RetrogeneDB ID: retro_onil_17

Retrocopy location

• Organism: Tilapia (Oreochromis niloticus)
• Coordinates: GL831217.1:1312301..1313414(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSONIG00000021384
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: SSTR5 (2 of 2)
• Ensembl ID: ENSONIG00000017693
• Aliases: None
• Description: somatostatin receptor 5 [Source:HGNC Symbol;Acc:11334]

Sequence

>retro_onil_17
ATGGACTCGTGGATCTTCCCGTCATCCCCTCCGAACCTGTCGGAGCACCTCCTGTACGACAGCTTCGTGCAGGACAATGA
GTCCATCCCCCACGGGAACTACACAGACCACAGCTTCACCAGAACCAGCACGGTGGTCATCACCTGCATGTACTTTCTGG
TTTGTGCTATGGGGCTGTGTGGAAACGCTCTCGTCATCTATGTCATTCTGCGCTACGCCAAGATGAAGACAGTTACCAAC
ATCTACATCCTCAACTTGGCGGTGGCTGACGTGCTCTTCATGCTTGGCCTGCCGTTCATTGCCATCCAGTTGGCGCTGGT
CCACTGGCCTTTTGGGCCTGTGCTATGCAGGGTCGTGATGACCGTCGACTCCCTCAACCAGTTCACTTCTATCTTCTGCC
TGATGGTCATGAGCATTGACCGCTACTTGGCCGTTGTGCATCCCATTAAATCCACAAAGTGGAGGAAGCCACGCATGGCC
AAGACTATCAATCTGGCAGTGTGGGGGGTGTCGCTGATGGTTAACCTGCCAATTGTTATCTACAGTGGTGTAATTACAAA
GCACGATGGCTGCTTCTGCACCATCGTATGGCCTGAACCTCAAGAGGCTTACTACACAGCATTCATGTTCTACACATTCA
TTCTAGGCTTCTTCCTGCCCCTCATGGTCATCTGCCTTTGCTACCTGTGCATCATCATCAAGGTGAAGTCCTCGGGCATC
CGTGTGGGCTCCTCCAAGAGGAAGCGCTCAGAGAGGAAAGTCACCCGGATGGTGTCCATCGTGGTGGCAGTGTTTGTTTT
CTGCTGGCTGCCTTTCTACGTTTTCAACGTCACATCAGTGACAGGCACCATCAGCACCACCCCGATCCTGAGAAGTACCT
TTGCATTCGTGGTGGTTCTAGGATATGCCAACAGCTGCGCTAACCCAATCCTTTATGCCTTCTTATCAGAGAACTTCAAG
AAGAGTTTCCAAAATGTCCTGTGTCTTAAAAATGTGGGAGGGCTGGACGAGGTCGATCGAAGTGATAGCCGGCAGGACAA
ATCTCGCATGATGAATGACCCGACGGAGACCCAGAGTACTCTGCTCAATGGGGACCTGCAGACAAGCATCTGA

Alignment

ORF - retro_onil_17 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.6 %
• Parental protein coverage: 70.27 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  FQGSSTLVTAVISLTVFVVGLTGNTLAIYVVLRYAKMKTVTNIYILNLAVADELYIVGLPFLTTQNVLSY
          F...ST.V.......V...GL.GN.L.IYV.LRYAKMKTVTNIYILNLAVAD.L...GLPF...Q..L..
Retrocopy FTRTSTVVITCMYFLVCAMGLCGNALVIYVILRYAKMKTVTNIYILNLAVADVLFMLGLPFIAIQLALVH

Parental  WPFGSFLCRVVMTADSMNQFTSIFCLTVMSIDRYLAVVHPIRSTKWRHPRVAKVVSAAVWAVSFVVVLPV
          WPFG..LCRVVMT.DS.NQFTSIFCL.VMSIDRYLAVVHPI.STKWR.PR.AK....AVW.VS..V.LP.
Retrocopy WPFGPVLCRVVMTVDSLNQFTSIFCLMVMSIDRYLAVVHPIKSTKWRKPRMAKTINLAVWGVSLMVNLPI

Parental  VIFSDVQDTFNS--CNMIWPEPKDVWSTAFILYTATVGFFGPLLIICLCYLLIVIKVKSSGARVGFSKRR
          VI.S.V........C...WPEP.....TAF..YT...GFF.PL..ICLCYL.I.IKVKSSG.RVG.SKR.
Retrocopy VIYSGVITKHDGCFCTIVWPEPQEAYYTAFMFYTFILGFFLPLMVICLCYLCIIIKVKSSGIRVGSSKRK

Parental  RSERKVTRMVVVIVVVFVLCWLPFFIINMVNLVVIIPESSATAGIYFFAVILSYANSCANPFLYGFLSDN
          RSERKVTRMV...V.VFV.CWLPF...N.......I...........F.V.L.YANSCANP.LY.FLS.N
Retrocopy RSERKVTRMVSIVVAVFVFCWLPFYVFNVTSVTGTISTTPILRSTFAFVVVLGYANSCANPILYAFLSEN

Parental  FKQSFRKVLCVRTMRCVANGVDDGDPSAPRTEKT
          FK.SF..VLC.........G.D..D.S..R..K.
Retrocopy FKKSFQNVLCLKNV----GGLDEVDRSDSRQDKS

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_17 retrocopy.

TSS

Oreochromis niloticus was not studied using FANTOM5 data.

Lab

retro_onil_17 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 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Gasterosteus aculeatus	ENSGACG00000018944	2 retrocopies	retro_gacu_1, retro_gacu_11,
Gadus morhua	ENSGMOG00000018538	1 retrocopy	retro_gmor_13,
Oreochromis niloticus	ENSONIG00000017693	1 retrocopy	retro_onil_17 ,
Tetraodon nigroviridis	ENSTNIG00000014076	1 retrocopy	retro_tnig_9,
Xiphophorus maculatus	ENSXMAG00000012731	1 retrocopy	retro_xmac_18,