVTSYNDNTLPAEQTLRKSSTDFDEPFEDFHTPAE

Legend:

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

Expression

RNA-Seq

Takifugu rubripes was not studied using RNA-Seq expression data.

ChIP-Seq

Takifugu rubripes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_trub_40 retrocopy.

TSS

Takifugu rubripes was not studied using FANTOM5 data.

Lab

retro_trub_40 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_trub_40 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 ,