RetrogeneDB ID: retro_olat_36

Retrocopy location

• Organism: Medaka (Oryzias latipes)
• Coordinates: 24:20808776..20810134(+)
• Located in intron of: ENSORLG00000017871

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSORLG00000001802
• Aliases: None
• Description: None

Sequence

>retro_olat_36
CAGCTTAGGGACGGACTGGAGAGGATTGATAAAAGCCACCTCCCAGGGAAATTCAAAGTGTGGTGCTACCAATTCATCCT
CTATCCACGCTTGATGTGGCCCCTGAAGATGATTACATCATCCACAGCAGCAAAGATGGATCCCAAAGCAAACAATTTCA
TCCGTAAGTGGCTTGGCTTACCTCGAAGTCTGTCCAACACAGGCCTTTTTGGGAGAAACACACTCCAGCTGCCACTGAAG
CCCATCAGCCTAGGCTACAGACAGGAGAAGACAAGGTTTGTGCTTAAGCTGAGAGACTCAACCGACCCAGTTGTAAGAAA
CACCAAGGCACCTGTCCGAACCGGAAGCAAATGGAAGGCAGAAGAGGCTGTTGACCAGGCCATCAGCAAGCTTAAGCACA
ACGAAGTCGTGGGAAAGACGCAGTCAGGCAGAGCTGGGTTAGGCTGGGGAACAGCCCCCAAGTTCTGGTCGAAAGCCAAA
AGAAGCAAGAGGAAAGAGCTGGTGATTGAAGAGGTGACCAGGAGCGTGGAAAACCAGTACAAGATCAAAGCACTCAGCCA
GCCACAACAAGGGCGTAGGACAAATGGGAAGGCGTGGTCAATAGGACCATAGGGTGGTCTGATATATGGAAGATGCCTCA
AGCAAGGCTGAGCTTCCTCATCCGGGCCACCTATGACACCCTACCCAGCCCCAGCAATCTGAGCCTATGGTTTGGCTCAG
AGGAAAACTGCCATCTCTGCAAGACTCCAAACCCTACGTTACAACACATCCTGTCCGGTTGCAAAGCAGCTCTGGCCCAG
GGTAGGCACAGATGGCGGCATGACCAGTCTTGAGGAAACTGGCAGAGGTCCTGGAAGTACGGAGGATGGAGGCAGCTAAA
GGACATCCCACGAAGACACCGTCTTTGATTCACTTTGTTGGAGAAGGGGCTGGAGCACAGAACACCAACCAGAGAGGGAC
ACCATCACTGCTAACACCAGGATGCGACTGGAACTTAAGGGTGGACCTTGACCGTCAGCTCAAGTTCCCACCAGAAATAA
CTACCACCTCTCTGCGACCAGACATCATCCTGTGGTCCTCTGCAGCCAAAGCAGCAATCCTGACAGAGCTCACAATCCCT
TCGGAGGGAGGAATGGATGCTGCATATGAAAGGGAGGAAGGAAAAATACACAGAGCTGGTAGCTGAGTGCCGAGATGCTG
GGTGGTCAACCATCATCTGCCCGGTGGAGGTTGGCTGCAGGGGCTTTGTTGGAACATCCACCCAGCTCCTCCTTAGGAAG
ATGGGAGTGACTGGGTCGAAATTGAAGAAGGCATCCGAGGACTTGGCGGATGAGGCGGAAAAAGCCAGTTTCTGGCTA

Alignment

ORF - retro_olat_36 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.9 %
• Parental protein coverage: 50.23 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  QLKDGLERIDKSHLPGKFKVWCYQFILNPRLMWPLKLCEITSSTVAKMDAKANNFIRKWLGLPQSLSNTG
          QL.DGLERIDKSHLPGKFKVWCYQFIL.PRLMWPLK...ITSST.AKMD.KANNFIRKWLGLP.SLSNTG
Retrocopy QLRDGLERIDKSHLPGKFKVWCYQFILYPRLMWPLKM--ITSSTAAKMDPKANNFIRKWLGLPRSLSNTG

Parental  LFGR----LPLKPISLGYRQEKTRLVLELRDSTNPVIRNTKAPVRTGSKWKAEEAVDQAISKLKHNKIVG
          LFGR....LPLKPISLGYRQEKTR.VL.LRDST.PV.RNTKAPVRTGSKWKAEEAVDQAISKLKHN..VG
Retrocopy LFGRNTLQLPLKPISLGYRQEKTRFVLKLRDSTDPVVRNTKAPVRTGSKWKAEEAVDQAISKLKHNEVVG

Parental  KTQSGRAGLGWRIAPKFWSKATRSEKKELVIEEVTRSEENQYKIKALSQPQQGRWTT-WD---QRTIVWS
          KTQSGRAGLGW..APKFWSKA.RS..KELVIEEVTRS.ENQYKIKALSQPQQGR.T..W.....RTI.WS
Retrocopy KTQSGRAGLGWGTAPKFWSKAKRSKRKELVIEEVTRSVENQYKIKALSQPQQGRRTN<WEGVVNRTIGWS

Parental  DIWKMPQARLSFLIRATYDTLPSPSNLSLWFGSEENCHLCKTPSPTLQHILSGCKAALAQGRYRWRHDQ-
          DIWKMPQARLSFLIRATYDTLPSPSNLSLWFGSEENCHLCKTP.PTLQHILSGCKAALAQGR.RWRHDQ.
Retrocopy DIWKMPQARLSFLIRATYDTLPSPSNLSLWFGSEENCHLCKTPNPTLQHILSGCKAALAQGRHRWRHDQ<

Parental  VLRKLAEVLEVRRMEAAKDPPTKTPSLIHFVGEGAGAQNTNQRGTPSLLTPGCDWNLRVDLDRQLNVCES
          VLRKLAEVLEVRRMEAAK..PTKTPSLIHFVGEGAGAQNTNQRGTPSLLTPGCDWNLRVDLDRQL.....
Retrocopy VLRKLAEVLEVRRMEAAKGHPTKTPSLIHFVGEGAGAQNTNQRGTPSLLTPGCDWNLRVDLDRQLKFPPE

Parental  IITWHL---IILWSSAAKAVILAELTIPWEGGMDAAYEK-KKDKYTELVAECRDAGWSTIICPVEVGCRG
          I.T..L...IILWSSAAKA.IL.ELTIP.EGGMDAAYE...K.KYTELVAECRDAGWSTIICPVEVGCRG
Retrocopy ITTTSLRPDIILWSSAAKAAILTELTIPSEGGMDAAYER>RKEKYTELVAECRDAGWSTIICPVEVGCRG

Parental  FVGTCTQLLLSKMGVTGSKLKKASKDLAEEAEKASFWL
          FVGT.TQLLL.KMGVTGSKLKKAS.DLA.EAEKASFWL
Retrocopy FVGTSTQLLLRKMGVTGSKLKKASEDLADEAEKASFWL

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_36 retrocopy.

TSS

Oryzias latipes was not studied using FANTOM5 data.

Lab

retro_olat_36 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_olat_36 has 0 orthologous retrocopies within teleost group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Oryzias latipes	ENSORLG00000001802	1 retrocopy	retro_olat_36 ,