RetrogeneDB ID: retro_olat_35

Retrocopy location

• Organism: Medaka (Oryzias latipes)
• Coordinates: 23:9574253..9575249(-)
• Located in intron of: ENSORLG00000012195

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSORLG00000014457
• Aliases: None
• Description: None

Sequence

>retro_olat_35
AAATGAAGGAGAGAATTGTCCCAGGACATTAGAAACAAAATTATAGGCAAACATTATAAAGGTAAAGGCTATAAAACCAT
CTCTAAGCAGCTTGAAGTTCCTGTGTCGACAGTGGCACATATTATTCAGAAGTTAAAGACCCACAAGACAGTAGACAACC
TCCCTGGACGTGGCAGGAAGAGGAAAATTGATGACAAATTGAGGAGACAGATAGTTGGAACTGTATCCAAAGAGCCCAGA
ACAACCTACAAAGACATTAAAGGTGAACTCCTAGATCAAGGTACATCAGTGTCAGATCGCACCATTCGTCGTTGTTTGAG
CCAGAGTGGATTTCATGGGAGATGACCAAGGAGGACACCACTGTTGAAAGGAAATCATAAAAAAGCCAGACTTGAATTTG
CAAAAATGCATGTTGACAATCCACAAAGCTTCTGGGAAAATGTCCTTTGGTCATATGAGACAAAACTGGAGCTTTTTGGT
AACGCACATCAGCTCTATGTTCGTAGACTCAAAAATGAAGCATACAATGAAAAGAATACTGTCCCTGCTGTGAAACATGG
AGGAGGCTCAGTTCTGTTTTGGGGCTGCATATGGCACAGGGTGTTGAAGTTGTGCAAGGTAAAATGAAATCTCAAGATTA
TTAAGGCATTCTGGATAGAAATGTGCTGCCTAGTGTCAGAAAGCTTAGTCTCAGTCGCAGGTCATGGGTCTTCCAACAGG
GCAACGATCCAAAACACACAGCCAGAAACCTCCAATAATGGCTCAGAGAAAAGCGTTGGACTATTCTGAAGTGGCCTTCT
ATGAGCCCAGATCTGAATCCCATTGAACATCTGTGGAAGGAGCTGAAGAAGACACCCGTCAAACCTAAGACAACTGGAAC
AGTTTGCTCATGAGGAGTTGGCCAAAATACCTGTCGACAGGTGCAGAAGGCTCATTGACAAATACAAAAACCATTTAATT
GCAGTGATTGCCTCAAAAGGTTGTGCAACAAAATAT

Alignment

ORF - retro_olat_35 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.96 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KPRRELSQDIRNKIIDKHRKGKGYKTISKQLEVPVTTVAHTIQKFKTHRTVVNLPGRRERAELRTR-KKE
          K.RRELSQDIRNKII.KH.KGKGYKTISKQLEVPV.TVAH.IQK.KTH.TV.NLPGR.............
Retrocopy K*RRELSQDIRNKIIGKHYKGKGYKTISKQLEVPVSTVAHIIQKLKTHKTVDNLPGRGRKRKIDDKLRRQ

Parental  LVMSVEKY---AFSEHQREYTHQGTSVSNHTIRGCLSQSGLHGRRPRRTPLLKGNHK-TRLEFAKMHVDK
          .V..V.K...........E...QGTSVS..TIR.CLSQSG.HGR.PRRTPLLKGNHK..RLEFAKMHVD.
Retrocopy IVGTVSKEPRTTYKDIKGELLDQGTSVSDRTIRRCLSQSGFHGR*PRRTPLLKGNHKKARLEFAKMHVDN

Parental  PQSFWENVLWTDETKLELFGKAHQLYVRRLKNEAYNEKSTVPTVKHGGGSVLFWGCF-AASGTECLEVVQ
          PQSFWENVLW..ETKLELFG.AHQLYVRRLKNEAYNEK.TVP.VKHGGGSVLFWGC...A.G.E...VVQ
Retrocopy PQSFWENVLWSYETKLELFGNAHQLYVRRLKNEAYNEKNTVPAVKHGGGSVLFWGCI<MAQGVE---VVQ

Parental  GQMKSPDYQGILGRNVLPSVRKLGLSRRSWVFQQDNDPKH-AKNPQEWLREKHWTILKWPSMSPDLNPIE
          G.MKS.DY.GIL.RNVLPSVRKL.LSRRSWVFQQ.NDPKH.A.N.Q.WLREK.WTILKWPSMSPDLNPIE
Retrocopy GKMKSQDY*GILDRNVLPSVRKLSLSRRSWVFQQGNDPKHTARNLQ*WLREKRWTILKWPSMSPDLNPIE

Parental  HLWKK-RRHP-SNLRQLEQFAHEEWARIPVDRCRRLIDKYRNSLIAVIASKGCATKY
          HLWK.....P.SNLRQLEQFAHEE.A.IPVDRCRRLIDKY.N.LIAVIASKGCATKY
Retrocopy HLWKELKKTP>SNLRQLEQFAHEELAKIPVDRCRRLIDKYKNHLIAVIASKGCATKY

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_35 retrocopy.

TSS

Oryzias latipes was not studied using FANTOM5 data.

Lab

retro_olat_35 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_olat_35 has 0 orthologous retrocopies within teleost group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryzias latipes	ENSORLG00000010891	1 retrocopy	retro_olat_22,
Oryzias latipes	ENSORLG00000013353	2 retrocopies	retro_olat_32, retro_olat_53,
Oryzias latipes	ENSORLG00000014457	2 retrocopies	retro_olat_35 , retro_olat_43,
Oryzias latipes	ENSORLG00000018922	1 retrocopy	retro_olat_31,
Oryzias latipes	ENSORLG00000019689	1 retrocopy	retro_olat_40,
Oryzias latipes	ENSORLG00000019879	1 retrocopy	retro_olat_28,
Oryzias latipes	ENSORLG00000020726	1 retrocopy	retro_olat_26,