RetrogeneDB ID: retro_onil_27

Retrocopy location

• Organism: Tilapia (Oreochromis niloticus)
• Coordinates: GL831333.1:213411..213918(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSONIG00000020506
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: mcl1b (2 of 2)
• Ensembl ID: ENSONIG00000006658
• Aliases: None
• Description: myeloid cell leukemia sequence 1b [Source:ZFIN;Acc:ZDB-GENE-030825-1]

Sequence

>retro_onil_27
CTGGAGAGAGAAACTAAACTCATTATTCACAGTTTTTTGGGAGACTTTACTGGACTTTCTCAGCCTCAACGAAAGGAAAC
CAAAGCACTAAAAATGATGAAAAGAGTTGTTGCGGACGTATTAGAAAAGCACAGATATGCTTACAACGGAATGATTAATA
AATTGTCATTGGATGAAAGAGAAGAAGATATGTCATTTGTAGCGAAGAGCCTCTTTGGAGACCACACGACCAACTGGGGT
CGTATTGTCAGCTTTGTGGCCTTCGGGGCAGTGGTGTCTCAGCACCTGAAGGAAAAGGGCAGGGACAACTGCGTGGTGCT
AGTGAGTCAAGAGATTTCTGCATACTTGCTGTCTGAACAGCGAGACTGGATTATCAAAAACAATGCATGGGATGGCTTTG
TGGCGTTCGTTCGAGTAGCAGACCCTGAGTCGATAGTCAGGAACACACTCATGGCCTTTGCTGGATTTGCTTGTATTGGG
GCAACACTGGCACTGTTGATCAGGTGA

Alignment

ORF - retro_onil_27 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.81 %
• Parental protein coverage: 61.51 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LERETKLLIHSFLGDFTGLSQPQRKETKALKTMKRVVADVLEKHRYAYNGMINKLSLDERHEDMSFVGAV
          LERETKL.IHSFLGDFTGLSQPQRKETKALK.MKRVVADVLEKHRYAYNGMINKLSLDER.EDMSF...V
Retrocopy LERETKLIIHSFLGDFTGLSQPQRKETKALKMMKRVVADVLEKHRYAYNGMINKLSLDEREEDMSF---V

Parental  AKSLFADHTTNWGRIVSFVAFGAVVSQHLKEKGRDNCVALVSQEVSAYLLSEQRDWIVKNNAWDGFVEFF
          AKSLF.DHTTNWGRIVSFVAFGAVVSQHLKEKGRDNCV.LVSQE.SAYLLSEQRDWI.KNNAWDGFV.F.
Retrocopy AKSLFGDHTTNWGRIVSFVAFGAVVSQHLKEKGRDNCVVLVSQEISAYLLSEQRDWIIKNNAWDGFVAFV

Parental  RVADPESTVRNTLMAFAGFAGIGATLALLIR
          RVADPES.VRNTLMAFAGFA.IGATLALLIR
Retrocopy RVADPESIVRNTLMAFAGFACIGATLALLIR

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_27 retrocopy.

TSS

Oreochromis niloticus was not studied using FANTOM5 data.

Lab

retro_onil_27 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 2 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Otolemur garnettii	ENSOGAG00000016421	4 retrocopies	retro_ogar_1048, retro_ogar_2493, retro_ogar_2494, retro_ogar_3400,
Oreochromis niloticus	ENSONIG00000006658	1 retrocopy	retro_onil_27 ,