RetrogeneDB ID: retro_olat_55

Retrocopy location

• Organism: Medaka (Oryzias latipes)
• Coordinates: scaffold378:271188..272712(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSORLG00000008831
• Aliases: None
• Description: None

Sequence

>retro_olat_55
AAATGGATCCAGCCCGACCTTCCCAGCCGCTGCAAATGAAGCCTGGGGGCGTCACAGGCCGACTCTCCTCATCTGCAAAT
TCCGAGGGCCCCCACTCCAACCGTCCTTCCCAACATCCTGCACAGGATTGGTGACACCCCCATGGTGCGCATCAACAAGA
TCCCCAAAGACTTTGGACTCAAGTGTGAACTATTGGCCAAGTGTGAGTTCTTCAATGCCGGCGGCAGCGTGAAGGACAGG
ATCAGCCTGCGCATGGTGGAGGACGGCGAGCGGGCCGGTATTCTCAAACCCGGAGACACCATCATCGAGCCCACGGCCGG
AAACACCGGGATCGGGCTGGCTCTGGCTGCCGCCGTTAAGGGATACCGCTGCATCATAGTCATGCCGGAGAAGATGAGCA
TGGAGAAGGTGGATGTCCTCCGAGCTCTTGGAGCTGAGATCGTCTGCACCCCTACCAGCGCTCGTTTCGATTCGCCAGAG
TCTCATGTGGGCGTGGCCTGGTGCCTCAAGAACGAGATCCCCAATTCGCACATCCTGGATCAGTACCGCAACCCAAGCAA
CCCCCTGGCTCACTATGACTCTACCGCAGAGGAAATCCTGGAGCAGTGTGATGGTAAAGTTGACATGCTGGTGGCTGGCG
CATGTACCGGCGGCACCATCATCGCTCGCAAGCTTAAGGACAAATGCCCAAACGTCAAGATTGTCGGTGTTGACCCTGAA
GGCTCCATCTTGGCTGAGCCTGAACACTTGAACAAAACTGATAAGGCCCAGTATGAGGTGGAGGGCATCGGCTATGATTT
TATTCCTACCGTGCTCGACAGATCAGTTGTTGATACTTGGTACAAATCCAACGGCGAGGAGTCCTTCAACATGTCCCGGA
TGCTCATCAGAGAGAAAGGCCTGTTGTGCGGAGGCAGCTCCGGGACCGCCATGGCCGCTGCCGTCGTGGTCACCAAAGAG
CTGAAGGAGGGCCAGCGCTGTGTGGTCATCCTGCCAAACTCCATCCGCAACTACATGTCCAAATTCTTGAACGACAAGTG
GATGTTTGAGAAAGGTTTCCTGAGCGAGGGGGTTTTGATGGTGAAGAAGCCCTGGTGGTGGAACTTGAAGCTGCAGGGTT
TGAACATGTCGGCCCCCTTAACCGTCCTTCCAACCGTCAGCTGCCAGAACACCATTAAAATCCTGAAGGAGAAAGGGTTC
GACCAGGCGCCTGTAGTGGACGATGCAGGGTTTATCCTGGGCATGGTGACTCTTGGGAACATGTTGTCGTCCATTCTTGC
AGGAAAGATCCGACTGTCCAACCCCATCAGTAAAGTCTACTACAAGCAGTTCCGACAGATTCGCCTGACTGACAACCTGG
GAAAGCTTTCCCGAATTCCTGAGACAGACCACTTTGCTCTGGTGGTTCACGAACAGATTCAGTATCTGACAGACGGATCC
GCCGTCCTGAAGCAGATGGTGTTCGGCATGATTACCGCCGTGGACCTGCTCAACTTTGTCACGGGCCGAGAAAGGAGGGA
GCGC

Alignment

ORF - retro_olat_55 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.08 %
• Parental protein coverage: 88.35 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KWIRPDLPSRCTWRPGAPVSESPHSHPERPKPASILPSVLDHIGHTPLIRLNKIPKEFGLKCEVLVKCEF
          KWI.PDLPSRC....GA....SPH....R......LP..L..IG.TP..R.NKIPK.FGLKCE.L.KCEF
Retrocopy KWIQPDLPSRCK*SLGASQADSPHLQIPRAPTPTVLPNILHRIGDTPMVRINKIPKDFGLKCELLAKCEF

Parental  FSAGGSIKDRIALRMVEDAERAGILQPGDTIIEPTSGNTGIGLALIAAVKGYKCIIVMPEKMSMEKEAVL
          F.AGGS.KDRI.LRMVED.ERAGIL.PGDTIIEPT.GNTGIGLAL.AAVKGY.CIIVMPEKMSMEK..VL
Retrocopy FNAGGSVKDRISLRMVEDGERAGILKPGDTIIEPTAGNTGIGLALAAAVKGYRCIIVMPEKMSMEKVDVL

Parental  KSLGADIVRTPTSAAFDSPESHICTAWRLKNEIPNSHILDQYRNASNPLAHYDTTAEEILEQCDGKLEML
          ..LGA.IV.TPTSA.FDSPESH...AW.LKNEIPNSHILDQYRN.SNPLAHYD.TAEEILEQCDGK..ML
Retrocopy RALGAEIVCTPTSARFDSPESHVGVAWCLKNEIPNSHILDQYRNPSNPLAHYDSTAEEILEQCDGKVDML

Parental  VAGAGTGGTLTGVSRKLKEKCPDVKIVGVDPEGSVLIHSE--GTDDHTTFEVEGIGYDFVPTVLDRSLVD
          VAGA.TGGT.....RKLK.KCP.VKIVGVDPEGS.L...E.....D....EVEGIGYDF.PTVLDRS.VD
Retrocopy VAGACTGGTI--IARKLKDKCPNVKIVGVDPEGSILAEPEHLNKTDKAQYEVEGIGYDFIPTVLDRSVVD

Parental  MWYKSNDAETFTMSRKLIREEGLLCGGSSGSAMAAAVKMAGDLKEGQRCVVILADSVRNYISKFLSDQWM
          .WYKSN..E.F.MSR.LIRE.GLLCGGSSG.AMAAAV.....LKEGQRCVVIL..S.RNY.SKFL.D.WM
Retrocopy TWYKSNGEESFNMSRMLIREKGLLCGGSSGTAMAAAVVVTKELKEGQRCVVILPNSIRNYMSKFLNDKWM

Parental  VERGFLSLEGQMNKKVWWWSHTVQSLQVPAPLTVAPSLSCQKAVQILRAKTFDQAPVVDETGAILGMVTL
          .E.GFLS....M.KK.WWW....Q.L...APLTV.P..SCQ....IL..K.FDQAPVVD..G.ILGMVTL
Retrocopy FEKGFLSEGVLMVKKPWWWNLKLQGLNMSAPLTVLPTVSCQNTIKILKEKGFDQAPVVDDAGFILGMVTL

Parental  GTILSSVHDGKVELSDAVGAVLCKDFQQVHLTDTLEKLSFFLKAHNFVLVVRDHIQYDSDGSAHLRHSVF
          G..LSS...GK..LS.....V..K.F.Q..LTD.L.KLS.......F.LVV...IQY..DGSA.L...VF
Retrocopy GNMLSSILAGKIRLSNPISKVYYKQFRQIRLTDNLGKLSRIPETDHFALVVHEQIQYLTDGSAVLKQMVF

Parental  GVVTPIDLLHYITSHADQER
          G..T..DLL...T.....ER
Retrocopy GMITAVDLLNFVTGRERRER

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_55 retrocopy.

TSS

Oryzias latipes was not studied using FANTOM5 data.

Lab

retro_olat_55 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_olat_55 has 0 orthologous retrocopies within teleost group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Loxodonta africana	ENSLAFG00000009950	1 retrocopy	retro_lafr_383,
Oryzias latipes	ENSORLG00000008831	1 retrocopy	retro_olat_55 ,
Sarcophilus harrisii	ENSSHAG00000017100	1 retrocopy	retro_shar_587,