RetrogeneDB ID: retro_onil_4

Retrocopy location

• Organism: Tilapia (Oreochromis niloticus)
• Coordinates: GL831138.1:8967171..8968155(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSONIG00000020458
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: MC5R
• Ensembl ID: ENSONIG00000006909
• Aliases: None
• Description: None

Sequence

>retro_onil_4
ATGAATGCCACAGAATACCATGGACTGATCCAAGGCTACCACAACAGGAGCCAAACCTCAGGCAATTTGCCATTTAACAA
AGACTTATCAGGAGAGGAAAAAGACTCATCTTCTGGATGTTATGAGCAGCTGCTTATTTCCACTGAGGTTTTCCTCACTC
TGGGCATCATCAGTTTGCTGGAGAACATCCTGGTTGTTGCTGCTATAATCAAAAACAAGAACCTTCATTCACCTATGTAC
TTTTTCATCTGTAGCCTTGCAGTTGCTGACATGCTCGTCAGTGTCTCTAATGCCTCAGAGACTATTGTTATAGCACTCAT
CAATGGAGGCAGCCTGACCATCCCCGTCACACTGATTAAAAGCATGGACAATGTGTTTGACTCTATGATCTGTAGCTCTC
TGTTGGCATCCATCTGCAGTTTGCTAGCGATCGCCATCGACCGCTATATCACCATCTTCTATGCCCTGCGATACCACAAC
ATTGTCACCCTGCGTCGTGCAATGCTGGTCATCAGCAGCATCTGGACGTGCTGCACCATTTCCGGCATCTTGTTCATCAT
CTACTCGGAAAGCACCACTGTACTCATCTGCCTCATCACCATGTTCTTCACCATGCTGGTGCTCATGGCATCACTCTACG
TCCACATGTTCCTGTTGGCTCGCCTGCACATGAAGCGGATCGCAGCCCTACCGGGCAACGCTCCCATCCAGCAGCGTGCC
AACATGAAGGGTGCCATCACCCTCACCATTCTCCTTGGGGTATTTGTGGTATGCTGGGCACCCTTTTTCCTCCACCTCAT
CCTTATGATCAGCTGCCCCAGGAACCCCTACTGCACCTGCTTCATGTCCCATTTCAACATGTACCTCATCCTCATCATGT
GCAACTCTGTCATTGACCCCATCATCTATGCTTTTCGCAGCCAAGAGATGAGAAAAACCTTCAAAGAGATTTTCTGCTGC
TCGCATGCTCTGCTGTATGTGTGA

Alignment

ORF - retro_onil_4 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.97 %
• Parental protein coverage: 82.95 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LSEKASTSKPAACEQVHIAIEVFLILGIISLLENILVITAIVKNKNLHSPMYFFVCSLAVADMLVSVSNA
          LS.....S.....EQ..I..EVFL.LGIISLLENILV..AI.KNKNLHSPMYFF.CSLAVADMLVSVSNA
Retrocopy LSGEEKDSSSGCYEQLLISTEVFLTLGIISLLENILVVAAIIKNKNLHSPMYFFICSLAVADMLVSVSNA

Parental  WETIIIYLLNNRQLVVEDHFIRQMDNMVDSMICISVVASMCSLLAIAVDRYVTIFYALRYHNIMTVRRAG
          .ETI.I.L.N...L......I..MDN..DSMIC.S..AS.CSLLAIA.DRY.TIFYALRYHNI.T.RRA.
Retrocopy SETIVIALINGGSLTIPVTLIKSMDNVFDSMICSSLLASICSLLAIAIDRYITIFYALRYHNIVTLRRAM

Parental  CIIGGIWTFCTGCGIVFIIYSDSTPVIICLISMFFAMLLIMASLYSHMFMLARSHVKRIAALPGYNSIHQ
          ..I..IWT.CT..GI.FIIYS.ST.V.ICLI.MFF.ML..MASLY.HMF.LAR.H.KRIAALPG...I.Q
Retrocopy LVISSIWTCCTISGILFIIYSESTTVLICLITMFFTMLVLMASLYVHMFLLARLHMKRIAALPGNAPIQQ

Parental  RTSMKGAITLTILLGIFIVCWAPFFLHLILMISCPRNLYCVCFMSHFNMYLILIMCNSVIDPLIYAFRSQ
          R..MKGAITLTILLG.F.VCWAPFFLHLILMISCPRN.YC.CFMSHFNMYLILIMCNSVIDP.IYAFRSQ
Retrocopy RANMKGAITLTILLGVFVVCWAPFFLHLILMISCPRNPYCTCFMSHFNMYLILIMCNSVIDPIIYAFRSQ

Parental  EMRKTFKEIICC
          EMRKTFKEI.CC
Retrocopy EMRKTFKEIFCC

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_4 retrocopy.

TSS

Oreochromis niloticus was not studied using FANTOM5 data.

Lab

retro_onil_4 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Gasterosteus aculeatus	ENSGACG00000003733	1 retrocopy	retro_gacu_8,
Oreochromis niloticus	ENSONIG00000006909	1 retrocopy	retro_onil_4 ,
Tetraodon nigroviridis	ENSTNIG00000013316	1 retrocopy	retro_tnig_17,