RetrogeneDB ID: retro_tnig_27

Retrocopy location

• Organism: Tetraodon (Tetraodon nigroviridis)
• Coordinates: 15:4555815..4557668(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSTNIG00000015341
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: fem1c
• Ensembl ID: ENSTNIG00000003195
• Aliases: None
• Description: fem-1 homolog c (C.elegans) [Source:ZFIN;Acc:ZDB-GENE-031008-3]

Sequence

>retro_tnig_27
ATGGACATATCGACGGCGGTTTTCAACGCGGCCAGAGATGGTAAGCTAAAACTTATCCAGAAGTTGCTGAGCAACAAAAC
TCCCGAGGAGTTGGAGGCGTTAGCCGAGGGAGAAAACACAGGGAGGCACACCTCTGTTGATAGCCTCCCGCTACGGGCAT
TTAGAGGTTGTCGATTACCTCCTTGAACACTGTAAAGCCAATGTCGAACTCGGGGGTGCGGTTAATTTTGACGGCGAGAC
CATCGAAGGTGCTCCGCCGCTGTGGGCGGCATCGGCAGCCGGTCACCTTCCCGTGGTGAAAACGCTTCTGAAACACGGCG
CCTCCGTCAACAATGCCACACTAACCAACTCAACACCCCTGCGAGCCGCCTGCTTCGACGGGCATCTGGGAGATCGTCCG
ATATCTGGTGGACCACAGAGCCGACATGGAGGTGGCCAACCGCCACGGCCACACCTGCCTCATGATCTCCTGTTACAAGG
GCCACAAGGAGATCGCCAAGTTTCTGCTGGACCGGGGGGCTGATGTCAACCGCAAGAGTGTGAAAGGCAACACTGCCCTG
CACGACTGTGCCGAGTCGGGCAGCCTCGACATCATGAAGATGCTGCTGAAGTGCGATGCTCACATGGAAAGGGACGGCTA
CGGCATGACCCCGCTGCTCGCCGCCAGTGTAACCGGTCACGCCAACATTGTGGTGCACCTCGTCCACCAGACACGGACCT
CCAGAGAGGAACGCGTTAATGCTCTCGAACTTCTTGGAGCCACGTCTGTGGACAAAAAGAGAGATCTGCTTGGTGCAATG
AGGTACTGGAGGTGGGCCATGGAGCTGAGGCACCCAGTGTATATAACTGAATCCCTGGCCAAGCCCCCACCTGGTCCTCC
CATCCCGGCATATGGCTGTGCCCAGGAGGTGAACACTGTGGAGGAGCTGGAAGCTTTGATCACAGACCCCGATGAAATGC
GGATGCAGGCATTGTTGATTCGAGAACGCATTCTGGGACCGTCTCATCCGGACACTTCGTATTATATCCGCTACAGGGGA
GCCGTATATGCCGACTCTGGCAACTTTGAACGGTGCATCAGCCTGTGGAAGTACGCTTTAGACATGCAGCAAAGCAACCT
CGACCCTCTCAGTCCAATGACTGCCTCCAGTTTCCTCTCCTTCGCAGAGCTCTTCTCTTTTGTCCTCCAGGACCGGGCCA
AGGGCACCATGTCCACACGCATCACCTTCTCCGACCTGATGACAGTGCTGGCGAAAAGTGTGAGGGAAGTCGAGAGAGCC
ATGGCACAAAGTGACAACCTACCCGAGGCCTCCCAGTTCACCAAAGCGCTCTCCATCATCCTGCACCTCATCTTCCTCCT
GGAGAAGCTGGACTGCAGTCCAGAGCAGGAGCACCAGAAGAAGCACACTTTGTACCGCCTGCTGAAGCTGAACCCTCGCG
GCCGCAGCGGCTTCACCCCCCTTCACATGGCCGTGGACAAAGAGACCACGTCGGTGGGCCGCTACCCTGTGGGCCGCTTC
CCCTCTCCGGCAGTGGCGGCGATACTCCTGGAGTGCGGCGCCGACATCGATTCCCGTGACTACGACAACAACACGCCACT
ACACATCGCCGCCGGCAACAGCTCCCCGGAGATTATGGCGCTGCTAATAAAGGCCGGGGCTCACTTTGACGCAAAGAACG
CACAAAGGAAGATGGCCTACGAGCTGTTGGATGAGCAGAGCAGTGGGCACCCCTCCATCTACCCGCTGAACTATGTCACC
CTTCAGTGCCTGGCAGCTCGCGCCATCGAGAAGCACAGACTCCCCTACAGGGGCCTTATTTCCGAAGAGATGGAGGCTTT
CATCGAGTTGCAC

Alignment

ORF - retro_tnig_27 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.87 %
• Parental protein coverage: 99.84 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MDLKTAVFNAARDGKLRLLQKLLENKDGHEVTKLMG-EKTNGATPLLMASRNGHLDLVEYLLECCSAPIE
          MD..TAVFNAARDGKL.L.QKLL.NK...E...L...EKT.G.TPLL.ASR.GHL..V.YLLE.C.A..E
Retrocopy MDISTAVFNAARDGKLKLIQKLLSNKTPEELEALAE>EKTQGGTPLLIASRYGHLEVVDYLLEHCKANVE

Parental  VGGSVNFDGETIEGAPPLWAASAAGHLKVVQSLLGHGASVNSTTLTNSTPLRAACFDGHL-DIVKYLVEH
          .GG.VNFDGETIEGAPPLWAASAAGHL.VV..LL.HGASVN..TLTNSTPLRAACFDGHL..IV.YLV.H
Retrocopy LGGAVNFDGETIEGAPPLWAASAAGHLPVVKTLLKHGASVNNATLTNSTPLRAACFDGHL>EIVRYLVDH

Parental  KADLEVANRHGHTCLMISCYKGHKDIAQFLLQNGADVNRKSVKGNTALHDCAESGSLEIMQMLLQYGASM
          .AD.EVANRHGHTCLMISCYKGHK.IA.FLL..GADVNRKSVKGNTALHDCAESGSL.IM.MLL...A.M
Retrocopy RADMEVANRHGHTCLMISCYKGHKEIAKFLLDRGADVNRKSVKGNTALHDCAESGSLDIMKMLLKCDAHM

Parental  EQDGYGMTPLLSASVTGHTNIVEYLTMHEQTRHTARIDALELLGATFVDKKRDLLGALKYWKRAMDLRY-
          E.DGYGMTPLL.ASVTGH.NIV..L.....T....R..ALELLGAT.VDKKRDLLGA..YW..AM.LR..
Retrocopy ERDGYGMTPLLAASVTGHANIVVHLVHQTRTSREERVNALELLGATSVDKKRDLLGAMRYWRWAMELRHP

Parental  MDSNNVVHKPEPKQLIMAYDYAKEVTNGEELDGLISDPDEMRMQALLIRERILGPQHPDTSYYIRYRGAV
          ........KP.P...I.AY..A.EV...EEL..LI.DPDEMRMQALLIRERILGP.HPDTSYYIRYRGAV
Retrocopy VYITESLAKPPPGPPIPAYGCAQEVNTVEELEALITDPDEMRMQALLIRERILGPSHPDTSYYIRYRGAV

Parental  YADSGNFERCINLWKYALDMQQSNLDPLSPMTASSLLSFAELFSFMLQDRAKGLLGTSISFEDLMGILSK
          YADSGNFERCI.LWKYALDMQQSNLDPLSPMTASS.LSFAELFSF.LQDRAKG...T.I.F.DLM..L.K
Retrocopy YADSGNFERCISLWKYALDMQQSNLDPLSPMTASSFLSFAELFSFVLQDRAKGTMSTRITFSDLMTVLAK

Parental  GVLEIERAVKHSGPTALDPAQLSKALSIILHLICLLEKVPCTAEQDHFKKETIYRFLKLQPCGKNGYSPL
          .V.E.ERA...S........Q..KALSIILHLI.LLEK..C..EQ.H.KK.T.YR.LKL.P.G..G..PL
Retrocopy SVREVERAMAQS-DNLPEASQFTKALSIILHLIFLLEKLDCSPEQEHQKKHTLYRLLKLNPRGRSGFTPL

Parental  HLAVDRNTTCVGRYPVCKFPSLTVASILLECGADVNSRDNDDNSPLHIAASNGHPDIMNLLISSGSHFDS
          H.AVD..TT.VGRYPV..FPS..VA.ILLECGAD..SRD.D.N.PLHIAA.N..P.IM.LLI..G.HFD.
Retrocopy HMAVDKETTSVGRYPVGRFPSPAVAAILLECGADIDSRDYDNNTPLHIAAGNSSPEIMALLIKAGAHFDA

Parental  TNAFQQTPCDLLDAKELSRNVIQPINHTTLQCLAARTIIKHSLSYQGNIPEKLEAFILLH
          .NA.......LLD........I.P.N..TLQCLAAR.I.KH.L.Y.G.I.E..EAFI.LH
Retrocopy KNAQRKMAYELLDEQSSGHPSIYPLNYVTLQCLAARAIEKHRLPYRGLISEEMEAFIELH

Legend:

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

Expression

RNA-Seq

Tetraodon nigroviridis was not studied using RNA-Seq expression data.

ChIP-Seq

Tetraodon nigroviridis was not studied using ChIP-Seq data.

EST

Tetraodon nigroviridis was not studied using EST data.

TSS

Tetraodon nigroviridis was not studied using FANTOM5 data.

Lab

retro_tnig_27 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_tnig_27 has 3 orthologous retrocopies within teleost group .

Species	RetrogeneDB ID
Gasterosteus aculeatus	retro_gacu_12
Oryzias latipes	retro_olat_3
Takifugu rubripes	retro_trub_16

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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,