RetrogeneDB ID: retro_tnig_14

Retrocopy location

• Organism: Tetraodon (Tetraodon nigroviridis)
• Coordinates: 1:1660801..1661377(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSTNIG00000000346
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: rhogb
• Ensembl ID: ENSTNIG00000006325
• Aliases: None
• Description: ras homolog gene family, member Gb [Source:ZFIN;Acc:ZDB-GENE-030131-8877]

Sequence

>retro_tnig_14
ATGCAGACCATAAAGTGTGTGGTGGTTGGTGACGGGGCAGTAGGTAAAACCTGCCTGCTCATCTCATACACGACTAATGC
CTTCCCAGAGGAGTACATACCCACTGTGTTTGACAACTACAGTGCTCAGATGAGCGTCGATGGCCGCACCGTTAGCCTTA
ACCTGTGGGACACAGCTGGCCAGGAGGAATATGACCGCCTGCGTACGCTCTCTTATCCACAAACCAACGTTTTCATCATT
TGCTTTTCCATTGGCAGTCCCTCCTCTCATGCCAATGTCAGACACAAGTGGCATCCCGAGGTGTCTCACCACTGCCCCAA
CGTGCCCATCCTGCTGGTGGGCACCAAGAAGGACCTAAGGGGTGATACCGAGACGGTGAAGAAGTTGAAGGAGCAAGGCC
TGGCTCCCACCACCCACCAGCAGGGCAATGCCTTGGCCAAGCAGATCGGTGCGGTCAAGTACATGGAATGCTCTGCTCTG
CTGCAGGATGGCGTCAAAGAAGTGTTTGCGGAAGCCGTAAGGGCAGTTTTGTATCCGGTAGCAAAAAAGAACCCCAAAAG
ATGCGTGCTGTTGTAA

Alignment

ORF - retro_tnig_14 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.96 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MQSVKCVVVGDGAVGKTCLLISYTTGAFPKEYIPTVFDNYSSQVTIDNRIVSLNLWDTAGQEEYDRLRTL
          MQ..KCVVVGDGAVGKTCLLISYTT.AFP.EYIPTVFDNYS.Q...D.R.VSLNLWDTAGQEEYDRLRTL
Retrocopy MQTIKCVVVGDGAVGKTCLLISYTTNAFPEEYIPTVFDNYSAQMSVDGRTVSLNLWDTAGQEEYDRLRTL

Parental  SYPQTNVFIICFAISSPASYENVKHKWHPEVSHHCPDVPILLVGTKSDLRSDPDTQKKLKEQNQTPVTHQ
          SYPQTNVFIICF.I.SP.S..NV.HKWHPEVSHHCP.VPILLVGTK.DLR.D..T.KKLKEQ...P.THQ
Retrocopy SYPQTNVFIICFSIGSPSSHANVRHKWHPEVSHHCPNVPILLVGTKKDLRGDTETVKKLKEQGLAPTTHQ

Parental  QGAALARQIQAVRYMECSALNQDGIKDVFSEAVRAFLNPQPTVSKRHCVLL
          QG.ALA.QI.AV.YMECSAL.QDG.K.VF.EAVRA.L.P........CVLL
Retrocopy QGNALAKQIGAVKYMECSALLQDGVKEVFAEAVRAVLYPVAKKNPKRCVLL

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_14 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_tnig_14 has 1 orthologous retrocopies within teleost group .

Species	RetrogeneDB ID
Takifugu rubripes	retro_trub_15

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Oreochromis niloticus	ENSONIG00000007414	1 retrocopy	retro_onil_25,
Tetraodon nigroviridis	ENSTNIG00000006325	1 retrocopy	retro_tnig_14 ,