RetrogeneDB ID: retro_olat_28

Retrocopy location

• Organism: Medaka (Oryzias latipes)
• Coordinates: 17:6984739..6985597(+)
• Located in intron of: ENSORLG00000005611

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSORLG00000019879
• Aliases: None
• Description: None

Sequence

>retro_olat_28
AGAAGAGTATTGTCCCAGGACATTAGAAACAAAATTATAGACAAACATGGTAAAGGTAAAGGCTATAAAACCATCTCTAA
GCAGCTTGAAGTTCCTGTGACCACAGTGGCACATATTATTCAGAAGTTTCAGACCCACGGGACTGCAGCCAACCTCCCTG
GATGTGGCAGGAAGAAGAAAATTGATGACAAATTGAGGAGACGGAGTTGGACCTGTATCCAAAGAGCCCAGAACAACCTC
CAAAGACATTAAAGGAGAACTCCTAGAGCAAAGTACATCAGTGTCAGATCGCACCATTCGTGGTTGTTTGAGCCAGAGAA
GAGTTCATGGTAGACGACAAAGGAGAACACCACTGTTGAAAGGAAATCATAAAAAAGTGAGACTGGAATTTGCAAAAATG
CATTTTGACAAGCCACAAAGCTTCTGGGAAAATGTCCTTTGGACAGATGAGACAAAACTGGAGCTTTTTGGTAAGGCACA
TCAGCTCTATGTTGGTAGACTCAAAAATGAAGCATACAACCAAAAGAACACTGTCCCTAATGTGAAACATGGAGGAGGCT
CAGTTCTGTTTTGGGGCTGCTTTGCTGCACAGGTTGTCTTGAAGTTGTACAAGGTAAAATGAAATCTCAAGATCATCAAG
GCATTCTGGATAGAAATCTGCTGCCTAGTGTCAGAAAGCTTGGTCTCAGTCGCAGGTCATGGGTCTTCCAACAGGACAAC
GATCCAAAACACACAAACGAAAACCCCCAAGAATGGCTAAGAGAAAAGTGTTGGACTATTCTGAAGTGGCCTTCTATGAG
CCCAGATCTGAATCCCATTGAACATCTGTGGAAGGAGCTGAAACATGCCATTTGGAGA

Alignment

ORF - retro_olat_28 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.35 %
• Parental protein coverage: 99.31 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  RRELSQDISNKIIDKHRKAKGYKTTSKQLEVPATTVAHIIQKFKTHGTVANLPGCGRKMKIDDKLKRRI-
          RR.LSQDI.NKIIDKH.K.KGYKT.SKQLEVP.TTVAHIIQKF.THGT.ANLPGCGRK.KI.D...RR..
Retrocopy RRVLSQDIRNKIIDKHGKGKGYKTISKQLEVPVTTVAHIIQKFQTHGTAANLPGCGRKKKI-DDKLRRR>

Parental  VGTVSKEPSTTFKDIKGEFIDQGTSVSDRTICRCLSQSYAFHHFCNDKKLLKGNNK--RLEFAKMHVDKP
          VG.VSKEP.TT.KDIKGE...Q.TSVSDRTI..CLSQ............LLKGN.K..RLEFAKMH.DKP
Retrocopy VGPVSKEPRTTSKDIKGELLEQSTSVSDRTIRGCLSQRRVHGRRQRRTPLLKGNHKKVRLEFAKMHFDKP

Parental  QRFWENVLWTDETKLELFGKAHQLYVGRLKNEAYNKNNTVPTVKHGGGSVLFW-GCFAASGTVCLEVVQG
          Q.FWENVLWTDETKLELFGKAHQLYVGRLKNEAYN..NTVP.VKHGGGSVLFW.G.....G..CLEVVQG
Retrocopy QSFWENVLWTDETKLELFGKAHQLYVGRLKNEAYNQKNTVPNVKHGGGSVLFW<GLLCCTG--CLEVVQG

Parental  QMKSQDYQGILDRNVLPSVRKLGLSRRSWVLQQDIDPKHTAKKTQEWLREERWTILKWPSMSPDLNPIEH
          .MKSQD.QGILDRN.LPSVRKLGLSRRSWV.QQD.DPKHT....QEWLRE..WTILKWPSMSPDLNPIEH
Retrocopy KMKSQDHQGILDRNLLPSVRKLGLSRRSWVFQQDNDPKHTNENPQEWLREKCWTILKWPSMSPDLNPIEH

Parental  LWKELKHAIWR
          LWKELKHAIWR
Retrocopy LWKELKHAIWR

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_28 retrocopy.

TSS

Oryzias latipes was not studied using FANTOM5 data.

Lab

retro_olat_28 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_olat_28 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,