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 summary: | ||
| 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] |
Retrocopy-Parental alignment summary:
>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
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 |
Tetraodon nigroviridis was not studied using RNA-Seq expression data.
Tetraodon nigroviridis was not studied using ChIP-Seq data.
Tetraodon nigroviridis was not studied using EST data.
Tetraodon nigroviridis was not studied using FANTOM5 data.
retro_tnig_4 was not experimentally validated.
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 |
Parental genes homology:
Parental genes homology involve 5 parental genes, and 5 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Danio rerio | ENSDARG00000067815 | 1 retrocopy | |
| Gasterosteus aculeatus | ENSGACG00000015271 | 1 retrocopy | |
| Oreochromis niloticus | ENSONIG00000010199 | 1 retrocopy | |
| Tetraodon nigroviridis | ENSTNIG00000015319 | 1 retrocopy |
retro_tnig_4 ,
|
| Xiphophorus maculatus | ENSXMAG00000019316 | 1 retrocopy |