RetrogeneDB ID: retro_gacu_12

Retrocopy location

• Organism: Stickleback (Gasterosteus aculeatus)
• Coordinates: groupIII:7686699..7688553(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSGACG00000015369
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: fem1c
• Ensembl ID: ENSGACG00000007406
• Aliases: None
• Description: fem-1 homolog c (C.elegans) [Source:ZFIN;Acc:ZDB-GENE-031008-3]

Sequence

>retro_gacu_12
ATGGATGTACCGACGGCGGTTTTCAACGCGGCCAGAGACGGTAAGCTGAAACTTATCCAGAAGTTGCTGAGCAACAAAAG
TCCAGAGGAGCTGGAGGCTTTAGCCGAGGAGAAGACGCAGGGAGGCACCGCTCTGCTGGTGGCCTCCCGCTACGGACACC
TGGAGGTCGTGGACTACCTCCTCGACCACTGCCGAGCCAACGTCGAACTCGGCGGCGCGGTCAACTTCGACGGCGAGACC
ATCGAGGGGGCTCCGCCGCTGTGGGCGGCCTCGGCCGCCGGTCACCTCCCCGTGGTGAAGGCGCTCCTGAAGCGGGGCGC
CTCGGTGAACAACGCGACGCTCACCAACTCCACGCCGCTGCGGGCCGCCTGCTTCGACGGCCACCTGGAGATCGTCCGCT
ACCTGGTGGAGCACAGGGCCGACATGGAGGTGGCCAACCGCCACGGGCACACCTGCCTCATGATCTCCTGTTACAAGGGC
CAGAAGGAGATCGCCAAGTTCCTCCTGGACCGCGGCGCCGACGTCAACCGCAAGAGCGTGAAGGGAAACACCGCCCTGCA
CGACTGCGCCGAGTCGGGCAGCCTGGACATCATGAAGATGCTGCTCAAGTGCAACGCGCGCATGGAGAGGGACGGCTACG
GGATGACCCCGCTGCTCGCCGCCAGCGTCACGGGTCACACCAACATCGTGGAGTACCTCGCCCACCAGCCTCGCACCTCC
AGGGAGGACCGCGTCGACGCCCTGGAACTGCTCGGGGCCACTTTCGTGGACAAGAAGCGGGATCTGCTGGGGGCCATGAG
GTACTGGAGGAGAGCGATGGAGCTGAGGCAACCGGGGGACAAAGCGGGCTGCTTGGGCAAGCCGCCACCCGGCCCCCCGG
TCCTTGCCTACGGCTGCGCGCAGGAGGTGGGCACAGCGGAGGAGCTGGAGGCTCTGATCACAGACCCCGATGAGATGAGG
ATGCAGGCTTTGTTGGTTCGCGAGCGCATCCTGGGGCCGTCGCACCCGGACACCTCCTATTACATCCGTTACCGGGGGGC
CGTGTACGCGGACTCGGGCAACTTTGAACGCTGCATCAGCCTTTGGAAATATGCTTTGGACATGCAGCAGAGCAACCTGG
ACCCTCTCAGCCCCATGACGGCCTCCAGTTTCCTGTCTTTTGCGGAGCTCTTCTCTTTTGTCCTTCAAGACCGGGCCAAA
GGCACCCTGTCCACCCGCGTCACCTTCCACGATCTGATGACCGTGCTGGGGAAAAGTGTGAGGGAGGTCGAGCGAGCCGT
GGCGCAGAAGGACAATCCCCCCGAGGCTCCTCAGTTCACCAAAGCGCTGTCCATCATCCTCCACCTCATCTTCCTCCTGG
AGAAGCTGGAGTGCAGCCCCGAGCAGGAGCATCAGAAGAAGCACACCGTGTACCGCCTGCTGAAGCTGAACCCCCGAGGC
CGCAGCGGCTTCACCCCCCTGCACATGGCCGTGGACAAGGAGACCACGTCCGTCGGCCGCTACCCCGTCGGCCGCTTCCC
CTCGCAGGCGGTGGCGGCGCTGCTCCTGGAGTGCGGCGCGGACGTGGACTCGCGCGACGGCGAGAACAACACGCCGCTGC
ACGTGGCCAGCAACAACGGCTGCCCGGAGATTATGGCGCTGCTCATGAAGGCCGGGGCGCACTTCGACGCCACAAACGCA
CAGAGGAAGACGGCGTACGAGCTGCTGGACGAGCAGAGCGGCGGGCACCCGGCCCTCTGCCCGCTGAACCATGTCACCCT
GCAGTGCCTGGCGGCGCGCGCCATTGAGAAGCACAGACTGCCCTACAGGGGACTCATCTCTGAGGAGATGGAGGCTTTCA
TCGAACTGCACTGA

Alignment

ORF - retro_gacu_12 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.23 %
• Parental protein coverage: 99.84 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MDLKTAVFNAARDGKLRLLQKLLENKDGHEVTKLTGDKTNGATPLLMASRYGHLDLVEYLLECCSAPVEV
          MD..TAVFNAARDGKL.L.QKLL.NK...E...L...KT.G.T.LL.ASRYGHL..V.YLL..C.A.VE.
Retrocopy MDVPTAVFNAARDGKLKLIQKLLSNKSPEELEALAEEKTQGGTALLVASRYGHLEVVDYLLDHCRANVEL

Parental  GGSVNFDGETIEGAPPLWAASAAGHLKVVQSLLGHGASVNSTTLTNSTPLRAACFDGHLDIVRYLVEHKA
          GG.VNFDGETIEGAPPLWAASAAGHL.VV..LL..GASVN..TLTNSTPLRAACFDGHL.IVRYLVEH.A
Retrocopy GGAVNFDGETIEGAPPLWAASAAGHLPVVKALLKRGASVNNATLTNSTPLRAACFDGHLEIVRYLVEHRA

Parental  DLEVANRHGHTCLMISCYKGHKEIAQYLLERGADVNRKSVKGNTALHDCAESGSLEIMRMLLQFGASMEQ
          D.EVANRHGHTCLMISCYKG.KEIA..LL.RGADVNRKSVKGNTALHDCAESGSL.IM.MLL...A.ME.
Retrocopy DMEVANRHGHTCLMISCYKGQKEIAKFLLDRGADVNRKSVKGNTALHDCAESGSLDIMKMLLKCNARMER

Parental  DGYGMTPLLSASVTGHTNIVDDLTTHQQTSHKARIDALELLGATFVDKKRDLLGALKYWKRAMDLRYM-D
          DGYGMTPLL.ASVTGHTNIV..L.....TS...R.DALELLGATFVDKKRDLLGA..YW.RAM.LR...D
Retrocopy DGYGMTPLLAASVTGHTNIVEYLAHQPRTSREDRVDALELLGATFVDKKRDLLGAMRYWRRAMELRQPGD

Parental  SNHVVHKAEAKQLIMAYDYAREVTNGEELDGLISDPDEMRMQALLIRERILGPQHPDTSYYIRYRGAVYA
          ......K........AY..A.EV...EEL..LI.DPDEMRMQALL.RERILGP.HPDTSYYIRYRGAVYA
Retrocopy KAGCLGKPPPGPPVLAYGCAQEVGTAEELEALITDPDEMRMQALLVRERILGPSHPDTSYYIRYRGAVYA

Parental  DSGNFERCINLWKYALDMQQSNLDPLSPMTASSLLSFAELFSFMLQDRAKGLLGTSVSFEDLMGILSKSV
          DSGNFERCI.LWKYALDMQQSNLDPLSPMTASS.LSFAELFSF.LQDRAKG.L.T.V.F.DLM..L.KSV
Retrocopy DSGNFERCISLWKYALDMQQSNLDPLSPMTASSFLSFAELFSFVLQDRAKGTLSTRVTFHDLMTVLGKSV

Parental  LEIERAVTQTGPMPPDPAQLSKALSIILHLICLLEKVPCTAEQDHFKKETIYKFLKLQPCGKNGYSPLHL
          .E.ERAV.Q....PP...Q..KALSIILHLI.LLEK..C..EQ.H.KK.T.Y..LKL.P.G..G..PLH.
Retrocopy REVERAVAQK-DNPPEAPQFTKALSIILHLIFLLEKLECSPEQEHQKKHTVYRLLKLNPRGRSGFTPLHM

Parental  AVDRNTTCVGRYPVCKFPSLTVASILLECGADVNSRDEDDNSPLHIAASNGHPDIMNLLISCGTHFDCTN
          AVD..TT.VGRYPV..FPS..VA..LLECGADV.SRD...N.PLH.A..NG.P.IM.LL...G.HFD.TN
Retrocopy AVDKETTSVGRYPVGRFPSQAVAALLLECGADVDSRDGENNTPLHVASNNGCPEIMALLMKAGAHFDATN

Parental  AFQQTAYDILHEKELSRNVIQPINHTTLQCLAARAIVKHSLAYRGNIPEKLEAFVLLH
          A...TAY..L.E.........P.NH.TLQCLAARAI.KH.L.YRG.I.E..EAF..LH
Retrocopy AQRKTAYELLDEQSGGHPALCPLNHVTLQCLAARAIEKHRLPYRGLISEEMEAFIELH

Legend:

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

Expression

RNA-Seq

Gasterosteus aculeatus was not studied using RNA-Seq expression data.

ChIP-Seq

Gasterosteus aculeatus was not studied using ChIP-Seq data.

EST

Gasterosteus aculeatus was not studied using EST data.

TSS

Gasterosteus aculeatus was not studied using FANTOM5 data.

Lab

retro_gacu_12 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_gacu_12 has 3 orthologous retrocopies within teleost group .

Species	RetrogeneDB ID
Oryzias latipes	retro_olat_3
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,