RetrogeneDB ID: retro_trub_13

Retrocopy location

• Organism: Fugu rubripes (Takifugu rubripes)
• Coordinates: scaffold_15:928301..930632(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSTRUG00000013856
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: elfn1b
• Ensembl ID: ENSTRUG00000015197
• Aliases: None
• Description: extracellular leucine-rich repeat and fibronectin type III domain containing 1b [Source:ZFIN;Acc:ZDB-GENE-080327-21]

Sequence

>retro_trub_13
GTGATGAGTGCCTTGTTTTGGTCTGTAGCCATTGTTTATTTGACTCAGATTGGCAGAGTGAGTGCAGACTGCTGGTTAAT
CGAGGGTGAAAAGGGCTTTGTATGGCTTGCAATCTGTAGCCAAAACCAACCACCTTACGAGGCCATCCCTCAGCATATCA
ACAGCACCATTGTGGACCTTCGTCTGAATGAAAACAAAATCAAAAGTATTCACTATTCTGCCCTTAGCCGCTTTGCCAAC
TTAACCTACCTAAACCTGACGAAGAATGAAATCTCCTACATCGAGGACGGGGCCTTTTCTGCTCAGTTTAACCTACAAGT
CCTTCAAATGGGCTTCAACAAGTTGAGAAACTTGACCGAAGGCATCCTCAGGGGTTTGGGAAAGCTGCAGTACCTCTACC
TCCAGGCAAATTTGATTGAGACTGTGACACCTAATGCCTTTTGGGAATGCCCCAACATTGAGAACATTGACCTCTCCATG
AACCGAATCCAGCAGTTAGATGGGTCCACATTCACCAGTTTGGCCAAACTGACCACCTGCGAGCTGTACACCAATCCTTT
TAACTGCTCCTGCGAGCTACTTGGATTTGTCAAATGGCTGTCGGTCTTCCCCAACAGAACAAACGAGCGGATGGTGTGCG
ACTCCCCATCTGGTGTCTCTGGTTATAGTTTACTCAGCCAGAATCCAAACAACCCAACATACAAAAATGCTCTTTATATG
CTCACCACCGTGTGTACTGATGACTACGTCACACCGTACACGCCAATCCCCACTGAGTCCATCACGCCCCCGCCAGACTC
AACACTGTGCGGTCTGGAGGATTGTCCCTCGGGGACAGAGCCGGAGGAGATCATCATCAGTACAACATATAACGATGTGG
AGGTAAACCCTGTCTTGAAGCTGAAACAGGTTACAAATACAGGCGCTACTATTACAGTTCAGATTCCGTATCCCTTCAAG
AAGATGTACATCCTGGTTCTGTACAACAACAGCTTTTTCACGGACATTCAAAACCTGAACAAAATAAAGGATGACATTGA
GCTGAAAAATCTCAATCCCCACACTAACTACACGTACTGTGTGGCTTCCATACGCAACTCCCTTCGCCATAATCACACTT
GTCTGACAATCACCACCGGCACCCGGAATGGGAAGGAAAGAAGCGTAAACAATGCAACTGCTACCCACTACATCATGACC
ATTTTAGGCTGCCTCTTCAGCATGGTCATCTTCCTCGGAGTTGTCTACTATTGTTTGCGGAGAAAGCGGCAACAAGATGA
AAAGCACAAAAAGTCAGGTAGCTTAAAGAAGAACATAATGGAGCTGAAATATGGACAGGAACTGGAAGGGGGGAATATTT
CTCGCATGTCACAGAAGCAGTTGTTGGCTGGGGACAGCATGGCACGCATGCCGTACCTACCACCTGCTGCCGAGATGGAG
CAGTACAAATTTCAAGAGATAGGTGACACCCCTAAAATGATGAAAGGGAACTACATGGAGGTGCGGAGCATGGACCACCA
CGACCGCAGGGAGTGCGAAATGGGAATGGCGGGGAATAGCCAGGGGTCGGTGGCCGAGATTTCCACCATAGCAAAAGAGG
TGGATAAAGTAAATCAGATTATTAACAACTGCATAGATGCGCTGAAGTCTGAATCCACCTCTTTTCAGGGCATGAAATCT
GGAGCGGTGTCCACCGCAGAGCCTCAGCTGGTGCTGATATCAGAGCACCCACAAGGTAAACCTGGCCTTCTGTCCCCCGC
ATATCAGGACAGCTACCACCACTCTCTGCAGAGGCATCGCTCGTCTGACATCTCGCCAAAGAGGCCCAGCACTGCCACAG
GAGGTCCAATGCGAAGCCCCAGGCCTTACCGCTCTGAATCCAAGTACATCGAGAAAACCTCCCCGACGGGAGAGACCATC
GTCACTGTAACGCCCACTGCAGCCATCCTGAGGGCTGAGGCGGACAAGATCCGCCAGTACAGCGACCATCGACACTCGTA
TCCCGACGCTCAGATTGAGGAGCTTGAAGGACCTGATGGCCACAAGTCATCCTTGTTAGAGCCTCTCACCCATTCCCGTT
CCAGAGACTTAGCGTACTCCCAACTGCCTTCCCAGTATCAAAATCTGAGCTACTCCTCCAGCCCCGAGTACTACTGCAAA
CCGCCACAGAGCATCTGGGGGCGATTCAAACTGCACCGGAAGCGGCACAAAGACGACGAGTACATGGCTGCCGGCCACGC
GCTGCGGAAGAAGGTCCAGTTTGCGAAGGACGAGGATCTGCACGACATTTTAGACTACTGGAAAGGTGTTTCAGCCCAGC
ATAAATCATAA

Alignment

ORF - retro_trub_13 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.9 %
• Parental protein coverage: 61.06 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VLSTFLCWLVVLSVMRLPVVTADCWLIEGEKGFVWLAICSMNQPPYESIPAHINSTIVDLRLNENKIRSV
          V.S................V.ADCWLIEGEKGFVWLAICS.NQPPYE.IP.HINSTIVDLRLNENKI.S.
Retrocopy VMSALFWSVAIVYLTQIGRVSADCWLIEGEKGFVWLAICSQNQPPYEAIPQHINSTIVDLRLNENKIKSI

Parental  HYSSLSRFGNLTYLNLTKNDISYVEDGAFSAQFNLQVLQMGFNKLRNLTEGMLRGLGKLQYLYLQANLIE
          HYS.LSRF.NLTYLNLTKN.ISY.EDGAFSAQFNLQVLQMGFNKLRNLTEG.LRGLGKLQYLYLQANLIE
Retrocopy HYSALSRFANLTYLNLTKNEISYIEDGAFSAQFNLQVLQMGFNKLRNLTEGILRGLGKLQYLYLQANLIE

Parental  TVTPNTFWECPNIENIDLSMNKIQVLDGSLFSGLSKLTTCELYTNPFNCSCELLGFLRWLSTFPNRTSER
          TVTPN.FWECPNIENIDLSMN.IQ.LDGS.F..L.KLTTCELYTNPFNCSCELLGF..WLS.FPNRT.ER
Retrocopy TVTPNAFWECPNIENIDLSMNRIQQLDGSTFTSLAKLTTCELYTNPFNCSCELLGFVKWLSVFPNRTNER

Parental  MVCDSPQGFFGYSLLSQNLRMSSQGNALHMLSVVCTDVDSSVTSFNGIGMVDFTTMLPDFASPCGLDDCA
          MVCDSP.G..GYSLLSQN.......NAL.ML..VCT..D..VT....I.....T...P.....CGL.DC.
Retrocopy MVCDSPSGVSGYSLLSQNPNNPTYKNALYMLTTVCT--DDYVTPYTPIPTESITP--PPDSTLCGLEDCP

Parental  SGTPPDEVINFSPIFSD--TNPIMTLKQVQHSSAVITVQLPHPYKKMYILALYNNSFFMDIQNLRRQRED
          SGT.P.E.I..S....D...NP...LKQV....A.ITVQ.P.P.KKMYIL.LYNNSFF.DIQNL.....D
Retrocopy SGTEPEEII-ISTTYNDVEVNPVLKLKQVTNTGATITVQIPYPFKKMYILVLYNNSFFTDIQNLNKIKDD

Parental  IELKNLKPNTNYTYCVASIRNSLRFNHTCLTISTGRQSGVERAVNKSSATHYIMTILGCLFGMLLFLGLI
          IELKNL.P.TNYTYCVASIRNSLR.NHTCLTI.TG...G.ER.VN...ATHYIMTILGCLF.M..FLG..
Retrocopy IELKNLNPHTNYTYCVASIRNSLRHNHTCLTITTGTRNGKERSVNNATATHYIMTILGCLFSMVIFLGVV

Parental  VHCLRKRRLMEEKERKMSRIQRTLIELKYGGDDDIEGGGVGPVSQK-LSAGDSLSRIPYLPQGGEIDPYK
          ..CLR..R...EK..K.........ELKYG.....EGG.....SQK.L.AGDS..R.PYLP...E...YK
Retrocopy YYCLRRKRQQDEKHKKSGSLKKNIMELKYG--QELEGGNISRMSQKQLLAGDSMARMPYLPPAAEMEQYK

Parental  LQEVIETPPHKPAKPNYMEVRGSGIERERERE
          .QE...TP..K..K.NYMEVR.......RE.E
Retrocopy FQEIGDTP--KMMKGNYMEVRSMDHHDRRECE

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_13 retrocopy.

TSS

Takifugu rubripes was not studied using FANTOM5 data.

Lab

retro_trub_13 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_trub_13 has 3 orthologous retrocopies within teleost group .

Species	RetrogeneDB ID
Gasterosteus aculeatus	retro_gacu_19
Oryzias latipes	retro_olat_18
Tetraodon nigroviridis	retro_tnig_5

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Gasterosteus aculeatus	ENSGACG00000016502	1 retrocopy	retro_gacu_19,
Oreochromis niloticus	ENSONIG00000000160	1 retrocopy	retro_onil_6,
Oryzias latipes	ENSORLG00000009720	1 retrocopy	retro_olat_18,
Tetraodon nigroviridis	ENSTNIG00000008254	1 retrocopy	retro_tnig_5,
Takifugu rubripes	ENSTRUG00000015197	1 retrocopy	retro_trub_13 ,
Xiphophorus maculatus	ENSXMAG00000014093	1 retrocopy	retro_xmac_1,