RetrogeneDB ID: retro_olat_26

Retrocopy location

• Organism: Medaka (Oryzias latipes)
• Coordinates: 15:20993523..20994516(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSORLG00000020726
• Aliases: None
• Description: None

Sequence

>retro_olat_26
AAGCGAAGGAGAGAATTGTCCCAGGACATTAGAAACAAAATTATAGACAAACATCATAAAGGTAAAGGCTGTAAAACCAA
CTCTAAGCAGCTTGAAGTTCCTGTGACAACAGTGGCACATATTATTCAGAAGTTTAAGACCTATAGGACAGTAGCCAACC
TCCCTGGACGTGGCCGGAAGAGGAAAATTGATGACAAATTCAGGAGACAGATAGTTGGAACTGTTTCCAAAGAGCCCAGA
ACAACCTCCAAAGACATTAAAGGTGAACTCCCAGATCAAGGTACATCAGTGTCAGATCGCACCATTCGTCGTTGTTTGAG
CCAGAGCGGACTTCATGGGAGACGACCAAGGAGGACACCACTGTTGAAAGGAAATCAATAAAAAGCCAGACTGGAATTTG
CAAAAATGCATGTTGACAAGCCACAAAGCTTCTGGGAAAATGTCCTTTGGACAGATGAGACAATACTGGAGCTTTTTGGT
AAGGCACATCAGCTTTATGTTGGTAACTCAAAAATGAAGCATCCAGCCAAAAGAACACTGTCCCTACTGTGAAACATGGA
GGAGGCTCAGTTCTGTGTTGGGGCTGCTTTGCTGCATCTGGCACAGGGTGTCTTGAAGTTAAAGGTAAAATGCAATCTCA
AGATTATCAAGGCATTCTGGATAGAAATGTGCTGCCTAGTGTCAGAAAGCTTGGTCTCAGTCGTGGGTCGTGGGTCTTCC
GACAGGACAAAACACACAGCCAAAAACACCAAATAACGGCTAAGAGAAAAGCGTTGGACTATTCTGAAGTGGCCTTCTAT
GAGTCTAGATCTGAATCCCATTGAACATCTGTGGAAGGAGGTGAAATACGCCATTTGGAGAAGACACTGGTCAAACCTGA
GACAACTGGAGCAGTTTGCTCATGAGAAGTGGGCAAAAATACCTGTGGACAGGTGCAGAAGGCTCATTGACAAATACAGA
AACCGTTTCATTGCAGTGATTGCCTCAAAAGGT

Alignment

ORF - retro_olat_26 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.0 %
• Parental protein coverage: 98.51 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KKCKVMSEDLRGKTVKKE-QSQGYESISRDLNVPLFTVGNIIKRFAAHGSVDNLPGC-RLPSRADKLRRR
          K.....S.D.R.K...K.....G....S..L.VP..TV..II..F.....V.NLPG..R.....DK.RR.
Retrocopy KRRRELSQDIRNKIIDKHHKGKGCKTNSKQLEVPVTTVAHIIQKFKTYRTVANLPGRGRKRKIDDKFRRQ

Parental  IVGTVPKEPRTTSKDIKGELLDQGTSVSHRTIRGCLSQSGLHGRRPRR-PLLKGNPKKARLEFAKMHVDK
          IVGTV.KEPRTTSKDIKGEL.DQGTSVS.RTIR.CLSQSGLHGRRPRR.PLLKGN..KARLEFAKMHVDK
Retrocopy IVGTVSKEPRTTSKDIKGELPDQGTSVSDRTIRRCLSQSGLHGRRPRRTPLLKGNQ*KARLEFAKMHVDK

Parental  PQSFWGNVLWTDETKLELFGKAHQLYVGR-LKNEASNQKNTVPTVKHGGGSVLFWGCFSASDTGCLEVVQ
          PQSFW.NVLWTDET.LELFGKAHQLYVG..LKNEAS.QKNTVPTVKHGGGSVL.WGCF.AS.TGCLEV..
Retrocopy PQSFWENVLWTDETILELFGKAHQLYVGN<LKNEASSQKNTVPTVKHGGGSVLCWGCFAASGTGCLEV-K

Parental  GQMKSQDDQGILDRNVLPSVRKLGLSLRSWIFQQDNDPKH-AKNPQEWLREKRWTILKWPSMSPDLNPIK
          G.M.SQD.QGILDRNVLPSVRKLGLS..SW.F.Q..D..H.AKN....LREKRWTILKWPSMS.DLNPI.
Retrocopy GKMQSQDYQGILDRNVLPSVRKLGLSRGSWVFRQ--DKTH>AKNTK*RLREKRWTILKWPSMSLDLNPIE

Parental  HLWKELKHAIWRRHPSNLRHLEQFAHEEWAKIPVDRCRRLIDKYRNRFIAVIASKG
          HLWKE.K.AIWRRH.SNLR.LEQFAHE.WAKIPVDRCRRLIDKYRNRFIAVIASKG
Retrocopy HLWKEVKYAIWRRHWSNLRQLEQFAHEKWAKIPVDRCRRLIDKYRNRFIAVIASKG

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_26 retrocopy.

TSS

Oryzias latipes was not studied using FANTOM5 data.

Lab

retro_olat_26 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_olat_26 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 ,