RetrogeneDB ID: retro_onil_14

Retrocopy location

• Organism: Tilapia (Oreochromis niloticus)
• Coordinates: GL831234.1:1769896..1771735(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSONIG00000021358
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: LINGO3 (1 of 2)
• Ensembl ID: ENSONIG00000010199
• Aliases: None
• Description: leucine rich repeat and Ig domain containing 3 [Source:HGNC Symbol;Acc:21206]

Sequence

>retro_onil_14
ATGGCCACGAGGGCCAGCCTGGGTCAGGATGTAGGCTGGCTGCTGCCTTTCCTTTTCTTGTTACTAATGATCACAGTGTC
ACCTGCCCAAAGCCAAGGATGTCCCCAGCGCTGTGAGTGCATTGCTAAGCTCAAGACTGTGTCTTGTTATGGTAAACGCT
TGTCTGCACTGCCAGATGGAATCCCACTGGACACCAAGATCCTGGACTTGAGTGGGAATAAACTGCGTTGGGTAGAACAC
GGAGACCTGCTTCCGTATTCACGTCTCGAAAAGCTAGACCTGAGTGAGAACATGATCAGTGTCCTGGAACCAAATGCTTT
TTCTAGCCTTCAGAACCTTAAGTCGCTTTCACTGAGGGGTAACCAACTGAAGCTGGTCCCAATGGGAGCTTTCTCCCGTC
TCTCCAACCTAACTTCATTGGACCTTAGTGGGAATAAGATTGTAATTCTGTTGGACTTTACTTTCCAAGACTTGAGAAGT
TTAAAGAACTTGGAGGTCGGTGACAATGATTTAGTTTATATCTCTAACAAGGCCTTTCTGGGTTTGGTGGGACTGAAGGA
ATTGACAATTGAGAGGTGTAACCTGACTTCGGTGTCCAGCCAGTCTTTGTCTTACCTGCATAACCTGGTGACTCTGCGGC
TCCGCTACCTCAGTATCTCTGCCTTAGAGGACCAAAACTTCCGGAAGCTGGGAAACCTGAGGGGCCTGGAGATTGATCAC
TGGCCCTTTTTGGAGTACATCTCTCCCCACAGCCTGCAGGGTCTCAACTTGTCCTGGCTGTCTATCACGCACACCAACAT
CACCTCTGTGCCCACCTCTGCCCTGCGTAGTTTGGCTCACCTCACCAGCCTCAACCTATCTTACAACCCCATCACTGTGT
TGGAGTCCTGGGCATTGCGGGATCTCGTAAGGCTGAAGGAGCTGCATCTAGTCAAAACCAACCTGGCAGTAGTGCAGCCC
TATGCGCTCGGTGGTCTAAGGCAAATCCGCCTTCTTAACCTTTCCTCTAACAGCCTGGTGACCCTGGAGGAGGGAGCCTT
TCAGTCTGTCAACACTCTGGAGACGCTGCGTTTGGATGGAAACCCTCTGGCCTGCGACTGCCGCTTGCTCTGGATCCTTC
AGCGGAGGAAGACCCTGAACTTTGATGGTGCCTCCCCGGTGTGTATGACACCTGTTGAAGTGCAAGGACGTGCTCTCAAT
GCTTTCTCTGATTCCGCTCTCTTTGACCACTTTACTTGTCAGAAGCCCAAAATCCGCAACAGGAAACTGCAGCAGATATC
TGCCCGCGAGGGACAGGTAGTGTCATTTATTTGCAGAGCAGAAGGTGAGCCCACACCGGTGATATTCTGGATTTCTCCTC
AGCGCCGCCGCATCACCACAAAGAGCAGCGGCCGCCTTACCGTGTTACCAGAAGGCACGCTAGAAATCCGCTACGCCCAG
GTCACAGATAGTGGGACGTACATTTGCATAGCCAGCAATGCCGGTGGAAATGACACATATTTTGCCACACTTACAGTGAG
TGGGCTGCCGCTGGATGCAGCCCTCATGGCCAACCGCACCTACTATGCTGGGGATCTTAATGACACAAATCTGAATGATA
CCAGAGTCTTCTTGAAGTTCACTCTGGACCTCAAGACGATCCTCATATCTACAGCCATGGGCTGTATCATGTTTCTCGGG
GTAGTCCTTTTCTGTTTCATTCTGCTGTTTGTGTGGAGTCGAGGGCGAGGACAGCACAAAAACAACTTCTCGGTAGAATA
TTCTTTTAGAAAAGTGGACGGGCCTGCAGCCAGTGGAGGACAAGGTGGAGCGCGGAAGTTCAACATGAAAATGATTTGA

Alignment

ORF - retro_onil_14 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.63 %
• Parental protein coverage: 96.78 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  WVLATSLVTMITLTLPGNSHACPPRCECSAQLRSVSCQRRRLTNIPEGIPTETRLLDLSKNRLRWVQAGD
          W.L............P..S..CP.RCEC.A.L..VSC...RL...P.GIP..T..LDLS.N.LRWV..GD
Retrocopy WLLPFLFLLLMITVSPAQSQGCPQRCECIAKLKTVSCYGKRLSALPDGIPLDTKILDLSGNKLRWVEHGD

Parental  LAPYPRLEEVDFSENLISTLEPNAFSTLQNLKVLKLRGNQLKLVPMGAFAKLGNLTSLDLSENKMVILLD
          L.PY.RLE..D.SEN.IS.LEPNAFS.LQNLK.L.LRGNQLKLVPMGAF..L.NLTSLDLS.NK.VILLD
Retrocopy LLPYSRLEKLDLSENMISVLEPNAFSSLQNLKSLSLRGNQLKLVPMGAFSRLSNLTSLDLSGNKIVILLD

Parental  YTFQDLKSLKHLEVGDNDLVYISHKAFSGLLGLEDLTIERCNLTSISGQTLSYLRSLVTLRLRHLSITAL
          .TFQDL.SLK.LEVGDNDLVYIS.KAF.GL.GL..LTIERCNLTS.S.Q.LSYL..LVTLRLR.LSI.AL
Retrocopy FTFQDLRSLKNLEVGDNDLVYISNKAFLGLVGLKELTIERCNLTSVSSQSLSYLHNLVTLRLRYLSISAL

Parental  EDQNFRKLSNLRGLDIDHWPYLEYISPLSFQGLDLHWLSITNTNITSVPSASFKNLVHLTHLNLSYNPIT
          EDQNFRKL.NLRGL.IDHWP.LEYISP.S.QGL.L.WLSIT.TNITSVP......L.HLT.LNLSYNPIT
Retrocopy EDQNFRKLGNLRGLEIDHWPFLEYISPHSLQGLNLSWLSITHTNITSVPTSALRSLAHLTSLNLSYNPIT

Parental  TLEPWAFKDLLRLKELIMVSTGLMTVEPHALGGLRQIRVLNFSSNDLQTLEEGSFHSVNSLETLRVDGNP
          .LE.WA..DL.RLKEL..V.T.L..V.P.ALGGLRQIR.LN.SSN.L.TLEEG.F.SVN.LETLR.DGNP
Retrocopy VLESWALRDLVRLKELHLVKTNLAVVQPYALGGLRQIRLLNLSSNSLVTLEEGAFQSVNTLETLRLDGNP

Parental  LMCDCRLLWILQRRKTLNFDGRVPVCAGPVEVQGVSLSSFTDSALFDHFTCQKPKIRNRKLQQMIAREGQ
          L.CDCRLLWILQRRKTLNFDG..PVC..PVEVQG..L..F.DSALFDHFTCQKPKIRNRKLQQ..AREGQ
Retrocopy LACDCRLLWILQRRKTLNFDGASPVCMTPVEVQGRALNAFSDSALFDHFTCQKPKIRNRKLQQISAREGQ

Parental  AVSFLCRAEGDPPPSIVWISPQRRRITTKSSGRIIVHPSGTLEIRYAQLTDSGTYICIASNAGGNDTYFA
          .VSF.CRAEG.P.P.I.WISPQRRRITTKSSGR..V.P.GTLEIRYAQ.TDSGTYICIASNAGGNDTYFA
Retrocopy VVSFICRAEGEPTPVIFWISPQRRRITTKSSGRLTVLPEGTLEIRYAQVTDSGTYICIASNAGGNDTYFA

Parental  TLTVRGQPLDAASAFFLNRSLYSSEFFNDTNLNSTRVFLKFTFDLTTILVSTAMGCITFLGVVLFCFLLL
          TLTV.G.PLDA..A...NR..Y.....NDTNLN.TRVFLKFT.DL.TIL.STAMGCI.FLGVVLFCF.LL
Retrocopy TLTVSGLPLDA--ALMANRTYYAGD-LNDTNLNDTRVFLKFTLDLKTILISTAMGCIMFLGVVLFCFILL

Parental  FVWSRGRGQRRNNFTVEYSFRKSE-PATGSSSGGTRKFNMKMI
          FVWSRGRGQ..NNF.VEYSFRK...PA.....GG.RKFNMKMI
Retrocopy FVWSRGRGQHKNNFSVEYSFRKVDGPAASGGQGGARKFNMKMI

Legend:

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

Expression

RNA-Seq

Oreochromis niloticus was not studied using RNA-Seq expression data.

ChIP-Seq

Oreochromis niloticus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_onil_14 retrocopy.

TSS

Oreochromis niloticus was not studied using FANTOM5 data.

Lab

retro_onil_14 was not experimentally validated.

Homology

Retrocopy orthology:

Oreochromis niloticus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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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,