RetrogeneDB ID: retro_tnig_4

Retrocopy location

• Organism: Tetraodon (Tetraodon nigroviridis)
• Coordinates: 1:13979654..13981394(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSTNIG00000004974
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: LINGO3 (1 of 2)
• Ensembl ID: ENSTNIG00000015319
• Aliases: None
• Description: leucine rich repeat and Ig domain containing 3 [Source:HGNC Symbol;Acc:21206]

Sequence

>retro_tnig_4
TGTCCCCAACGCTGCGAGTGCATCGCCAAAATCAAGGCGGTGTCCTGCTTCGGTAAACGCATGTCCGCGTTTCCAGATGG
CATCCCAGCGGACACCAAGGTCCTGGACTTAAGTGGGAATAAACTCCGCTGGGTCGAGCACGGCGACCTGCTCCCGTACC
ATCGGCTGGAAAAGCTGGATTTGAGCGACAACACGATAAGCGTGCTGGAGCCCAATGCGTTCTCGTCCCTCCAGAACCTG
CAGTTTCTCTCACTCAGAGGGAACCAGCTGAAGCTTGTCCCCATGGGGGCTTTCTCTCGCCTGTCCAACCTAACCTCTTT
GGACCTCAGCGGGAACAAGATTGTGATTCTTTTAGACTTTACTTTCCAAGACTTGAGAAGTCTGAAAACGCTGGAGGTGG
GAGACAACGATTTGGTTTATATCTCCAACAAGGCCTTTCTGGGACTGGTGGGCCTGAGGGAGCTGACCATCGAGAGGTGT
AATTTGACCTCTGTGTCCAGCCAGTCCTTGTCCTACCTGCAGAACCTGGTGATGCTACGCCTCCGCTACCTCAGCATCTC
TGCCTTAGAGGACCAAAATTTCCGTAAGCTAGGCAACCTGCGGGGCCTGGAGATCGACCACTGGCCCTTCCTGGAGCACG
TTTCCCCTCACAGCCTGCAGGGTCTGAACCTGTCTTGGCTGTCCATCACGCACACCAACATCACCACCGTGCCCACCTCT
GCCCTGCGCAGCCTGGCTCACCTCACCAGCCTCAACCTCTCCTACAACCCCATTGCTGTGTTGGAGTCGTGGGCCCTCAG
AGACCTTATTAGGCTGAAGGAGCTGCATCTGGTCAACACTAACCTGGCTGTGGTGCAACCATATGCACTAGGTGGTCTGA
GGCAGATCCGCCTTCTCAATCTCTCCACAAACAACCTGGTCACCTTGGAAGAGGGAGCTTTCCAGTCCGTCAACACTCTG
GAGACGCTGCGTTTAGACGGCAACCCCCTGGCCTGCGACTGCCGTTTGCTGTGGATCCTCCAGCGCAGGAAAACCCTGAA
TTTTGAAGGTGCCCCCCCTGTGTGTACCACACCTGTGGAGGTGCAGGGCCGGGCCCTCAACGCCTTCTCTGACTCGGCTC
TCTTTGACCACTTTACCTGTCAGAAGCCCAAAATTCGCAACCGGAAGCTGCAACAGATCTCTGCTCGGGAGGGCCAGGTG
GTGTCGTTCGTTTGCCGAGCGGAAGGTGAGCCGGCGCCGGTGATCTTCTGGATCTCTCCTCAACGCCGGCGCATCACCAC
AAAGAGCAACGGCCGCCTGACTGTGCTGCCAGAAGGCACGTTAGAAATACGCTACGCTCAGGTGATGGACAGCGGCACCT
ACATCTGCATCGCCAGCAACGCGGGCGGAAACGACACTTATTTCGCTACGCTGACCGTCAGCGGCCTTCCGCTGGACGCA
GCCCTGATGGCCAATCGCACTTACTACGCCGGCGATCTCAACGACACTAATCTCAACGACACCAGGGTCTTCTTGAAGTT
CACGCTGGACCTGAAGACCATCCTCATATCCACAGCCATGGGCTGCATCATGTTCCTCGGGGTGGTGCTGTTCTGTTTCA
TTCTGCTTTTCGTGTGGAGTCGGGGCAGGGGGCAGCACAAGAACAATTTTTCCGTGGAATACTCCTTCAGAAAGGTGGAT
GGGCCTGCGGCCAGCGGAGGGCAGGGGGGAGCGCGCAAGTTCAACATGAAAATGATCTGA

Alignment

ORF - retro_tnig_4 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.85 %
• Parental protein coverage: 92.52 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  CPPRCECSAQLRSVSCQRRRLTNIPEGIPTETQLLDLSKNRLRWVQTGDLTPYPRLEEVDLSENLIATLE
          CP.RCEC.A....VSC...R....P.GIP..T..LDLS.N.LRWV..GDL.PY.RLE..DLS.N.I..LE
Retrocopy CPQRCECIAKIKAVSCFGKRMSAFPDGIPADTKVLDLSGNKLRWVEHGDLLPYHRLEKLDLSDNTISVLE

Parental  PNAFAGLQSLKVLKLRGNQLKLVPMGAFAKLGNLTSLDLSENKMVILLDYTFQDLKSLKHLEVGDNDLVY
          PNAF..LQ.L..L.LRGNQLKLVPMGAF..L.NLTSLDLS.NK.VILLD.TFQDL.SLK.LEVGDNDLVY
Retrocopy PNAFSSLQNLQFLSLRGNQLKLVPMGAFSRLSNLTSLDLSGNKIVILLDFTFQDLRSLKTLEVGDNDLVY

Parental  ISHKAFSGLLGLEVLTIERCNLTSISGQTLSYLRSLVTLHLRYLSVSALEDQNFRKLSNLRGLEIDHWPY
          IS.KAF.GL.GL..LTIERCNLTS.S.Q.LSYL..LV.L.LRYLS.SALEDQNFRKL.NLRGLEIDHWP.
Retrocopy ISNKAFLGLVGLRELTIERCNLTSVSSQSLSYLQNLVMLRLRYLSISALEDQNFRKLGNLRGLEIDHWPF

Parental  LEYISPYSFQGLDLHWLSITNTNITSVPSASFKNLAHLTHLNLSYNPISTLEPWAFKDLLRLKELIMVNT
          LE..SP.S.QGL.L.WLSIT.TNIT.VP......LAHLT.LNLSYNPI..LE.WA..DL.RLKEL..VNT
Retrocopy LEHVSPHSLQGLNLSWLSITHTNITTVPTSALRSLAHLTSLNLSYNPIAVLESWALRDLIRLKELHLVNT

Parental  GLLTVELHAFGGLRQIRVLNFSSNDLQTLEEGTFHSVNSLETLRVDGNPLVCDCRLLWILQRRRTLNFDG
          .L..V...A.GGLRQIR.LN.S.N.L.TLEEG.F.SVN.LETLR.DGNPL.CDCRLLWILQRR.TLNF.G
Retrocopy NLAVVQPYALGGLRQIRLLNLSTNNLVTLEEGAFQSVNTLETLRLDGNPLACDCRLLWILQRRKTLNFEG

Parental  RVPVCAGPVEVQGVSLSSFTDSALFDHFTCQKPKIRNRKMQQVIAHEGQAVSFLCRAEGDPVPAIVWISP
          ..PVC..PVEVQG..L..F.DSALFDHFTCQKPKIRNRK.QQ..A.EGQ.VSF.CRAEG.P.P.I.WISP
Retrocopy APPVCTTPVEVQGRALNAFSDSALFDHFTCQKPKIRNRKLQQISAREGQVVSFVCRAEGEPAPVIFWISP

Parental  QRRRITAKTSGRITVLPSGTLEIRYAKLTDSGTYICIASNAGGNDTYFATLTVRGQPLDAASAFFLNRSL
          QRRRIT.K..GR.TVLP.GTLEIRYA...DSGTYICIASNAGGNDTYFATLTV.G.PLDA..A...NR..
Retrocopy QRRRITTKSNGRLTVLPEGTLEIRYAQVMDSGTYICIASNAGGNDTYFATLTVSGLPLDA--ALMANRTY

Parental  YSSDFFNDTNLNSTHVFLKFTLDLTTILVSTAMGCITFLGVVLFCFLLLFVWSRGRGQRKNNFTVEYSFR
          Y..D..NDTNLN.T.VFLKFTLDL.TIL.STAMGCI.FLGVVLFCF.LLFVWSRGRGQ.KNNF.VEYSFR
Retrocopy YAGD-LNDTNLNDTRVFLKFTLDLKTILISTAMGCIMFLGVVLFCFILLFVWSRGRGQHKNNFSVEYSFR

Parental  KSE-PATGSSSGGIRKFNMKMI
          K...PA.....GG.RKFNMKMI
Retrocopy KVDGPAASGGQGGARKFNMKMI

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_4 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_tnig_4 has 2 orthologous retrocopies within teleost group .

Species	RetrogeneDB ID
Gasterosteus aculeatus	retro_gacu_3
Danio rerio	retro_drer_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,