RetrogeneDB ID: retro_onil_21

Retrocopy location

• Organism: Tilapia (Oreochromis niloticus)
• Coordinates: GL831172.1:1193487..1194816(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSONIG00000020497
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: SFPQ
• Ensembl ID: ENSONIG00000017737
• Aliases: None
• Description: None

Sequence

>retro_onil_21
ATGCAAGGAAACAGAGGACCCCAGCAGAACCGCGGCCCAAACCGCCTGGGAGAGCAGCTGAAAAGCGAAGGAACAAACAG
CAACGGGCAGCAGCCAGAGCCCAGCGAGCAGACCAACCCCAACGAGGCCTTAACCCTGGACCTGCAGAGCTTCAGAAAGC
CCGGGGAAAAGACCTTTACCCAGCGGAGCAGGCTGTTTGTAGGTAACTTACCAACAGGTGTTACCGAGGAGGACCTGGAG
AAGCTGTTCACCAAGTATGGAAAAGCCAGCGAGATATTTATTAACAAGGAAAGAGGCTTCGGCTTCATTAGGCTCGAAAC
GAGAATCATAGCAGAGATCGCCAGAGCCGAGCTAGATGATACTCCCTTCAGAGGCAGGCCCATACGGGTGAGGTTTGCGA
CACACGGAGCTGCTTTAACTGTGAAGAATCTGCCAGAGTTTGTGTCCAACGAGCTCCTGGAGGAGGCCTTCGCAGTCTTT
GGCCAGATAGAAAGAGCTGTGGTCATAGTGGATGACCGAGGGAGGCCTACGGGGAAGGGCATAGTGGAGTTCACCTCAAA
GCCAGCTGCAAGAAAGGCTTTGGATAAGTGCTCTGATGGTGCTTATCTTATGACAGCTTTCCCCCGGCCTGTTACAGTGG
AGCCTATGGAACAGTTTGATGAAGAGGAGGGACTGCCAGAAAAGTTGGTCAACAAAAACCAGCAGTATCACAAAGAGCGT
GAGCAGCCGCCACGATTCGCTCAGCCCGGCTCCTTCGAGTATGAGTATGCCATGCGATGGAAGGCCCTGATGGAGATGGA
GAAGCAGCAGTATGAGATGGTGGACCGCAACATGAAAGAGGCGCAGGAGAAGCTGGAGGCTGAGATGGAGGCGGCCAGAC
ACGAGCATCAGGTGATGCTGATGAGGCAGGACCTCCTGAGGCGGCAGGAAGAGCTGCGAAGGATGGAGGAGCTCCACAAT
CAGGAAGTGCAGAAGAGGAAACAAGCCGAGCTCCGACAGGAGGAGGAACGCCGCAGGAGAGAGGAGGAGATGAGGCTGCG
CAATGAGGAGATGATGAAGAGGCAGCAGGAGGGCTTCAGGGGCAACTTCTCTGAGAACAGGGAGCAAGACATGAGGATGC
ATATGGGTGGTCATGGGATGCCCATGAACAGAAACTCTCTGGGTGGCAGCTCTGGTCCAGCTGGTACTCCTGGCTTGGCT
GCAGAGAATTCTCCAATGTTGCCAGGGCCAGGAAACAACAGCATGCCTGGAGGTGGTCAGGGTGGCTTCCCCAGAGGCCT
CCCTGGCCCTGGAGATTATGGACCTCCCAATAAACAACGCAGATTTTGA

Alignment

ORF - retro_onil_21 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.32 %
• Parental protein coverage: 59.22 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SEESQSKAEFKATLSMLLKPGEKSYTQRCRLFVGNLPNDITEDDFRRMFAKYGEPTEVFINKGKGFGFIR
          SE...........L....KPGEK..TQR.RLFVGNLP...TE.D....F.KYG...E.FINK..GFGFIR
Retrocopy SEQTNPNEALTLDLQSFRKPGEKTFTQRSRLFVGNLPTGVTEEDLEKLFTKYGKASEIFINKERGFGFIR

Parental  LESRALAEIAKAELDDTPMKGRPLRVRFATHSAALSVKNLSPFVSNELLEEAFSQFGMVERAIVVVDDRG
          LE.R..AEIA.AELDDTP..GRP.RVRFATH.AAL.VKNL..FVSNELLEEAF..FG..ERA.V.VDDRG
Retrocopy LETRIIAEIARAELDDTPFRGRPIRVRFATHGAALTVKNLPEFVSNELLEEAFAVFGQIERAVVIVDDRG

Parental  RSTGRGIVEFASRPAARKALERCNEGVFLLTTSPRPVVVEPLEQYDSEDGLPEKLAQKNPKYKTEREEPP
          R.TG.GIVEF.S.PAARKAL..C..G..L.T..PRPV.VEP.EQ.D.E.GLPEKL..KN..Y..ERE.PP
Retrocopy RPTGKGIVEFTSKPAARKALDKCSDGAYLMTAFPRPVTVEPMEQFDEEEGLPEKLVNKNQQYHKEREQPP

Parental  RFARPGTFEFEYAKRWKSLDEMEKQQRQQVEKNMREARDKLESEMEDAYHEHQANLLRQDLLRRQEELRR
          RFA.PG.FE.EYA.RWK.L.EMEKQQ...V..NM.EA..KLE.EME.A.HEHQ..L.RQDLLRRQEELRR
Retrocopy RFAQPGSFEYEYAMRWKALMEMEKQQYEMVDRNMKEAQEKLEAEMEAARHEHQVMLMRQDLLRRQEELRR

Parental  MEEMHNQEMQKRKEMQLRQEEERRRQEEEMLRKRELEEQMRRQREENYRMGSFMDRDREMRMHPGG-ALG
          MEE.HNQE.QKRK...LRQEEERRR.EEEM...R...E.M.....E..R......R...MRMH.GG....
Retrocopy MEELHNQEVQKRKQAELRQEEERRRREEEM---RLRNEEMMKRQQEGFRGNFSENREQDMRMHMGGHGMP

Parental  MGDMSFGGSSQKFSMGGLGFESQQGMGGPG
          M...S.GGSS......GL..E......GPG
Retrocopy MNRNSLGGSSGPAGTPGLAAENSPMLPGPG

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_21 retrocopy.

TSS

Oreochromis niloticus was not studied using FANTOM5 data.

Lab

retro_onil_21 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 12 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000003595	1 retrocopy	retro_cfam_198,
Callithrix jacchus	ENSCJAG00000001431	4 retrocopies	retro_cjac_1073, retro_cjac_2542, retro_cjac_2697, retro_cjac_486,
Felis catus	ENSFCAG00000031287	1 retrocopy	retro_fcat_1989,
Gasterosteus aculeatus	ENSGACG00000002034	1 retrocopy	retro_gacu_13,
Gadus morhua	ENSGMOG00000011950	1 retrocopy	retro_gmor_20,
Macropus eugenii	ENSMEUG00000014082	1 retrocopy	retro_meug_164,
Oryctolagus cuniculus	ENSOCUG00000001877	1 retrocopy	retro_ocun_1834,
Oreochromis niloticus	ENSONIG00000017737	1 retrocopy	retro_onil_21 ,
Sarcophilus harrisii	ENSSHAG00000016107	1 retrocopy	retro_shar_36,
Tetraodon nigroviridis	ENSTNIG00000011331	1 retrocopy	retro_tnig_32,
Takifugu rubripes	ENSTRUG00000003783	1 retrocopy	retro_trub_8,
Drosophila melanogaster	FBgn0004227	1 retrocopy	retro_dmel_11,