RetrogeneDB ID: retro_olat_21

Retrocopy location

• Organism: Medaka (Oryzias latipes)
• Coordinates: 12:24804842..24806127(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSORLG00000003375
• Aliases: None
• Description: None

Sequence

>retro_olat_21
CAATCTCTTCCGGTAAACATTCCGGTGTCAACTTTCAACGTGATAAACAAAATGATAACTCAATTTATATGGCAGCGAAA
AAGACCCAGAATTAGATTAAAAACATTATTCTTGCCAAGAAATAAGGGAGGTTTGGCTCTACCAAACCTAAACTTTTACT
ATTGGGCAGCTCAGTTGACAGCGATCGTGGCCTGGATTAGAGAGGATGAGGAAGTAAAATGGATTAAAGTGGAACAAGGT
GAAACTAAAGGGGTGCGGCTGTCTACGCTTCCATTTACTGAACTAAAATCTGTCAACAAAATCAAAATTGGAAACAGTTG
GATCAAACATACTCTAAAGATTTGGACGGTAGTTAGAAAAAATGTTACTTGATACAGGGTCAATTTCCAGAGCAATGCCT
ATTGTTGGTAAAATAGATTTTCCGCCTTCAACGTGGGATCCCACCTTTAAGACATGGGCCACTAAAGGCCTTATAACTCT
TAACCAGTTGTCCGATGTAACGGAACTTAATTCCTTTTCACAGCTTCAAGGACAATTTGGCCTTCTGCCGAATGATTTTT
ATAAATATCTCCAAATCAGGCATTACATCATGAAGCACAAAGAGCGAGACAGAATCAACAAATCCCAAACTGCATAGAAC
AATATTTTACTATAATCGCAGAAAAAAACTTTCCAACGCATAAACATGTTTCCAACTTGTATAAGAGACTCTCAACTGCC
ACCAGACAGAATACATATAATATCAAAGAAAAATGGGAATTGGAATCTAACTGTTTAATAGAAGATGAACAATAGGATAA
ATTGTGTGAGGACAGCCATATAGGAATTAATAGCCAACTATGGAAAGAGTTTGACTGGAAAATTAAAATGCGTTTTTTTC
ACACACCCCTGTTGATTTCTAATTTTGCCAAGGGCTCATCCACAGCCTTATGTTGGAGGCAATGTGAAAAATTGGTGATC
ATACACATATTTTCTTTGATTGCCCAGTTATCTGTGAATTTTGGAAAGATATTAAGAGGGAGATTGAAACTATTGTAAAA
CATGACATTCCTTTAAGTGCTCTGTCGTATCTGCTTGGTGTATTTCCAAAAGACTTTGATGCTGATCAAATATATATAAT
GCGCATTTTACTACTGGTCGCAAAAAAAGCCATAACAGGAAATTGGAAAAATGTAACATCACCTTCTGTAACTGAATGGA
AACAAAGTATCAAACACGTTTATTTGATGGAAAAATGACAGCATTGCTACAACTAAAATCAGATGTCTTTGAACGTCGAT
GGCAC

Alignment

ORF - retro_olat_21 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.47 %
• Parental protein coverage: 90.08 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  QSLAVNIPVSTFNVLNKMITQFIRQQKRPRIRLKTLFLPKNKGGLAIP-LKFYYWAAQLTTIVAWIKEDE
          QSL.VNIPVSTFNV.NKMITQFI.Q.KRPRIRLKTLFLP.NKGGLA.P.L.FYYWAAQLT.IVAWI.EDE
Retrocopy QSLPVNIPVSTFNVINKMITQFIWQRKRPRIRLKTLFLPRNKGGLALPNLNFYYWAAQLTAIVAWIREDE

Parental  EVKWFKVEQGETKGVRLSTLPFTDLKSVNKIKIGNNWIKHTLKIWTVVKK-MLLDTGSISRAMPIVGNID
          EVKW.KVEQGETKGVRLSTLPFT.LKSVNKIKIGN.WIKHTLKIWTVV.K.MLLDTGSISRAMPIVG.ID
Retrocopy EVKWIKVEQGETKGVRLSTLPFTELKSVNKIKIGNSWIKHTLKIWTVVRK>MLLDTGSISRAMPIVGKID

Parental  FPPSMWDPTFKTWATKGLITLNQLFDGTELKSFSQLQRQFGLLPNDFYKYLQIRHYIMKHKERDRINKT-
          FPPS.WDPTFKTWATKGLITLNQL.D.TEL.SFSQLQ.QFGLLPNDFYKYLQIRHYIMKHKERDRINK..
Retrocopy FPPSTWDPTFKTWATKGLITLNQLSDVTELNSFSQLQGQFGLLPNDFYKYLQIRHYIMKHKERDRINKS<

Parental  PNCIEQYFTTIAEKNFPTHKHVSNLYKSLSTATGQHTYNIKEKWELESNCIIEDEQWDKLCEDSHIGINS
          PNCIEQYFT.IAEKNFPTHKHVSNLYK.LSTAT.Q.TYNIKEKWELESNC.IEDEQ.DKLCEDSHIGINS
Retrocopy PNCIEQYFTIIAEKNFPTHKHVSNLYKRLSTATRQNTYNIKEKWELESNCLIEDEQ*DKLCEDSHIGINS

Parental  QLWKEFDWKIKMRFFFTHPC----FAEGSSTALCWRQCG-KIGDHTHIFFDCPAICEFWKDNKREIETIV
          QLWKEFDWKIKMR.FF..P.....FA.GSSTALCWRQC..KIGDHTHIFFDCP.ICEFWKD.KREIETIV
Retrocopy QLWKEFDWKIKMR-FFHTPLLISNFAKGSSTALCWRQCE<KIGDHTHIFFDCPVICEFWKDIKREIETIV

Parental  NHDIPLSTLSYLLGGSPQRTSRMADQKYIMRILLLVANKTITGNWKNVTSPSVTEWKQRIKHVYLME-KT
          .HDIPLS.LSYLLG..P......ADQ.YIMRILLLVA.K.ITGNWKNVTSPSVTEWKQ.IKHVYLME.K.
Retrocopy KHDIPLSALSYLLGVFPKDFD--ADQIYIMRILLLVAKKAITGNWKNVTSPSVTEWKQSIKHVYLME<KM

Parental  TALLQLKSDIFERRWH
          TALLQLKSD.FERRWH
Retrocopy TALLQLKSDVFERRWH

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_21 retrocopy.

TSS

Oryzias latipes was not studied using FANTOM5 data.

Lab

retro_olat_21 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_olat_21 has 0 orthologous retrocopies within teleost group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryzias latipes	ENSORLG00000003375	1 retrocopy	retro_olat_21 ,
Oryzias latipes	ENSORLG00000014268	1 retrocopy	retro_olat_56,