RetrogeneDB ID: retro_olat_15

Retrocopy location

• Organism: Medaka (Oryzias latipes)
• Coordinates: 5:26944600..26945578(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSORLG00000013930
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: mafba
• Ensembl ID: ENSORLG00000009479
• Aliases: None
• Description: v-maf musculoaponeurotic fibrosarcoma oncogene family, protein B (avian) [Source:ZFIN;Acc:ZDB-GENE-980526-515]

Sequence

>retro_olat_15
GCCAGCTGCAGTTTCATGAGCTCTGAGGCGCTTTCACATCTAAAAATCCCCATGGATTTCGTGGGCGACTTTGACTTGAT
GAAATTCGGCGTGAAGAAGGAGACGATGCAGAGTCTGGAACGCGCATTCGTCGGGCCGTGCAGTCAGCTCCAAAGGCCAG
ACTCCGTCTCCTCCACCCCTGGCACCACTCCGTGCAACTCGGTGCCCTCCTCTCCAAACATCAACCCGCACGAGCAGAGA
AACACCCCCGGGGGCGACCACTTCTGGATGCACAACAACGGCGGATACCCTCATCAGATGTACCCCCAAGCTTTTGGTCT
GACCCCCGAGGACGCAATGGAGGCCCTCATTGACGCGACGCAGCAGGGGCACCCCACTGCGCCCCACATCCACCACCCTC
AGCCCTTCCAGGGTGACTACGAGGGCTACGCTCACCTGAACGAGCCTGTCCACCACTACGCGGGCCTCCCCGGTCACCCC
GACATGCAGGGCGTCCCGAGCAGCCACTGCCAGGACACATATCTCAAGGATGAAATCGGGTGCGAGTCCCCGCAGTCGCC
GGAGGCCCAGCAGGTCGTGGGTGCGCACCACCCTCTCCAGCAACCGCACCGGCGATCCACCAGCGAGATGCACTTCTCAG
ACGACCAGCTGGTGTCCATGTCCGTCAGAGAGCTGAATCGGCTGCTGAGGGGCCTGAGCAAGGACGAGGTGATGCGTCTG
AAGCAGAAGCGGCGGACCTTGAAAAACAGAGGTTACGCACAGTCCTGCCGCTACAAGCGGGTGCAGCAGAAACACATCCT
GGAGCACGAAAAGACCAGCCTGGTGTCACAGGTCGAGCAGCTGAAACACGAACTCAGCAGGCTGGTCCGAGAGAGGGACG
CATACAAACTCAAATGTGAGAAACTGTCCGGGGCGAACTGCTACCACGAAACCGGCTCCACCAGTGACAACCCGTCTTCT
CCTGAGTATTTAATATGA

Alignment

ORF - retro_olat_15 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.38 %
• Parental protein coverage: 73.7 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  YWMPNSG-YHQQIDPQTLNLTPEDAVEALIGATAHGHPPPPHVQQQLQQQGAFEGYRGPYAGSMQHHTEE
          .WM.N.G.Y..Q..PQ...LTPEDA.EALI.AT..GHP..PH.......QG..EGY.........HH...
Retrocopy FWMHNNGGYPHQMYPQAFGLTPEDAMEALIDATQQGHPTAPHIHHPQPFQGDYEGYA--HLNEPVHHYAG

Parental  LSGHPGGHNHPHGQHHHHHSQDPES-PSPVSPEAHQTLSQSAAHHSSGSGLSVEDRFSDEQLVSMSVREL
          L.GHP.....P..........D.....SP.SPEA.Q.................E..FSD.QLVSMSVREL
Retrocopy LPGHPDMQGVPSSHCQDTYLKDEIGCESPQSPEAQQVVGAHHPLQQPHRRSTSEMHFSDDQLVSMSVREL

Parental  NRHLRGFTKDEVIRLKQKRRTLKNRGYAQSCRFKRVQQKHVLENEKTQLMNQVEQLKAEISRLARERDAY
          NR.LRG..KDEV.RLKQKRRTLKNRGYAQSCR.KRVQQKH.LE.EKT.L..QVEQLK.E.SRL.RERDAY
Retrocopy NRLLRGLSKDEVMRLKQKRRTLKNRGYAQSCRYKRVQQKHILEHEKTSLVSQVEQLKHELSRLVRERDAY

Parental  KLKCEKLTGSGATNGFREAGSTSDNPSSPEFFM
          KLKCEKL.G....N...E.GSTSDNPSSPE...
Retrocopy KLKCEKLSGA---NCYHETGSTSDNPSSPEYLI

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Oryzias latipes was not studied using RNA-Seq expression data.

ChIP-Seq

Oryzias latipes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_olat_15 retrocopy.

TSS

Oryzias latipes was not studied using FANTOM5 data.

Lab

retro_olat_15 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_olat_15 has 0 orthologous retrocopies within teleost group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Oryzias latipes	ENSORLG00000009479	1 retrocopy	retro_olat_15 ,