RetrogeneDB ID: retro_onil_20

Retrocopy location

• Organism: Tilapia (Oreochromis niloticus)
• Coordinates: GL831134.1:9756672..9758526(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSONIG00000021435
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: FEM1C
• Ensembl ID: ENSONIG00000015041
• Aliases: None
• Description: None

Sequence

>retro_onil_20
ATGGATATATCGACGGCGGTTTTCAACGCGGCCAGAGATGGTAAGCTGAAACTTATCCAGAAGTTGCTGAGCAACAAAAG
TCCAGAGGAGCTGGAGGCTTTGGCTGAGGAGAAAACACAGGGGGGAACCCCTTTGCTGATAGCCTCTCGATACGGACATT
TAGAGGTGGTGGACTACCTCCTTGAACATTGTAAAGCGAATGTTGAACTCGGGGGTTCGGTGAACTTTGACGGCGAGACC
ATCGAGGGGGCTCCGCCGCTCTGGGCGGCTTCGGCAGCCGGTCACCTCCCTGTAGTGAAGACGCTACTGAAACACGGTGC
CTCGGTAAACAATGCAACACTAACTAACTCAACGCCGCTCCGAGCTGCCTGCTTCGACGGTCACCTGGAGATCGTCCGCT
ACCTGGTGGAGCACAGAGCCGACATGGAGGTCGCCAACCGCCACGGCCACACCTGCCTCATGATCTCCTGCTACAAGGGC
CACAAGGAGATAGCCAAGTTCCTCCTGGATCGCGGTGCGGATGTTAACCGCAAGAGTGTGAAAGGAAACACTGCCCTACA
CGACTGTGCCGAGTCAGGTAGTCTGGACATCATGAAGATGTTGCTGAAGTGCAATGCCCGCATGGAGAGAGACGGATACG
GGATGACCCCGCTCCTGGCTGCAAGCGTGACGGGTCACACCAACATTGTGGAGTATCTCGCCCACCAGCCTCGTACCTCC
AGAGAGGAGCGCATCGATGCACTTGAACTCCTAGGGGCTACTTTTGTGGACAAAAAGCGTGATCTGTTGGGCGCCATGAG
GTACTGGAGGAGGGCGATGGAGCTGAGGCAGCCGGGGGAAAAGACCGGTTCTCTTGCCAAGCCTCCACCCGGCCCCCCGA
TCCCCGCCTATGGATGCGCACAGGAGGTGTGCACTGCAGAGGAACTGGAGGCTTTGATCACCGACCCGGACGAAATGAGG
ATGCAGGCCCTGTTGATTCGCGAGCGCATCCTGGGCCCATCCCATCCAGACACGTCTTATTACATCCGCTATAGGGGAGC
TGTGTACGCTGACTCAGGCAACTTCGAGCGCTGCATAAGTCTGTGGAAGTACGCTTTAGACATGCAGCAAAGCAACCTGG
ACCCTCTCAGTCCCATGACAGCCTCAAGTTTCCTGTCTTTTGCAGAACTCTTCTCATTTGTTCTTCAAGACCGGGCAAAA
GGCTCGCTGTCAACACGCATCACCTTCCATGATCTCATGACTGTGTTGGGCAAAAGCGTGAGGGAGGTAGAGAGAGCTGT
GGCACAAAGGGATAATCCCCCAGAAGCTCCTCAGTTCACCAAAGCCCTCTCCATCATCCTCCACCTCATCTTTCTACTGG
AGAAGCTTGAGTGCAGCCCGGAGCAGGAGCACCAGAAGAAGCACACGGTGTACCGACTTCTAAAGCTGAACCCCCGAGGG
CGGAGCGGCTTCACCCCCCTGCACATGGCCGTAGACAAGGAAACGACATCTGTCGGCCGCTACCCGGTAGGCCGCTTCCC
CTCCCAGGCGGTGGCTGCGCTGCTCCTAGAGTGCGGCGCGGACGTTGATTCGCGGGACTGTGAGAACAACACACCGCTGC
ACATTGCTGCTAACAACGGTTGTCCGGAGATTATGGCGCTCCTCATGAAGGCTGGAGCTCACTTCGATGCCACAAACGCA
CAGAGGAAGACGGCCTACGAGCTGTTGGATGAGCACAGCAGCGGGCACCCGGCGCTCTACCCGCTAAACTACGTCACCCT
TCAGTGCCTGGCAGCACGTGCAATCGAAAAGCACAGACTGCCCTACAGGGGACTCATCTCTGAAGAGATGGAGGCTTTCA
TTGAGCTGCACTGA

Alignment

ORF - retro_onil_20 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.68 %
• Parental protein coverage: 99.84 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MDLKTAVFNAARDGKLRLLQKLLENKDGHEVTKLMGEKTNGATPLLMAARYGHLDLVEYLLECCSAPVEV
          MD..TAVFNAARDGKL.L.QKLL.NK...E...L..EKT.G.TPLL.A.RYGHL..V.YLLE.C.A.VE.
Retrocopy MDISTAVFNAARDGKLKLIQKLLSNKSPEELEALAEEKTQGGTPLLIASRYGHLEVVDYLLEHCKANVEL

Parental  GGSVNFDGETIEGAPPLWAASAAGHLKVVQSLLGHGASVNSTTLTNSTPLRAACFDGHLDIVKYLVEHNA
          GGSVNFDGETIEGAPPLWAASAAGHL.VV..LL.HGASVN..TLTNSTPLRAACFDGHL.IV.YLVEH.A
Retrocopy GGSVNFDGETIEGAPPLWAASAAGHLPVVKTLLKHGASVNNATLTNSTPLRAACFDGHLEIVRYLVEHRA

Parental  DLEVANRHGHTCLMISCYKGHKEIAQYLLEKGADVNRKSIKGNTALHDCAESGSLEIMRMLLQYGATMEQ
          D.EVANRHGHTCLMISCYKGHKEIA..LL..GADVNRKS.KGNTALHDCAESGSL.IM.MLL...A.ME.
Retrocopy DMEVANRHGHTCLMISCYKGHKEIAKFLLDRGADVNRKSVKGNTALHDCAESGSLDIMKMLLKCNARMER

Parental  DGYGMTPLLSASVTGHTNIVDYLTTHQQTRHTERIDALELLGATFVDKKRDLLGALKYWKRAMDLRYM-D
          DGYGMTPLL.ASVTGHTNIV.YL.....T...ERIDALELLGATFVDKKRDLLGA..YW.RAM.LR....
Retrocopy DGYGMTPLLAASVTGHTNIVEYLAHQPRTSREERIDALELLGATFVDKKRDLLGAMRYWRRAMELRQPGE

Parental  SNNIIQKPEPKQLIMAYDYAREVTNAEELDGLISDPDEMRMQALLIRERILGPQHPDTSYYIRYRGAVYA
          ......KP.P...I.AY..A.EV..AEEL..LI.DPDEMRMQALLIRERILGP.HPDTSYYIRYRGAVYA
Retrocopy KTGSLAKPPPGPPIPAYGCAQEVCTAEELEALITDPDEMRMQALLIRERILGPSHPDTSYYIRYRGAVYA

Parental  DSGNFERCINLWKYALDMQQSNLDPLSPMTSSSLLSFAELFSFMLQDRAKGLLGTSVSFEDLMGILSKSV
          DSGNFERCI.LWKYALDMQQSNLDPLSPMT.SS.LSFAELFSF.LQDRAKG.L.T...F.DLM..L.KSV
Retrocopy DSGNFERCISLWKYALDMQQSNLDPLSPMTASSFLSFAELFSFVLQDRAKGSLSTRITFHDLMTVLGKSV

Parental  MEIERAIKQSGPMPPDPAQLSKALSIILHLICLLEKVPCTAEQDHFKKETIYRFLKLHPCGKNGFSPLHL
          .E.ERA..Q....PP...Q..KALSIILHLI.LLEK..C..EQ.H.KK.T.YR.LKL.P.G..GF.PLH.
Retrocopy REVERAVAQR-DNPPEAPQFTKALSIILHLIFLLEKLECSPEQEHQKKHTVYRLLKLNPRGRSGFTPLHM

Parental  AVDRNTTCVGRYPVCKFPSLTVASILLECGADVNSRDDDDNSPLHIAATNGHPDIMNLLISCGTHFDSTN
          AVD..TT.VGRYPV..FPS..VA..LLECGADV.SRD...N.PLHIAA.NG.P.IM.LL...G.HFD.TN
Retrocopy AVDKETTSVGRYPVGRFPSQAVAALLLECGADVDSRDCENNTPLHIAANNGCPEIMALLMKAGAHFDATN

Parental  AFQQTACDLLDEKELARNVIQPINHTTLQCLAARAIIKHGLDYRGNIPEKLEAFVLLH
          A...TA..LLDE.........P.N..TLQCLAARAI.KH.L.YRG.I.E..EAF..LH
Retrocopy AQRKTAYELLDEHSSGHPALYPLNYVTLQCLAARAIEKHRLPYRGLISEEMEAFIELH

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Oreochromis niloticus was not studied using RNA-Seq expression data.

ChIP-Seq

Oreochromis niloticus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_onil_20 retrocopy.

TSS

Oreochromis niloticus was not studied using FANTOM5 data.

Lab

retro_onil_20 was not experimentally validated.

Homology

Retrocopy orthology:

Oreochromis niloticus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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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,