RetrogeneDB ID: retro_drer_4

Retrocopy location

• Organism: Zebrafish (Danio rerio)
• Coordinates: 22:20894207..20896025(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSDARG00000061970
• Aliases: lingo3a, si:dkey-172o19.1
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: LINGO3 (1 of 2)
• Ensembl ID: ENSDARG00000067815
• Aliases: None
• Description: leucine rich repeat and Ig domain containing 3 [Source:HGNC Symbol;Acc:21206]

Sequence

>retro_drer_4
ATGGCGGGTTGTCCACACCTGAGTTTATCAGGGCTGCTTGTGCTCCTAATCACTGCATCCATAACACATGGCCAGAGCTG
CCCACAGCGCTGTGACTGTATCCCTCACCAGAGAGCAGTGATGTGCCAGAACAAGCGCCTGGGATCTATTCCTGGGGGCA
TCCCGGCTGACACACGGCTGCTGGATTTGAGCTGCAACAGTTTGCGCTGGGTGGAGTACAATGACTTGTCGACACTCTTG
AGACTTGAGGAGCTAGACCTGAGCGAGAATCTCATCAGTGTGTTGGAGCCTAACGCCTTCTCCAGCTTGCTTAACCTTAG
AGTATTGCGTCTTAGAGCCAACCAGCTTAAACTCGTGCCCATGGGTGCCTTTTCACGTCTCACCAACCTCACAACTCTGG
ACCTAAGTGGGAATAAACTAGTAATCCTGTTAGACTTCACCTTTCAGGACTTGAGGAACCTCCGCAATTTGGAGGTTGGT
GATAATGACCTGGTGTACATTTCCAACAAAGCTTTCCTGGGATTGGTGGGACTGCGGGAGTTAACCATTGAGAGGTGTAA
TCTGACTTCCATAAGTGGACAGTCTCTTTCCTACCTTCGTGGCTTGGTGACTCTTCGATTACGCTACCTCAGTATCGCTT
CGTTAGAAGAGCAGAACTTTCGCAAATTGGGTGGACTACGGGGTCTTGAGATTGACCACTGGCCATTCCTTGAGTACATC
TCTCCACACAGCTTCCAAGGTCTCAACCTTTCCTGGCTTTCGATTACCAACACCAACATTTCCACCGTGCCTACTGGTGC
TCTTCGCAACCTAATTCACTTGGCTAGCCTCAATCTGTCCTACAATCCCATCTCGGTTCTTGAGTCCTGGGCCTTGCGGG
ACCTTGTTCGATTGAAAGAACTGCATCTAGTTGGTACAAATCTGATCTCCGTGCAACCCTACGGTCTTGGAGGTCTGCAA
CAGATACGATTGCTTAACTTATCAAACAACGGATTAGTGACCCTGGAGGAAGGATCCTTCCACTCCGTCAACACACTGGA
GACGCTGCGTGTAGATGGCAACCCTTTGTCCTGTGACTGCCGCCTACTGTGGATTCTGCAGCGCAGGAAGACCCTCAATT
TTGATGGAAAGTCACCCGTTTGCACTGCACCCGTAGAAGTGCGAGGAAAATCGCTTAGTACATTCACAGACTCTGCACTT
TTTGACCACTTCACCTGCCAGAGGCCCAAAATCCGCAATCGCAAGCTTCAACAGCTGACAGCACGTGAAGGCCAGGTTGT
GTCGTTTGTATGTAGAGCTGAAGGAGACCCAACTCCGGTCATCTTTTGGATTTCACCTCAGCGTCGACGTATCACCACAA
AGAGTACTGGGAGAGTTATTGTCCTGCCTGAAGGTACTCTGGAGATTCGTTATGCCCAGGTAACAGACACTGGGACCTAT
ATATGCATAGCAAGCAATGCTGGTGGCAACGATACCTACTTCGCCACCCTAACAGTCAGTGGATTGCCACTAGATAGTGC
TTTGTCTGCTAATCGCACATACTACGTAGGTGATCTCAATGACACAAATTTAAACGACACGCGTGTCTTCCTGAAGTTCA
CATTGGATCTCAAAACCATTCTTGTGTCCACAGCAATGGGTTGTATAATGTTTTTGGGGGTAGTTCTTTTCTGTTTCATT
CTCCTGTTTGTGTGGAGCCGAGGACGAGGTCAGCACAAGAACAATTTCTCAGTAGAGTATTCATTCAGAAAGGTAGACGG
CCCTGCTGCCAGCGGGGGTCAAGGAGGGGCACGGAAATTTAACATGAAGATGATATAA

Alignment

ORF - retro_drer_4 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.42 %
• Parental protein coverage: 95.04 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VLGLLLALAAPSCSGCPPRCDCAAQLRSVSCQRRRLSAVPEGVPTETRLLDLSRNRLRWVAAGDLAPYPR
          .L.LL..........CP.RCDC....R.V.CQ..RL...P.G.P..TRLLDLS.N.LRWV...DL....R
Retrocopy LLVLLITASITHGQSCPQRCDCIPHQRAVMCQNKRLGSIPGGIPADTRLLDLSCNSLRWVEYNDLSTLLR

Parental  LEELDLSENLISTLEPNAFANLQALRTLRLRANQLKLVPMGAFARLTNLTTLDLSENRIVILLDFTFQDL
          LEELDLSENLIS.LEPNAF..L..LR.LRLRANQLKLVPMGAF.RLTNLTTLDLS.N..VILLDFTFQDL
Retrocopy LEELDLSENLISVLEPNAFSSLLNLRVLRLRANQLKLVPMGAFSRLTNLTTLDLSGNKLVILLDFTFQDL

Parental  RSLKNLEVGDNDLVYISHKAFSGLLSLEDLTMARCNLTSISGQTLSYLRGLVTLRLRHLSISTLEEQNFR
          R.L.NLEVGDNDLVYIS.KAF.GL..L..LT..RCNLTSISGQ.LSYLRGLVTLRLR.LSI..LEEQNFR
Retrocopy RNLRNLEVGDNDLVYISNKAFLGLVGLRELTIERCNLTSISGQSLSYLRGLVTLRLRYLSIASLEEQNFR

Parental  KLTALRGLEIHDWPFLEFISPLSFQGLNLSWLFITNTNITSVPSASFRNLAYLTALNLSYNPISTLESWA
          KL..LRGLEI..WPFLE.ISP.SFQGLNLSWL.ITNTNI..VP....RNL..L..LNLSYNPIS.LESWA
Retrocopy KLGGLRGLEIDHWPFLEYISPHSFQGLNLSWLSITNTNISTVPTGALRNLIHLASLNLSYNPISVLESWA

Parental  FRDLIRLKELHMVSTNLLTVEPHALGGLRQIRVLNLSNNDLVTLEESSFHSVNSLETLRVDGNPLSCDCR
          .RDL.RLKELH.V.TNL..V.P..LGGL.QIR.LNLSNN.LVTLEE.SFHSVN.LETLRVDGNPLSCDCR
Retrocopy LRDLVRLKELHLVGTNLISVQPYGLGGLQQIRLLNLSNNGLVTLEEGSFHSVNTLETLRVDGNPLSCDCR

Parental  LLWILQRRRTLNFDGKMPVCAGPPEVQGYLLSMFTDSALFDYFTCQKPKIRNRKMQQVMVHEGQPVSFLC
          LLWILQRR.TLNFDGK.PVC..P.EV.G..LS.FTDSALFD.FTCQ.PKIRNRK.QQ....EGQ.VSF.C
Retrocopy LLWILQRRKTLNFDGKSPVCTAPVEVRGKSLSTFTDSALFDHFTCQRPKIRNRKLQQLTAREGQVVSFVC

Parental  RAEGEPTPAIIWISPQRRRITSKSNGRVTVLPGGTLEIRYAQLTDSGTYICIASNAGGNDTYFATLTVKG
          RAEG.PTP.I.WISPQRRRIT.KS.GRV.VLP.GTLEIRYAQ.TD.GTYICIASNAGGNDTYFATLTV.G
Retrocopy RAEGDPTPVIFWISPQRRRITTKSTGRVIVLPEGTLEIRYAQVTDTGTYICIASNAGGNDTYFATLTVSG

Parental  QPVDAAIFSNRSMYAMDFNETGLNSTRVFLKFTLDLTTILVSTAMGCIMFLGVVLFCFLLLFVWSRGRGQ
          .P.D.A...NR..Y..D.N.T.LN.TRVFLKFTLDL.TILVSTAMGCIMFLGVVLFCF.LLFVWSRGRGQ
Retrocopy LPLDSALSANRTYYVGDLNDTNLNDTRVFLKFTLDLKTILVSTAMGCIMFLGVVLFCFILLFVWSRGRGQ

Parental  RKNNFTVEYSFRKTEGPATTGSSGGTRKFNMKMI
          .KNNF.VEYSFRK..GPA..G..GG.RKFNMKMI
Retrocopy HKNNFSVEYSFRKVDGPAASGGQGGARKFNMKMI

Legend:

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

Expression

RNA-Seq

Danio rerio was not studied using RNA-Seq expression data.

ChIP-Seq

Danio rerio was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_drer_4 retrocopy.

TSS

Danio rerio was not studied using FANTOM5 data.

Lab

retro_drer_4 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_drer_4 has 2 orthologous retrocopies within teleost group .

Species	RetrogeneDB ID
Gasterosteus aculeatus	retro_gacu_3
Tetraodon nigroviridis	retro_tnig_4

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Danio rerio	ENSDARG00000067815	1 retrocopy	retro_drer_4 ,
Gasterosteus aculeatus	ENSGACG00000015271	1 retrocopy	retro_gacu_3,
Oreochromis niloticus	ENSONIG00000010199	1 retrocopy	retro_onil_14,
Tetraodon nigroviridis	ENSTNIG00000015319	1 retrocopy	retro_tnig_4,
Xiphophorus maculatus	ENSXMAG00000019316	1 retrocopy	retro_xmac_14,