RetrogeneDB ID: retro_onil_39

Retrocopy location

• Organism: Tilapia (Oreochromis niloticus)
• Coordinates: GL831164.1:5024687..5026145(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSONIG00000004482
• Aliases: None
• Description: None

Sequence

>retro_onil_39
ACCATCCAGAACACATTCAGCTCTCGAGTCAATGACTTCACCATGATTCTGTTCACTGTGGACTCAGATCCTACAGCTCC
AGCTGTTGTTAACTTTGTGAAAAAAAACCAGGACATCCAGGAGCTCTGTGAGAGCTGTGGCAGAAGATCTGTTGTTCTCA
ACATTAACAACAAACAGCAGATCCCACAGCTGGTCCAGGCTGTGGAAAAGGTTAGAGAGACAGGACCCAAATCCTTCACA
AAAGACATGTTCATATTAGCTCAGATGGAGAGAGTGGTAGAACAGAAAAACATTAACACAAGACTTAAAGCTGAAATGCT
GGATTTAAGAAAAAAAAGGGATATGTGTGTTCATGATAGAAATCAGAACAATGAATGTCTCAGGATGGTTCTGATTGGAA
AGACTGGCAGTGGAAAGAGCGCAACTGGAAACACCATTCTGGGCCTACGGCAAGGGAAAGAACGTTTTAAATCTAAACCC
AGCGGGAAGTCAGTGACAAAGTACTGTGAGAAAGCAGAAGGAGAGGTCGATGGACGTCCTGTTGTTGTGGTCGACACCCC
CGGTCTGTTTGACACGAGTCTGTCCAATGATGAAGTTGAGCAGGAGCTTGTGAAATGCATCACCATGTTGTCTCCTGGAC
CTCATGTGATCTTACTGGTGCTGTCAATTGGCCGGTTTACAAAGGAGGAAAAAGATACCGTTGAACTGATCAAGAAATAC
TTTGGGAAAAATTCACAACATTTCATTATTGTTACATTCACCAGGAAAGATGAACTGGGCGATCAAACATTTGAGACTTA
CATAAAAGAAGATTGTGATGAATTTGTACAAAAATTGATTTATGACTGTGGAGACAGATATCATGTCTTTAATAATAAGG
ATGCAAAGAATCGGGCTCAGGTCAGTGAGCTGCTGACAAAGGTTGAGGTAATGGTGCACGAAAATGGAGGCAGCTGCTAC
ACCACTGAGATGTTCCAAGAGGCTGAGGTGGCAATAAAGAAGGAAGTGAAGAGGATCCTAAAAGAGAAGGAAGAGGAGAT
GATGAGACAGAAAGAAGAGCTTGAACAAAAACATGAGGAACAGATAAAAGCAATGGAAAAAAGAATGGAAGAACAGAGAG
TGGAAACTGAACAGGAGAGAAAACTGATAGAAAAACAACTTAAAAGAATGGAGGATAACATAAAGGATGAACGTGAACAG
AGAAAAAGAGAACAGGAAAGGCGAGAAGCAGAGGACCGCCAAAGGAAAATACAAGATGAACTTCAACAACAAGAGTGGGA
ACGAAAGCGTATAGATCTGGAGAAAAAACTAAAGGCAGAATCAAAGGAAAAGGAAATAACTGACCGACAGCTGGAACAAA
GCAGAGAAGAGATGAGAAACCAACGAGAGAAGTGGGAAAAGGAAAAGAGTGAGTGGTGGGACAAACGACATCAAGAAAAT
GAACAGAAACAAGCAAAA

Alignment

ORF - retro_onil_39 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.62 %
• Parental protein coverage: 63.19 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TIQNTFSSRVNDFTMILFTVDSDPTDPAVSN-LKDNKDIQELCESCGGRSVVLNINDKQQIPQLVQAVEK
          TIQNTFSSRVNDFTMILFTVDSDPT.PAV.N......DIQELCESCG.RSVVLNIN.KQQIPQLVQAVEK
Retrocopy TIQNTFSSRVNDFTMILFTVDSDPTAPAVVNFVXXXQDIQELCESCGRRSVVLNINNKQQIPQLVQAVEK

Parental  VRA---KSFTKDMFILAQMERVVEQKNINTRLQAEM-DLRKNRAMCVDDRNQNRECLRMVLIGKTGSGKS
          VR....KSFTKDMFILAQMERVVEQKNINTRL.AEM.DL.....MCV.DRNQN.ECLRMVLIGKTGSGKS
Retrocopy VRETGPKSFTKDMFILAQMERVVEQKNINTRLKAEMLDLXXXXDMCVHDRNQNNECLRMVLIGKTGSGKS

Parental  ATGNTIL----GKQRFKSRPSGRSVTKFCEKAEGEVDGRPVVVVDTPGLFDTSLSNDEVEQELIKCITML
          ATGNTIL....GK.RFKS.PSG.SVTK.CEKAEGEVDGRPVVVVDTPGLFDTSLSNDEVEQEL.KCITML
Retrocopy ATGNTILGLRQGKERFKSKPSGKSVTKYCEKAEGEVDGRPVVVVDTPGLFDTSLSNDEVEQELVKCITML

Parental  APGPHVILLVLSIGRFTNEEKQTVELIKKYFGKNSQHFIIVTFTRKDELKGQTFESYIENDSGEFVQKLI
          .PGPHVILLVLSIGRFT.EEK.TVELIKKYFGKNSQHFIIVTFTRKDEL..QTFE.YI..D..EFVQKLI
Retrocopy SPGPHVILLVLSIGRFTKEEKDTVELIKKYFGKNSQHFIIVTFTRKDELGDQTFETYIKEDCDEFVQKLI

Parental  HDCGGRYHVFNNNDAKNRAQVSELLTKIEVMVHKNGDSCYTSEMFQEAEVAIKKEVERILKEKEEEMKRQ
          .DCG.RYHVFNN.DAKNRAQVSELLTK.EVMVH.NG.SCYT.EMFQEAEVAIKKEV.RILKEKEEEM.RQ
Retrocopy YDCGDRYHVFNNKDAKNRAQVSELLTKVEVMVHENGGSCYTTEMFQEAEVAIKKEVKRILKEKEEEMMRQ

Parental  QEELEQKHKEQIKAMKKRMEEQRAETEQQRKLIEKQLKKKEDNIKHEREQRKREQEREKKLKAESKEKET
          .EELEQKH.EQIKAM.KRME.............EKQLK..EDNIK.EREQRKREQER.....AE......
Retrocopy KEELEQKHEEQIKAMEKRMEXXXXXXXXXXXXXEKQLKRMEDNIKDEREQRKREQERR---EAEDRQRKI

Parental  TDRQLEQSREEMRNHREKWEKERNKRKE-EDRMRRDQEERERKELEENYKKKLQEMKTKYEEEARKQAE
          .D....Q..E..R...EK..K...K.KE..DR......E..R...E...K.K.........E...KQA.
Retrocopy QDELQQQEWERKRIDLEKKLKAESKEKEITDRQLEQSREEMRNQREKWEKEKSEWWDKRHQENEQKQAK

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_39 retrocopy.

TSS

Oreochromis niloticus was not studied using FANTOM5 data.

Lab

retro_onil_39 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Oreochromis niloticus	ENSONIG00000004482	1 retrocopy	retro_onil_39 ,