RetrogeneDB ID: retro_tnig_3

Retrocopy location

• Organism: Tetraodon (Tetraodon nigroviridis)
• Coordinates: 11:7439485..7440466(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSTNIG00000000015
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: neurod
• Ensembl ID: ENSTNIG00000003533
• Aliases: None
• Description: neurogenic differentiation [Source:ZFIN;Acc:ZDB-GENE-990415-172]

Sequence

>retro_tnig_3
ATGATCAAACCGTACGTGAGACAAAGTGAGGAAGAGGAGGTGGCTGGCCCTCAGCAGTGGATGGACGGGGACGTGAGCTC
GCCCGACGGAGGCACGGCCGTCCCGCCGCACCGCTACCGAGCGGGTGGAGGGAGCCAACAGGCCCCGGAGATGGGCAGCG
AGGACGCCGAGGAAGAGGAGGAAGACGAAGAGGCCCAGGGCGACGAGGGCGAGTCCAAACGGCGAGGGCCCAAGAAAAAG
CGCATGACCAAGGCCCGTGTGGAGCGGTTCCGCGCCCGGCGCATCAAGGCCAACGCTCGGGAGCGCTCGCGCATGCACGG
TTTGAACGACGCGCTGGAGAACCTGCGCAGCATCATGCCCTGCCACTCCAAGACACAGAAACTGTCCAAGATCGAGACCT
TACGGCTGGCCCGCAACTACATCTGCGCCCTGTCCGAGGCCCTGGAGGCGGGGCTCTCCACCGAGAGCAGGGCCTTCATG
GAGACGCTGTGCAAGGGCCTCTCGCAGCCCACCACCAACCTGGTGGCCGGCTGCTTGCAGATGGCGCCCGCCCCTGGAGC
AGGCAACAGGCCCGAGGACAGACCCAGAGCCCGGGCTCCTCATGCTCCTCTGGGCGTGGTCAGCTACGCCTCCCCGGGCC
TGCCGAGTCCACCGTACGGCACTTTTGACTCTGCTCACCTGCTGCACCTCAGGGCCATGAAGGGGGGGGTGTATGAGAAC
CCCTCGCCCAGCGACTACAACTCCGGCCTGGGGACGCCTCCGTACGACGGACCCCCGACGCCGCCGCTCAGCATCAGCAC
CAACGCAGTCCCCAAACAGGAGCCGTCCCCACACTACCCACCACCACACCACTACTCGCCCTCCCCCGTGGAGCAGGACA
TGTATCAGACAGGCTACGACGTGCACCTGGAGGCGTCCTACGACACCTATCACCCGCCCTCATTGCCCCCCCGACAGATA
ACCTCCATCTACAGAGACTGA

Alignment

ORF - retro_tnig_3 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.21 %
• Parental protein coverage: 69.51 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EEQQESENKPKRRGPKKKKMTKARLQRFKVRRMKANARERNRMHGLNDALESLRKVVPCYSKTQKLSKIE
          EE.Q..E...KRRGPKKK.MTKAR..RF..RR.KANARER.RMHGLNDALE.LR...PC.SKTQKLSKIE
Retrocopy EEAQGDEGESKRRGPKKKRMTKARVERFRARRIKANARERSRMHGLNDALENLRSIMPCHSKTQKLSKIE

Parental  TLRLAKNYIWALSEVLRSGKAPDLMSFVQVLCKGLSQPTTNLVAGCLQLNPRTFLPEQTPDLPTHLPPAG
          TLRLA.NYI.ALSE.L..G.......F...LCKGLSQPTTNLVAGCLQ..P.........D.P....P..
Retrocopy TLRLARNYICALSEALEAGLSTESRAFMETLCKGLSQPTTNLVAGCLQMAPAPGAGNRPEDRPRARAPHA

Parental  AVAYPAHFPFQSPGLTAGLPSPPYGTMEPSHIFH--QVKGQSYGALEPFFDSVLLSDGPAFDPPLSPPLS
          ...........SPGL....PSPPYGT....H..H....KG..Y....P......L...P..D.P..PPLS
Retrocopy PLGVVSY---ASPGL----PSPPYGTFDSAHLLHLRAMKGGVYENPSPSDYNSGLGTPP-YDGPPTPPLS

Parental  INGN
          I..N
Retrocopy ISTN

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_3 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_tnig_3 has 0 orthologous retrocopies within teleost group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Tetraodon nigroviridis	ENSTNIG00000003533	1 retrocopy	retro_tnig_3 ,