RetrogeneDB ID: retro_olat_43

Retrocopy location

• Organism: Medaka (Oryzias latipes)
• Coordinates: 8:4642586..4643435(-)
• Located in intron of: None

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_43
AAGTGAAGGAGAGAATTGTCCCAGGACATTATAAACAAAATTATAGACAAACATAGTAAAGGTAAAGGCTATAAAACCAT
CTCTAAGCAGCTTGAAGTTTCTGTGACGACAGTGGCATATATGATTCAGAAGTTTAAGACCCACGGGACAGTAGCCAACC
TCCCTGGACGTGGCAGGAAGAGGAAAATTGAGGAGACGGATAGTTGGAACTGTATCCAAAGAGACAAGAACAACCTCCAA
AGACGTTAAAGGTGACCTCCTAGATCAAGGTACATCAGTGTCAGATCGCACCATTCATCACTGTTTGAGCCAGAGTGGAC
TTCATGGGAGACGACCAAGGAGGACACCACTGTTGACAGGAAATCATAAAAAAGCCAGACTGGAATTTACCAAAATGCAT
GTTGACAAGCCCCAAAGCTTCTGGGAAAATGTCCTTTGGACAGATGAGACCAAACTGGAGCTTTTTGGTAAGGCACATCA
GCTCTATTTTTGTAGACTCAAAAATGAAGCATACAACCAAAAGAACACTGTCCCTACTGTGAAACATGGAGGAGGCTCAG
TTCTGTTTTGGGGCTGCTTTGCTGCATCTGGCACAGGGTGTCTTGAAGTTGTGCAAAGGAAAATGAAATCTCCAGATTAT
CAAGGCATTCTGGATAGAAATGTGCTGCCAAGTGTCAGAAAGCTTAGTCTCAGTTGCAGGTCATGGGTCTTCAAACAGGA
CACCGATCCAAAACACACAGCCAAAACCCCCCAAAAATGGCTCAGAGAAAAGCGTTGGAATATTCTGAAGTGGCCTCTAT
GAGCCCAGATCTGAATCCCATTGAACATCTGTGGAAGGAGCTGAAACAT

Alignment

ORF - retro_olat_43 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.54 %
• Parental protein coverage: 85.67 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KPRRELSQDIRNKIIDKHRKGKGYKTISKQLEVPVTTVAHTIQKFKTHRTVVNLPGRRE-RAELRTRKKE
          K.RRELSQDI.NKIIDKH.KGKGYKTISKQLEV.VTTVA..IQKFKTH.TV.NLPGR...R..LR.R...
Retrocopy K*RRELSQDIINKIIDKHSKGKGYKTISKQLEVSVTTVAYMIQKFKTHGTVANLPGRGR>RGKLRRRIVG

Parental  LVMSVEKYAFSEHQREYTHQGTSVSNHTIRGCLSQSGLHGRRPRRTPLLKGNHK-TRLEFAKMHVDKPQS
          .V.................QGTSVS..TI..CLSQSGLHGRRPRRTPLL.GNHK..RLEF.KMHVDKPQS
Retrocopy TVSKETRTTSKDVKGDLLDQGTSVSDRTIHHCLSQSGLHGRRPRRTPLLTGNHKKARLEFTKMHVDKPQS

Parental  FWENVLWTDETKLELFGKAHQLYVRRLKNEAYNEKSTVPTVKHGGGSVLFWGCFAASGTECLEVVQGQMK
          FWENVLWTDETKLELFGKAHQLY..RLKNEAYN.K.TVPTVKHGGGSVLFWGCFAASGT.CLEVVQ..MK
Retrocopy FWENVLWTDETKLELFGKAHQLYFCRLKNEAYNQKNTVPTVKHGGGSVLFWGCFAASGTGCLEVVQRKMK

Parental  SPDYQGILGRNVLPSVRKLGLSRRSWVFQQDNDPKH-AKNPQEWLREKHWTILKWP-SMSPDLNPIEHLW
          SPDYQGIL.RNVLPSVRKL.LS.RSWVF.QD.DPKH.AK.PQ.WLREK.W.ILKWP.SMSPDLNPIEHLW
Retrocopy SPDYQGILDRNVLPSVRKLSLSCRSWVFKQDTDPKHTAKTPQKWLREKRWNILKWP<SMSPDLNPIEHLW

Parental  KKRRH
          K...H
Retrocopy KELKH

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_43 retrocopy.

TSS

Oryzias latipes was not studied using FANTOM5 data.

Lab

retro_olat_43 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_olat_43 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,