RetrogeneDB ID: retro_tnig_15

Retrocopy location

• Organism: Tetraodon (Tetraodon nigroviridis)
• Coordinates: 13:10538886..10540200(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSTNIG00000016028
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: gpr22
• Ensembl ID: ENSTNIG00000007247
• Aliases: None
• Description: G protein-coupled receptor 22 [Source:ZFIN;Acc:ZDB-GENE-041210-48]

Sequence

>retro_tnig_15
ATGCATATCCTCCCCTGCCAGAAACAAGAAGCCACCATGAGCAACGTCACGGTCACAGACAACACCGAACCCATCAGCCA
CACCATGAGTACGGCCAGCCCCAGCCCCAATCCCTACCCCTTAAGTTTTCAAGTATCCATTACTGGATTTCTCATGCTGG
AGATCCTCTTGGGCCTGAGCTCTAACCTGACTGTTTTGGCCCTCTACTGTATGAAATCAAATCTCATTAGTTCCGTCAGT
AACATCGTGACTATGAACCTTCATGTCCTGGATGTCCTGATCTGTGTGTGCTGCATCCCTCTTACCATTGTGGTGGTGCT
GCTTTCCTTGGAAAGAGACACCGCTCTGGTCTGTTGCTTCCATGAAGCCTGTGTCTCATTTGCTAGCGTTGCCACTGCTG
CTAACGTCCTGGCCATCACCCTCGATCGCTACGACATCTCAGTCAAACCAGCCAACAGAGTGCTTACTATGGGCCGTGCT
CTGGCCCTCTTGGCTGCAATTTGGGTGCTATCCTTTATTAGCTTCCTCGTTCCCTTTATCGAGGTGGGTTTCTTTGCCCA
GGGGAATGCTGAGCTGAACCAGACTGTGGTGGAGAACGTAGTCCACGCGAACCAGTACTACACAGAACTGGGACTTTATT
ACCACCTGCTGGCCCAGATTCCCATTTTCTTCTTCACTGCTGTCGTCATGCTCATCACCTACTCAAAAATCCTGCAAGCT
CTTAACATTCGCATCGGCACGCGTTTCCACGCATCACAGAAGAAGGCTCGCAGGAAAAAGCGTCCATCTATGACAGCGAT
GACAACACAGCAGGAAGCCACGGACGCATCCCAGAGCAGCGGCAGCCGCAACACTACCCTGGGGATGCGCACCTCGGTCT
CTGTCATCATTGCACTGCGCAGGGCCGTGAAGCGCCACAGAGAACGACGAGAACGCCAAAAAAGGGTTTTCAGAATGTCC
CTCCTGATCGTCTCCACCTTCCTTCTGTGTTGGACACCAATCACAGTACTCAACACGGTCATCCTGAGCGTGGGACCCAG
CGACCTCATGGTCAAGCTGAGACTAGGTTTCCTGGTCATGGCTTACGGGACCACCATCTTTCACCCTCTGCTCTACGCCT
TTACGAGGCAGAAGTTCCAGAAGGTCTTAAAAAGCAAGATGAAGAAGCGGGTAGTATCAATCATTGAGGCAGACCCCACG
CCCAACAACGCCATTATCCACAACTCGTGGATTGATCCAAAGAGGAACAAAAAAGTGACATTTGTGGACAAAGATGCCCA
ACAGAAATGTATTTCTTCTGAGGACGTGGAGTGA

Alignment

ORF - retro_tnig_15 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.43 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MHISRVLILTGTMSNRTVLDTTEPYNNEQTSAQ---DIYPLSFQVSLICFLVVEIVLGLSSNLTVLILYC
          MHI........TMSN.TV.D.TEP.......A......YPLSFQVS...FL..EI.LGLSSNLTVL.LYC
Retrocopy MHILPCQKQEATMSNVTVTDNTEPISHTMSTASPSPNPYPLSFQVSITGFLMLEILLGLSSNLTVLALYC

Parental  MKQNLISSVSNIITMNLHVVDVLVCVCCIPLTAVVVLLPLEAEKAQLCCFHEACVSFASVATAANVLAIT
          MK.NLISSVSNI.TMNLHV.DVL.CVCCIPLT.VVVLL.LE...A..CCFHEACVSFASVATAANVLAIT
Retrocopy MKSNLISSVSNIVTMNLHVLDVLICVCCIPLTIVVVLLSLERDTALVCCFHEACVSFASVATAANVLAIT

Parental  LDRYDISVRPANRVLTMARAVALLGSIWALSFFSFLVPFMEVGFFIEWGSDAVNQTAAFTAFGTNESNAE
          LDRYDISV.PANRVLTM.RA.ALL..IW.LSF.SFLVPF.EVGFF...G....NQT........N....E
Retrocopy LDRYDISVKPANRVLTMGRALALLAAIWVLSFISFLVPFIEVGFFAQ-GNAELNQTVVENVVHANQYYTE

Parental  RGLYYHLLAQIPIFFFTAVVMLITYYKILQALNIRIGTRFQHNLPKKKPKSKNAISLGAATPAESTDVSQ
          .GLYYHLLAQIPIFFFTAVVMLITY.KILQALNIRIGTRF.H...KK....K........T..E.TD.SQ
Retrocopy LGLYYHLLAQIPIFFFTAVVMLITYSKILQALNIRIGTRF-HASQKKARRKKRPSMTAMTTQQEATDASQ

Parental  NSAGARSGASAPLGMRASVSVIIALRRAVKRHRERRERQKRVFRMSLLIISTFLLCWTPITVLNTIILST
          .S.G.R......LGMR.SVSVIIALRRAVKRHRERRERQKRVFRMSLLI.STFLLCWTPITVLNT.ILS.
Retrocopy -SSGSR---NTTLGMRTSVSVIIALRRAVKRHRERRERQKRVFRMSLLIVSTFLLCWTPITVLNTVILSV

Parental  GPSDFTARLRLGFLMMAYGTTIFHPLLYAFTRQKFQKVLKSKM-KRVVSVVEAEPKPKNAVIHNSWIDPR
          GPSD....LRLGFL.MAYGTTIFHPLLYAFTRQKFQKVLKSKM.KRVVS..EA.P.P.NA.IHNSWIDP.
Retrocopy GPSDLMVKLRLGFLVMAYGTTIFHPLLYAFTRQKFQKVLKSKMKKRVVSIIEADPTPNNAIIHNSWIDPK

Parental  RTKKVTFEDTKVRQKCLHSHD
          R.KKVTF.D....QKC..S.D
Retrocopy RNKKVTFVDKDAQQKCISSED

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_15 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_tnig_15 has 1 orthologous retrocopies within teleost group .

Species	RetrogeneDB ID
Gasterosteus aculeatus	retro_gacu_4

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Gasterosteus aculeatus	ENSGACG00000019247	1 retrocopy	retro_gacu_4,
Oreochromis niloticus	ENSONIG00000014203	1 retrocopy	retro_onil_13,
Tetraodon nigroviridis	ENSTNIG00000007247	1 retrocopy	retro_tnig_15 ,