RetrogeneDB ID: retro_olat_22

Retrocopy location

• Organism: Medaka (Oryzias latipes)
• Coordinates: 13:5352225..5353148(+)
• Located in intron of: ENSORLG00000002616

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSORLG00000010891
• Aliases: None
• Description: None

Sequence

>retro_olat_22
GGCTATAAAACCATCTCTAAGCAGCTGGAAGTTCCTGTGACAACAGTGGCACATATTATTCAGAAGTTTAAGACCCACGG
AACAGTAGCCAACCTCCCTGGACGTGGCCTGAAGAGGAAAATTGATGACAAATTGAGGAGACGGATGGTTAGAACTGTAT
CCAAAGAGCCCAGAACAACCTCCAAAGACGTTAAAGGTGAACTCCTAGATCAAGGTACATCAGTGTCAGATTGCACCATT
TGTCGTTGTTCGAGCCAGAGTGGACTTCATGGGAGACGACCAAGGAGGACACCAATGTTCAGGAAAGGAAATCATAAAAA
AGACTGGAATTTGCAAAAATGCATGTTGACAAGCCACAAAGCTTCTGGGAAAATGTCCTTTGGACAGATGAGACGAAACT
GTAGCTTTTTGGTAAGGCACATCAGCTCTATGTTTGTAGACTCAAAAATGAAGCACACAAGGAAAAGAACACTGTCCCAA
CTGTGAAACATGGAGGAGGCTCAGTTCTGTTTTGGGGCTGCTTTGCTGCATCTGGCACAGGGAAATCTCAAGATTATCAA
GGCATTCTGGATATAAATGTGCTGCCTAGTGTCAGAAAGCTTGGTCTCAGTCGCAGGTCATGGGTCTTCCAACAGGACAA
CGATCCAAAACACACAGCCAAAAACCGCCAAGAATGGCTAAGAGAAAAGCGTTGGACTATACTTAAGTGGCCTTCTATGA
GCCCAGATCTGAATCCCATTGAACATCTGTGGAAGGAGCTGAAACATGCCATTTGTAGAAGACACCCATCAAACCTGAGA
CAACTGGAGCAGTTTGCTCATGAGGAGTGGGCCAAAATACCTGTGGACAGGTGCAGAAGGCTCATTGACAAATACAGAAA
CCGTTTAATTGCAGTGATTGCCTCAAAAGGTTGTGCAACAAGA

Alignment

ORF - retro_olat_22 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.47 %
• Parental protein coverage: 92.99 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GKEKINTHLSTXVTTVAHISQKFKTHGTVANLTGRW-KRNIDDKLRTRIVGTVSKEPRTTSKDIKSKLLD
          G...I...L...VTTVAHI.QKFKTHGTVANL.GR..KR.IDDKLR.R.V.TVSKEPRTTSKD.K..LLD
Retrocopy GYKTISKQLEVPVTTVAHIIQKFKTHGTVANLPGRGLKRKIDDKLRRRMVRTVSKEPRTTSKDVKGELLD

Parental  QSTSVSDRTIHGSFSQSGLHRRRPRRTPLLKGNHTKA-RLELAKMHVNKAQSFWENVLWTDETKLELFGE
          Q.TSVSD.TI....SQSGLH.RRPRRTP.......K..RLE.AKMHV.K.QSFWENVLWTDETKL.LFG.
Retrocopy QGTSVSDCTICRCSSQSGLHGRRPRRTPMFRKGNHKK<RLEFAKMHVDKPQSFWENVLWTDETKL*LFGK

Parental  AHQLYVHRLKNEASNEKNTVPTVKHGGGSVLFWGCSAASATGCLEVVQDYQGIPGRNVLHSVRKLGLSWR
          AHQLYV.RLKNEA..EKNTVPTVKHGGGSVLFWGC.AAS.TG......DYQGI...NVL.SVRKLGLS.R
Retrocopy AHQLYVCRLKNEAHKEKNTVPTVKHGGGSVLFWGCFAASGTGKSQ---DYQGILDINVLPSVRKLGLSRR

Parental  SWVCQQANDPKHTAKTPEKRWTILKWPSMS-PHLNP----IEHQWKELKHAIWRRHPSNLRQLKQFVHEE
          SWV.QQ.NDPKHTAK..........W.....P...P....IEH.WKELKHAI.RRHPSNLRQL.QF.HEE
Retrocopy SWVFQQDNDPKHTAKNRQEWLREKRWTILKWPSMSPDLNPIEHLWKELKHAICRRHPSNLRQLEQFAHEE

Parental  WAKIPVDRCRRLIDKYRNRFIAVVTSKGCATK
          WAKIPVDRCRRLIDKYRNR.IAV..SKGCAT.
Retrocopy WAKIPVDRCRRLIDKYRNRLIAVIASKGCATR

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_22 retrocopy.

TSS

Oryzias latipes was not studied using FANTOM5 data.

Lab

retro_olat_22 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_olat_22 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,