RetrogeneDB ID: retro_olat_3

Retrocopy location

• Organism: Medaka (Oryzias latipes)
• Coordinates: 17:22661838..22663692(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSORLG00000014774
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: FEM1C
• Ensembl ID: ENSORLG00000004946
• Aliases: None
• Description: None

Sequence

>retro_olat_3
ATGGATATAAACACGGCGGTTTTCTGCGCGGCCAGAGAGGGTAAGCTAAAACTTCTCCAGAAGTTGCTGAGCAACAAAAG
TCCAGAGGAGCTGGAGGTTTTGGCCGGGGAGAAAACGCAGGGAGGCACCGCATTGCTGATCGCCTCCCGGAACGGACACT
TGGAGGTGGTGGACTACCTGGTGGCTCACTGTAAGGCGAACGTGGAGCTCGGCGGCTCCGTCAACTTTGACGGGGAGACC
ATCGAGGGGGCTCCGCCGCTGTGGGCGGCTTCGGCCGCCGGTCACCTCCCGGTGGTGAAGACGCTTCTGAAACACGGCGC
GTCGGTGAACAACGCCACTCTGACCAATTCTACGCCGCTCCGCGCCGCCTGCTTTGACGGTCACCTGGAGATCGTCCGCT
ACCTGGTGGAGCACAAAGCCGACATGGAGGTGGCCAACCGCCACGGTCACACCTGCCTCATGATCTCCTGCTACAAAGGC
CACAAGGAGATCGCCAAATTCCTCCTTGATCGAGGTGCGGACGTGAACCGCAAAAGCGTGAAGGGGAACACCGCCCTCCA
CGACTGCGCAGAGTCCGGGAGCCTGGAGATCATGAAGATGCTGTTGAAGTGCAATGCCCGAATGGAGAGGGATGGCTACG
GAATGACCCCCCTGCTGGCTGCAAGTGTCACGGGTCACACTAAAATCGTGGAATATCTCGCCCACCAGCCTTGGACCTCC
AGAGAGGAGCGCATTGATGCTCTGGAACTGTTAGGAGCCACCTTTGTGGACAAAAAGCGAGATCTGATGGGGGCCATTAG
GTACTGGAGGAGAGCCATGGAGCTGAGGCAGCCAGGGGACCAAGCCGGACCGCTGGCCAAGCCTCCACCCGGACCCCCGA
TCTCTGCGTATGGCTGTGCACAGGAGGTGAGCTCGGCAGAGGAGCTGGAGGCTTTGATCACAGACCCAGATGAAATGCGG
ATGCAGGCTTTGTTGGTCCGGGAGCGCATCCTCGGGCCGTCCCACCCAGACACCTCATTTTACATCCGCTACAGGGGCGC
TGTGTACGCCGACTCTGGCAACTTTGAGCGCTGTATCAGCCTGTGGAAGTATGCCTTAGACATGCAGCAGAGCAACCTGG
ATCCTCTGAGTCCCATGACGGCCGCCAGCTTCCTGTCTTTTGCAGAGCTTTTCTCTTTTGTTCTTCAGGACAGGTCCAAA
GGCACGCTGTCGACTAGCATCACCTTCCAGGATCTGATGACTGTGCTGGTGAAGAGCGTGAGGGAGGTTGAGAGGGCCGT
GGCCCAGAGGGATAGCCCCCCAGAGGCCCCCCAGTTCACCAAGGCCCTCTACATCATCCTCCACCTCATTTTTTTACTGG
AGAAGCTGGAGTGCACGCCGGAGCAGGAGCACCAGAAGAAGCACACCGTGTACCGGCTCCTGAAGCTGAACCCCAGAGGT
CGGGGCGGCTTCACTCCCCTCCACATGGCGGCGGACAAGGAAACCACGTCGGTGGGCCGCTACCCTGTGGGCCGCTTCCC
CTCGCTGCCGGTGGCGGCGCTGCTCCTGGAATGCGGTGCAGATGTGGATTCACGCGATTGTGAGAACAACACGCCACTGC
ACGTCGCAGCGAACAATAGCTGTCCGGAGATCATGGCGCTGCTCATGAAGGCCGGCGCCCACTTTGACACCACAAATGCA
CAGAAGAAGATGGCCTGCGAGCTGCTGGACGAGCACAGCGGCGGGCACCCGGCTCTTTATACTTTAAACTACATCACCCT
CCAGTGCCTAGCGGCGCGGGCGATAGAGAAGCACAGGCTGCCTTACAGAGGACTGATATCTAAAGAAATAGAGGCTTTTA
TTGAGCTGCACTGA

Alignment

ORF - retro_olat_3 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.09 %
• Parental protein coverage: 99.84 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MDLKTAVFNAVRDGKLRLLQKLLENKDGHEVIKLMGEKTNGATPLLMAARYGHLELVEYLLECCSAPVEV
          MD..TAVF.A.R.GKL.LLQKLL.NK...E...L.GEKT.G.T.LL.A.R.GHLE.V.YL...C.A.VE.
Retrocopy MDINTAVFCAAREGKLKLLQKLLSNKSPEELEVLAGEKTQGGTALLIASRNGHLEVVDYLVAHCKANVEL

Parental  GGSVSFDGETIEGAPPLWAASAAGHLKVVQSLLGHGASVNSTTLTNSTPLRAACFDGHLDIVKYLVEHSA
          GGSV.FDGETIEGAPPLWAASAAGHL.VV..LL.HGASVN..TLTNSTPLRAACFDGHL.IV.YLVEH.A
Retrocopy GGSVNFDGETIEGAPPLWAASAAGHLPVVKTLLKHGASVNNATLTNSTPLRAACFDGHLEIVRYLVEHKA

Parental  DLEVANRHGHTCLMISCYKGHKDIAQYLLEKGADVNRKSVKGNTALHDCAESGSLEIMQMLLQYGATMEQ
          D.EVANRHGHTCLMISCYKGHK.IA..LL..GADVNRKSVKGNTALHDCAESGSLEIM.MLL...A.ME.
Retrocopy DMEVANRHGHTCLMISCYKGHKEIAKFLLDRGADVNRKSVKGNTALHDCAESGSLEIMKMLLKCNARMER

Parental  DAYGMTPILSASVTGHTNIVDYLTTLPQTSHTKRIDALELLGATFVDKKRDLLGALKYWKRAMDLRYV-D
          D.YGMTP.L.ASVTGHT.IV.YL...P.TS...RIDALELLGATFVDKKRDL.GA..YW.RAM.LR...D
Retrocopy DGYGMTPLLAASVTGHTKIVEYLAHQPWTSREERIDALELLGATFVDKKRDLMGAIRYWRRAMELRQPGD

Parental  SNSIVHKPEPKHLVMAYDYAREVTNAEELDSLISDPDEMRMQALLIRERILGPQHPDTSYYIRYRGAVYA
          ......KP.P.....AY..A.EV..AEEL..LI.DPDEMRMQALL.RERILGP.HPDTS.YIRYRGAVYA
Retrocopy QAGPLAKPPPGPPISAYGCAQEVSSAEELEALITDPDEMRMQALLVRERILGPSHPDTSFYIRYRGAVYA

Parental  DSGNFERCINLWKYALEMQQSNLDPLSPMTASSLLSFAELFSFMLQDRAKGLLGTSVSFEDLMGILSKSV
          DSGNFERCI.LWKYAL.MQQSNLDPLSPMTA.S.LSFAELFSF.LQDR.KG.L.TS..F.DLM..L.KSV
Retrocopy DSGNFERCISLWKYALDMQQSNLDPLSPMTAASFLSFAELFSFVLQDRSKGTLSTSITFQDLMTVLVKSV

Parental  MEIERAIKQSGPMPPDPAQLSKALSIILHLICLLEKVPCTAEQDHFKKETIYRFLKLQPCGKNGYSPLHL
          .E.ERA..Q....PP...Q..KAL.IILHLI.LLEK..CT.EQ.H.KK.T.YR.LKL.P.G..G..PLH.
Retrocopy REVERAVAQR-DSPPEAPQFTKALYIILHLIFLLEKLECTPEQEHQKKHTVYRLLKLNPRGRGGFTPLHM

Parental  AVDRNTTCVGRYPVCKFPSLTVASILLECGADVNSKDEDDNSPLHIAASNGHPDIMNLLISNGTHFDSTN
          A.D..TT.VGRYPV..FPSL.VA..LLECGADV.S.D...N.PLH.AA.N..P.IM.LL...G.HFD.TN
Retrocopy AADKETTSVGRYPVGRFPSLPVAALLLECGADVDSRDCENNTPLHVAANNSCPEIMALLMKAGAHFDTTN

Parental  AFQQTACDLLDEKELARNVIQPINHTTLQCLAARAIVKHSLAYQGNIPEKLEAFILLH
          A....AC.LLDE...........N..TLQCLAARAI.KH.L.Y.G.I....EAFI.LH
Retrocopy AQKKMACELLDEHSGGHPALYTLNYITLQCLAARAIEKHRLPYRGLISKEIEAFIELH

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

1 EST(s) were mapped to retro_olat_3 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
AM327821	22661709	22662359	100	650	0	650

TSS

Oryzias latipes was not studied using FANTOM5 data.

Lab

retro_olat_3 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_olat_3 has 3 orthologous retrocopies within teleost group .

Species	RetrogeneDB ID
Gasterosteus aculeatus	retro_gacu_12
Takifugu rubripes	retro_trub_16
Tetraodon nigroviridis	retro_tnig_27

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Gasterosteus aculeatus	ENSGACG00000007406	1 retrocopy	retro_gacu_12,
Gadus morhua	ENSGMOG00000005806	1 retrocopy	retro_gmor_12,
Oreochromis niloticus	ENSONIG00000015041	1 retrocopy	retro_onil_20,
Oryzias latipes	ENSORLG00000004946	1 retrocopy	retro_olat_3 ,
Tetraodon nigroviridis	ENSTNIG00000003195	1 retrocopy	retro_tnig_27,
Takifugu rubripes	ENSTRUG00000012022	1 retrocopy	retro_trub_16,
Xiphophorus maculatus	ENSXMAG00000015297	1 retrocopy	retro_xmac_5,