RetrogeneDB ID: retro_trub_32

Retrocopy location

• Organism: Fugu rubripes (Takifugu rubripes)
• Coordinates: scaffold_210:382128..383775(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSTRUG00000008859
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: DSE
• Ensembl ID: ENSTRUG00000006239
• Aliases: None
• Description: None

Sequence

>retro_trub_32
CACCCCAACCTTTATTTCAGCCCGGAGGACGTGCTGCTCCTGAGGCAGAGGTCGTCCACCACCCACAGCCACATATTCAA
AGTCGTGCGGTTGGCGGTGCTCACCATGCTCGCCAACGTCCCCTTCTACATGCCGCCGGCGAAACACGAGGATTTTACGA
GCAAATGGAACGAGATTTACGGCAACAACCTGCCCCCCCTGGCTCTCTACTGCCTGCTGTGCCCAGAGGACTCTGCCGCT
CTGCAGTTTCTCCTCAAATTTATGGACAGGATGGCCGAGTACCCGGACTGGAAGGTGACCAGCGCGCCCAACGACGAGGT
CCCCACAGCGCATTCCCTCACTGGATTCGCCACCGCGTACGACTTCGTCTACAGCTACCTGGACGAGCAGCGCAGGAAAG
TTTACCTCAAGAAAATCCGCTCCGAGACGGAGGAGCTGTATGAGCTGTCAAAGCACCGGGGGTGGGGCAAGCAGTATCTC
CAGAATCATCAGACCACCAACATACTGGCTGTCCTGACTGGTGCCATCGTAGTGGGATCACACAAAGACCCAGAGTCCAT
GTTGTGGAAGCAGGTGGCGGTGAACTACATGGAGAAAACCATGTTTCTTCTCAATCACGTGGTGGACGGCTCGCTGGATG
AGGGGGTCGCCTATGGGAGCTACACGGCCAAGTCTGTCACCCAGTATGTTTTCCTAGCGCAGCGCCACTTTGATATCGAC
AATCTTCAGAACAACTGGCTGCGGGGCCACTTCTGGTTCTATTACGCCACCCTGTTGCCAGGGTTTCAGCGGAGCGTCGG
CATCGCAGACTCCAACTACAACTGGTTCTATGGGCCGGAGAGCCAGCTCGTTTTTCTCGACTCCTTCGTCATGAGGAACG
GGACGGGGAACTGGTTGGCCCAGCAGATCAGGAAACACCGGCCCAAGGACGGACCCATGGGACAATCCTCTGCCCAGCGC
TGGGCGACGCTTCACACCGAGTACATCTGGTACAACCAGCACCTCACACCGCAGCCCCCACAGGACTTTGGGAAAGCCAG
GATGCATATTTTCTCTAACTGGGGTGTGGTTACCTACGGAGCGGGGCTGCCCAGCAGTCAGGGTAATACTTTTCTCTCCT
TTAAGTCCGGCAAGCTGGGTGGCCGTGCTGTCTACGACATCGTCCATGACAAGCCTTATTCCTGGGTGGAGGGCTGGAAC
AGCTTTAATCCGGGCCACGAGCACCCTGACCAGAACTCTTTCACTTTCGCCCCTAATGGGCAGGTGTTTGTGTCTGAAGC
ACTTTACGGACCCAAGTACAGCTATCTCAACAATGTTCTGGTTTTCAGCCCATCGCCCACCAGCCAGTGTAACAACCCCT
GGGAGGGGCAGTTAGGGGAATGTGCTAAGTGGCTTCGCTGGACCGATGATGGTGTGGGTGACGCCAGAGGGGAGGTGATC
GTGGCCTCTTCGCATAGTGACATGATGTTTGTGAGCGGCGAGGCGGCGTTGGCTTACTCCCCCGCCATGAGGCTAAAGAG
TGTATTCCGGGCTTTAGTTCTGCTAAACTCTCAGACGCTGCTGGTGCTGGACCATGTGGAGAAGTTTGGAGACTCGCCCC
TCTCGTCTCTGAGCGCGTTTTTCCACAACCTTGACATCGACTTTAAG

Alignment

ORF - retro_trub_32 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.72 %
• Parental protein coverage: 87.62 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  HPMLYFSRGDVEEMQYAAAGTHRDMAKRIRDAGEAMLEHPEEYLPPWSPAEFTARWNEVYGNNLGVLSMF
          HP.LYFS..DV.........TH....K..R.A...ML.....Y.PP.....FT..WNE.YGNNL..L...
Retrocopy HPNLYFSPEDVLLLRQRSSTTHSHIFKVVRLAVLTMLANVPFYMPPAKHEDFTSKWNEIYGNNLPPLALY

Parental  CLLYPHRAGALDLVKDYMERMAAQPSWLVKDAPWDEVPLAHSLVGFATAYDFMHEYLNKDQQERFLQVIG
          CLL.P....AL......M.RMA..P.W.V..AP.DEVP.AHSL.GFATAYDF...YL........L..I.
Retrocopy CLLCPEDSAALQFLLKFMDRMAEYPDWKVTSAPNDEVPTAHSLTGFATAYDFVYSYLDEQRRKVYLKKIR

Parental  NASRLMYEKSYVRGWGFQYLHNHQPTNCVALLTGSLVYMTQAKKEAYLWTKQVLSIMEKSMVLLQDVTDG
          ......YE.S..RGWG.QYL.NHQ.TN..A.LTG..V.......E..LW.......MEK.M.LL..V.DG
Retrocopy SETEELYELSKHRGWGKQYLQNHQTTNILAVLTGAIVVGSHKDPESMLWKQVAVNYMEKTMFLLNHVVDG

Parental  SLYEGVAYGTYTTRSLFQYMFLVQRHFAIGHFRHPWLLKHFAFLYRTILPGFQRTVAIADSNYNWFYGPE
          SL.EGVAYG.YT..S..QY.FL.QRHF.I......WL..HF.F.Y.T.LPGFQR.V.IADSNYNWFYGPE
Retrocopy SLDEGVAYGSYTAKSVTQYVFLAQRHFDIDNLQNNWLRGHFWFYYATLLPGFQRSVGIADSNYNWFYGPE

Parental  SQLVFLDRYVMRNGSGNWLADLIHQNRVMEGPGQAGKGQRWCTLHTEFIWYDPGLIPKPPSDFGTSQLHY
          SQLVFLD..VMRNG.GNWLA..I...R...GP......QRW.TLHTE.IWY...L.P.PP.DFG....H.
Retrocopy SQLVFLDSFVMRNGTGNWLAQQIRKHRPKDGPMGQSSAQRWATLHTEYIWYNQHLTPQPPQDFGKARMHI

Parental  FEDWGVVTYGSALPADTNRTFLSFKSGKLGGRAIYDIVHRNKYKEWVKGWRNFNAGHEHPDQNSFTFAPN
          F..WGVVTYG..LP.....TFLSFKSGKLGGRA.YDIVH...Y..WV.GW..FN.GHEHPDQNSFTFAPN
Retrocopy FSNWGVVTYGAGLPSSQGNTFLSFKSGKLGGRAVYDIVHDKPY-SWVEGWNSFNPGHEHPDQNSFTFAPN

Parental  GVPFVAEALYGPKYTLLNNVVLFGSSVSDSCFKPWAGQVTETCDSKWLKYKVGQAADTQGRVEAAMRREG
          G..FV.EALYGPKY..LNNV..F..S....C..PW.GQ..E....KWL........D..G.V..A.....
Retrocopy GQVFVSEALYGPKYSYLNNVLVFSPSPTSQCNNPWEGQLGEC--AKWLRWTDDGVGDARGEVIVASSHSD

Parental  MVFIRGEGHSAYNPELKIRNFQRNLLLLHPQLLLLVDHIHLQTDSPTRAMSAFFHNTDLPFQ
          M.F..GE...AY.P........R.L.LL..Q.LL..DH.....DSP....SAFFHN.D..F.
Retrocopy MMFVSGEAALAYSPAMRLKSVFRALVLLNSQTLLVLDHVEKFGDSPLSSLSAFFHNLDIDFK

Legend:

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

Expression

RNA-Seq

Takifugu rubripes was not studied using RNA-Seq expression data.

ChIP-Seq

Takifugu rubripes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_trub_32 retrocopy.

TSS

Takifugu rubripes was not studied using FANTOM5 data.

Lab

retro_trub_32 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_trub_32 has 0 orthologous retrocopies within teleost group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000013791	1 retrocopy	retro_acar_15,
Callithrix jacchus	ENSCJAG00000004530	1 retrocopy	retro_cjac_1174,
Homo sapiens	ENSG00000111817	1 retrocopy	retro_hsap_4178,
Gorilla gorilla	ENSGGOG00000026746	2 retrocopies	retro_ggor_1419, retro_ggor_2802,
Nomascus leucogenys	ENSNLEG00000013106	1 retrocopy	retro_nleu_2476,
Pongo abelii	ENSPPYG00000016948	2 retrocopies	retro_pabe_3418, retro_pabe_3517,
Pan troglodytes	ENSPTRG00000018529	1 retrocopy	retro_ptro_2833,
Sorex araneus	ENSSARG00000010799	1 retrocopy	retro_sara_560,
Takifugu rubripes	ENSTRUG00000006239	1 retrocopy	retro_trub_32 ,
Xenopus tropicalis	ENSXETG00000032776	1 retrocopy	retro_xtro_8,