RetrogeneDB ID: retro_onil_68

Retrocopy location

• Organism: Tilapia (Oreochromis niloticus)
• Coordinates: GL832157.1:1786..2728(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: auh (1 of 2)
• Ensembl ID: ENSONIG00000011227
• Aliases: None
• Description: AU RNA binding protein/enoyl-Coenzyme A hydratase [Source:ZFIN;Acc:ZDB-GENE-040801-95]

Sequence

>retro_onil_68
CGCGTGCAGTCAGCACATCGACAAAGTGCGTGTAGGCTAGCCGCTGCCTTCTGCTCCCGACGGTATGTTCTGTCCAACAG
AGTCGTGCTTTGTCCTCGCCTGAACGGCCACAGTGCTGTTATGCGATACTACAGCTCCGACTCAAAGGATGAGCTGCACG
TTAGATACCTGGACGGAGAAGACAGCGGTATTGTCGTCGTTGGAATAAATCGACCAAAAGCCAAAAATGCCATAAACAAA
AATCTTGTGAAAGTGATGTTTGAAGCTGTGGAGGACATCAAGAAGAATAAAAAAGTGCGCAGTGTAATTTTATGTAGTTT
AGTTCCTGGTATATTTTGTGCAGGTGCAGATCTGAAGGAGAGGGCCAAGATGCACCAGAGCGAAGTGGGACCATTTGTAT
CCAAAGCAAGAGCCCTCATTACAGAGCTAGGAAACCTGCCAGTACCAACAATTGCTGCAATTGATGGTGCTGCCTTAGGA
GGAGGTTTGGAAATGGCCCTTGCTTGTGACATCAGGATTTCCTCCAATATTGCCAAAATGGGACTAGTTGAGACTACACT
TGCAATTATTCCTGGAGCAGGTGGTACACAACGTCTCCCTAGGGTGATTGGCGTCTCTCTAGCCAAGGAGCTCATCTTTG
CTGCACGAGTGGTTGATGGGACACAGGCGCAACAAATGGGTCTTGTCAGTCATTCTGTGGAGCAGAATAACAGTGGAGAT
GCTGCCTACTTGAGGGCTCTGGAGCTTGCACGGGAGATTAACCCCCAGGGCCCAATTGCAATAAGGATGGCAAAGTTGGC
AATTAACCAGGGGATAGAGGTGGATTTATCTACAGGTCTGGCAATAGAAGAGGCTTGTTATTCCCAGGTGATACCAACCA
AAGACCGTTTGGAAGGCTTGTCTGCTTTCAAAGAGAAGAGGCAGCCTCAGTACAAAGGGGAA

Alignment

ORF - retro_onil_68 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.86 %
• Parental protein coverage: 95.73 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RVQSAHRQSACRLAAAFFSRRYVLSNRVVLCPRLNGHGAVTRYYSSDSKDDLRVRYLDGEDSGIVVVGIN
          RVQSAHRQSACRLAAAF.SRRYVLSNRVVLCPRLNGH.AV.RYYSSDSKD.L.VRYLDGEDSGIVVVGIN
Retrocopy RVQSAHRQSACRLAAAFCSRRYVLSNRVVLCPRLNGHSAVMRYYSSDSKDELHVRYLDGEDSGIVVVGIN

Parental  RPKAKNAISKNLVKMMFEAVEDIKKNKKVRSVILCSLVPGIFCAGADLKERAKMHQSEVGPFVSKARALI
          RPKAKNAI.KNLVK.MFEAVEDIKKNKKVRSVILCSLVPGIFCAGADLKERAKMHQSEVGPFVSKARALI
Retrocopy RPKAKNAINKNLVKVMFEAVEDIKKNKKVRSVILCSLVPGIFCAGADLKERAKMHQSEVGPFVSKARALI

Parental  TELGSLPVPTIAAIDGAALGGGLEMALACDIRISSNTAKMGLVETKLAIIPGAGGTQRLPRVIGVSLAKE
          TELG.LPVPTIAAIDGAALGGGLEMALACDIRISSN.AKMGLVET.LAIIPGAGGTQRLPRVIGVSLAKE
Retrocopy TELGNLPVPTIAAIDGAALGGGLEMALACDIRISSNIAKMGLVETTLAIIPGAGGTQRLPRVIGVSLAKE

Parental  LIFAARVVDGTQAQQMGLVSHSVEQNDSGDAAYLRALELSREINPQGPIAIRMAKLAINQGIEVDLSTGL
          LIFAARVVDGTQAQQMGLVSHSVEQN.SGDAAYLRALEL.REINPQGPIAIRMAKLAINQGIEVDLSTGL
Retrocopy LIFAARVVDGTQAQQMGLVSHSVEQNNSGDAAYLRALELAREINPQGPIAIRMAKLAINQGIEVDLSTGL

Parental  AIEEACYSQVIPTKDRLEGLAAFKEKRQPQYKGE
          AIEEACYSQVIPTKDRLEGL.AFKEKRQPQYKGE
Retrocopy AIEEACYSQVIPTKDRLEGLSAFKEKRQPQYKGE

Legend:

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

Expression

RNA-Seq

Oreochromis niloticus was not studied using RNA-Seq expression data.

ChIP-Seq

Oreochromis niloticus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_onil_68 retrocopy.

TSS

Oreochromis niloticus was not studied using FANTOM5 data.

Lab

retro_onil_68 was not experimentally validated.

Homology

Retrocopy orthology:

Oreochromis niloticus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000005695	1 retrocopy	retro_cjac_93,
Cavia porcellus	ENSCPOG00000001066	1 retrocopy	retro_cpor_503,
Oreochromis niloticus	ENSONIG00000011227	1 retrocopy	retro_onil_68 ,
Pan troglodytes	ENSPTRG00000021099	1 retrocopy	retro_ptro_1612,