RetrogeneDB ID: retro_trub_22

Retrocopy location

• Organism: Fugu rubripes (Takifugu rubripes)
• Coordinates: scaffold_68:167960..168839(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSTRUG00000005151
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: lrrc30
• Ensembl ID: ENSTRUG00000002387
• Aliases: None
• Description: leucine rich repeat containing 30 [Source:ZFIN;Acc:ZDB-GENE-050506-25]

Sequence

>retro_trub_22
ATGGGGGGGAAGCATTCCCGCGGCGTCCCCAAGGAGCTGAGCGATGTGAGTCAAAGGAGAAACGGTTCCAGAGACGGGCA
GTTCAGCGTGCCCTCGGCCACAGAGAGGTTCCGCAGACACACCATGATCCACTTTGGCTACAGCACCCTCAGTCTGGCCA
TGCAGGGTCTGAGCAGGACCCCTGCGGAGCTGTGGGAACTCAGAGAGCTGCAAAAACTCAACTTGTCCATGAACTGCCTG
TGCTCCCTGCCCGCTGCCGTAGGCTCTTTGGACAACCTTGTGATCCTTAACCTGTGGGGCAACAACCTGTCCAGCCTGCC
GCCTGAGATCGGCTTGCTGAAGAAGCTGCGCGTCCTCTTTGCCTGCCGAAACCGACTGAGTGAGGTCCCGGAGGAGCTGG
GCTCCTGCACCTGCCTGGAGGTTCTGAGTTTGGCCAACAACCAGATCGCGAGCCTCCCCGGCAGCTTGGCCACCATGCAC
AACCTGACCAAACTTAATCTCAGCTACAACCACATCGTTCACATCCCCACCTGCGTGTATAGCATGAAGGGCTTGGTCTT
TCTCCACCTGGCTTGCAACCGTCTGGAGACCATTGCAGACCAGATCCAGGATTTGGTCAACCTGAAGATTCTCATTGTGG
AGGGAAACAGTATCCACACTCTTCCCAAGACGCTGTGCTCTATGAACTCTCTCGAACTCCTCAACGTCGACTTCAACGAG
CTGCAAAATGTCCCAGTGGAAATGTATCTTCTGAGCAGACTTGGGAGACTCGCCTGCCACCCACTGGATAAAGGACTTCA
TATTGTTCACAACCCTCTCCTCAAACCCATCCAGGAGGTTCTACAAGGTGGACTCAGCGCCCTCTATAACTACCTCAAA

Alignment

ORF - retro_trub_22 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.0 %
• Parental protein coverage: 93.02 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VVTLLFRVQLSSLPAEIGRLQKLRVLFAYRNRLTEVPEELGACTKLEVLSLANNQLSTLPASFSNLTQLK
          V...L....LSSLP.EIG.L.KLRVLFA.RNRL.EVPEELG.CT.LEVLSLANNQ...LP.S......L.
Retrocopy VILNLWGNNLSSLPPEIGLLKKLRVLFACRNRLSEVPEELGSCTCLEVLSLANNQIASLPGSLATMHNLT

Parental  KLNLSHNLIAHVPACVYNMKALVFLHLACNRLDNLAENIQALVELKILIVEGNSLQSLPKALCCLTRLEL
          KLNLS.N.I.H.P.CVY.MK.LVFLHLACNRL...A..IQ.LV.LKILIVEGNS...LPK.LC....LEL
Retrocopy KLNLSYNHIVHIPTCVYSMKGLVFLHLACNRLETIADQIQDLVNLKILIVEGNSIHTLPKTLCSMNSLEL

Parental  LNLDFNHIKDVPQELHQLTRLQRLACHPLDTGLHIVHNPLLKPVKEVLEGGLGALYNYLR
          LN.DFN....VP.E...L.RL.RLACHPLD.GLHIVHNPLLKP..EVL.GGL.ALYNYL.
Retrocopy LNVDFNELQNVPVEMYLLSRLGRLACHPLDKGLHIVHNPLLKPIQEVLQGGLSALYNYLK

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Takifugu rubripes was not studied using RNA-Seq expression data.

ChIP-Seq

Takifugu rubripes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_trub_22 retrocopy.

TSS

Takifugu rubripes was not studied using FANTOM5 data.

Lab

retro_trub_22 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_trub_22 has 1 orthologous retrocopies within teleost group .

Species	RetrogeneDB ID
Tetraodon nigroviridis	retro_tnig_8

---

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,