RetrogeneDB ID: retro_tnig_8

Retrocopy location

• Organism: Tetraodon (Tetraodon nigroviridis)
• Coordinates: 15_random:1990154..1991036(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSTNIG00000014871
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: lrrc30
• Ensembl ID: ENSTNIG00000005041
• Aliases: None
• Description: leucine rich repeat containing 30 [Source:ZFIN;Acc:ZDB-GENE-050506-25]

Sequence

>retro_tnig_8
GGGAAGCATTCACGCAGCGTCCCCGAGGAGCCAAACGAGGTGAGTCCCAGGGGGAAGGGTTCCAGGGAGGAGCAGTTCGG
CGTGCCCTCGGCCACAGAGAGGATTCGCAGACACACCATGATCCACTTCGGCTACAGCACCCTCAGTCTGGCCATGCGGG
GTCTCAGCAGGCCCCCTGCTGAGCTGTGGGAGCTCAGAGAACTGCAGAAGCTCAACCTGTCTATGAACTGCCTGTGCTCC
CTGCCGCCTGCCGTCGGCTCTTTGGACAACCTTGTGATCCTCAACCTGTGGGGGAACAACCTGTCCAGCCTGCCGCCCGA
GATCGGCCTGCTGAAGAAGCTGCGCGTGCTCTTTGCCTGTCGTAACCGTCTGAGCGAGGTCCCGGAGGAGCTGGGCTCCT
GCACCTGCCTGGAGGTTCTCAGCCTGGCCAACAACCAGATCACGAGCCTGCCTGGCAGCTTGGCCACCATGCACAACCTG
ACCAAACTGAATCTCAGCTACAACCACATCGTCCACATCCCCACCTGTGTGTACAGCATGAAGGGCTTGGTGTTTCTCCA
CCTGGCTTGCAACCGCCTGGAGACCATTGCGGACCAGATCCAGGATTTGGTCAACCTGAAGATTCTCATCGTGGAGGGAA
ACAGCATCCACACGCTTCCCAAGACGCTGTGCTCGATGAACTCTCTAGAACTCCTCAACGTTGACTTCAACGAGCTGCAA
AACGTGCCGGTGGAGATGTATCTCCTGAGCAGATTGGGGAGACTGGCCTGCCACCCGCTGGATAAAGGACTTCATATCGT
TCACAACCCTCTCCTCAAACCCATCCAGGAGGTGCTTCAAGGAGGACTCAGCTCCCTTTATAACTACCTCAAACCCACCT
GA

Alignment

ORF - retro_tnig_8 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.73 %
• Parental protein coverage: 98.8 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GSTSLSLARRGLQELPEELWELLQLEKLNVSLNSLTVVPAQLALLSNLEVLNLWGNQLSRLPPEIGRLQK
          G...LSLA.RGL...P.ELWEL..L.KLN.S.N.L...P.....L.NL..LNLWGN.LS.LPPEIG.L.K
Retrocopy GYSTLSLAMRGLSRPPAELWELRELQKLNLSMNCLCSLPPAVGSLDNLVILNLWGNNLSSLPPEIGLLKK

Parental  LRVLFAYRNRLSEVPEELGACTQLEVLSLAGNQLSTLPASLSDLSRLRKLNLSHNLVAHVPACVYHMRSL
          LRVLFA.RNRLSEVPEELG.CT.LEVLSLA.NQ...LP.SL.....L.KLNLS.N...H.P.CVY.M..L
Retrocopy LRVLFACRNRLSEVPEELGSCTCLEVLSLANNQITSLPGSLATMHNLTKLNLSYNHIVHIPTCVYSMKGL

Parental  VFLHLASNRLESLAENIQALVELKILIVEGNRLHSLPKAVCCLTRLELLNLDFNQLRDVPQEMHQLTRLR
          VFLHLA.NRLE..A..IQ.LV.LKILIVEGN..H.LPK..C....LELLN.DFN.L..VP.EM..L.RL.
Retrocopy VFLHLACNRLETIADQIQDLVNLKILIVEGNSIHTLPKTLCSMNSLELLNVDFNELQNVPVEMYLLSRLG

Parental  RLACHPLDTGLHIQHNPLLKPVKEVLQGGLDALYAYLR
          RLACHPLD.GLHI.HNPLLKP..EVLQGGL..LY.YL.
Retrocopy RLACHPLDKGLHIVHNPLLKPIQEVLQGGLSSLYNYLK

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_8 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_tnig_8 has 1 orthologous retrocopies within teleost group .

Species	RetrogeneDB ID
Takifugu rubripes	retro_trub_22

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Oreochromis niloticus	ENSONIG00000009892	1 retrocopy	retro_onil_3,
Tetraodon nigroviridis	ENSTNIG00000005041	1 retrocopy	retro_tnig_8 ,
Takifugu rubripes	ENSTRUG00000002387	1 retrocopy	retro_trub_22,
Xiphophorus maculatus	ENSXMAG00000002735	1 retrocopy	retro_xmac_4,