RetrogeneDB ID: retro_tnig_29

Retrocopy location

• Organism: Tetraodon (Tetraodon nigroviridis)
• Coordinates: Un_random:17082361..17083133(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSTNIG00000006723
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSTNIG00000010978
• Aliases: None
• Description: None

Sequence

>retro_tnig_29
GTCAGCCTCCTGTTGCTTCTCCTCGGCCTCTCTCAGGCACAACCTGTCAAAGAGGAAGGAGGCAACGCCGTGGGTGAAGA
CGATCCTGTTGACATCAGCGCCAGAATCCTCTCCTCCAACAATGGCAGCCGGGAGATCCTGCTGGAGGGGGACATGGTGG
CCCCTAAAAACAGAAATGCCATGAAGTGCTGGTCCCAGAGCTGTCTGTGGCCCAAAAACTCCAACGGCTTGGTGGTCATC
CCCTACACCATCGGCTATGAGTACCAAAAACTGGGAGAGGCAGGCCATCGAAACTGCCTTGCAGTCCTTCCACGGCAGCA
CCTGCATCCGCTTCACGCCGCGGAAGAACGAGTACGACTACATCAAGGTGGAGAGCGGAGATGGATGCTACTCCTCTCTG
GGCAGAGTGGGAAACGGACAGACGCTGTCCATCAACACGGCCGGCTGTCTCTACCACGGAGTCATTCAGCATGAAACCAT
GCACGCTCTGGGCTTCCAGCACGAGCAGACCAGGAGTGACCGCGACTACTATGTCAGGATCAACTGGGATAACATCGATC
CTAATATGGCCTTCAACTTTTACAAGCAGGACACCAACAACCTGAACACTCCGTATGACTACGGTTCCGTCATGCACTAC
GGAAGAACGGCCTTCACCATGTATGCTGGCGTGGACACCATCACCCCCATCCCAGACTCCAGGGTCCAGATTGGCCAAAG
GAATGGCTTGTCCTACTGGGACATCCAGAGGGTCAACCTGCTCTACGGCTGC

Alignment

ORF - retro_tnig_29 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.08 %
• Parental protein coverage: 96.63 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VSLLLLLLGFCSADDDNLHEHEKVDPTKGEDITSTILRMNNESADFLLEGDLFIPKKRNAMKCLNDAFNC
          VSLLLLLLG...A..........V......DI...IL..NN.S...LLEGD...PK.RNAMKC......C
Retrocopy VSLLLLLLGLSQAQPVKEEGGNAVGEDDPVDISARILSSNNGSREILLEGDMVAPKNRNAMKCWSQS--C

Parental  LWPKSSDGKVWLPYLISEKYDQD-EVDTILKALKDFHTKTCIRFKPRQGERMYLSFEPKHGCFSAMGRVG
          LWPK.S.G.V..PY.I...Y....E...I..AL..FH..TCIRF.PR..E..Y...E...GC.S..GRVG
Retrocopy LWPKNSNGLVVIPYTIGYEYQKL>ERQAIETALQSFHGSTCIRFTPRKNEYDYIKVESGDGCYSSLGRVG

Parental  EKQTVSLQRFGCVRHGVIQHEVLHALGFYHEHTRSDRDKYISILWDNIIDHYVYNFDKKETNNLNTPYDY
          ..QT.S....GC..HGVIQHE..HALGF.HE.TRSDRD.Y..I.WDNI......NF.K..TNNLNTPYDY
Retrocopy NGQTLSINTAGCLYHGVIQHETMHALGFQHEQTRSDRDYYVRINWDNIDPNMAFNFYKQDTNNLNTPYDY

Parental  GSIMHYGRDAFGINR-KETMIPIPDSSVDIGQREVMSAIDVLRVNKLYKC
          GS.MHYGR.AF.......T..PIPDS.V.IGQR...S..D..RVN.LY.C
Retrocopy GSVMHYGRTAFTMYAGVDTITPIPDSRVQIGQRNGLSYWDIQRVNLLYGC

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_29 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_tnig_29 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	ENSTNIG00000010978	1 retrocopy	retro_tnig_29 ,