RetrogeneDB ID: retro_ttru_1397

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: scaffold_112278:83072..84536(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: SMEK2
• Ensembl ID: ENSTTRG00000000027
• Aliases: None
• Description: SMEK homolog 2, suppressor of mek1 (Dictyostelium) [Source:HGNC Symbol;Acc:29267]

Sequence

>retro_ttru_1397
ATGGTGGGCAACCAGCGCTACGTAAAAGTCTACACCCTGAAAGATGAACAACAGTGGGTCATTCTAGACACAGGGTACAT
CTCATCCACTTATGAGGAGGGGGCCCAGGCCATGTTTCTGCTAGTTAGATCCAAGTCCGATGACTCACTGATCTTGGAGT
CAAAGATAAATCCAGACATGTACTATGAGAAAGATGGAACGTTAATTTTTTGGTTTGAGGCTGAGAACCGTGGTACAGCG
ATACATTTCCAGGACACGGCAATTTGTCATAAGGTCTGGAAAGCCATTTGCCAGGTTCACAGTAAAGTCCCATGTGTCGA
AACTATACATGACATCATGGATGAATCAGAAGCCAAAGAGGGTGATGACTCGCCAAAAACCAGTGAACTGCTCGACCTGC
CAAACTGCAAACTCGATAAACTTGGAGAGATTGTTGACTTAGTTACCTTGAGTCTCACCTCACCTATGGATAAAGAACTC
CTGGCTCTGCTCTTGGAAAGGGAGGACTATATTCAAAAACTACTGCAGTTGTTCCACACTTGTGAGAACCTAGAGTATAC
TGAAGGCTTATACCATTTGCATGAAATTATTAAAGGAATCTTATTCCTCGACAATACATCTCTGTTTGAGATCCTGTTTT
CTGATGAGTGTATCATGGATGTGGTGGGATGCCTTGAATATGACCCTGCTTTGGCTCAGCCAAAAAGGCATAGGGAATTC
TTAACCCAAAATGCACACTTCAGGGAAGTTATACCAATAACAGACAGTGAAATTCGACAAAAAATACATCAGACATACAG
GGTACAGTACATTCACGACATCCTTTTGCCTATACCATCCAAGTTTCAAGACAATATTCTTCCTAATCTTACAAGTTTTA
TTTTTTTTAACAAGGTTGAGCTAGTCAACATGTTGCAGGAAGATGACGAGTATTTGGCTGAAGTTTTTGCACAGATGAGG
GATGAGACCACAGATGATGATAAACGGCGTGACCTGGTATTTTTTTTAAAGGAATTCTGTGTATTTTCTCATCTATTACG
TTCTGAAAGCAGGTGTGCACTATTCACAACACTGACAGAATTGGGAATTCTTCCTGCTCTTAAAATTGTAATGGGCATGG
ATGATTTGCAAATAAGGTTAGCTGCTACTGATATACTTGGTGATCTAGTGAAGTATACTCCATTCATTGTCCAAAGATTT
ATGATGGACGAAGCCCAGCAAAGTGAAGATGGCAAACTTTTCACTAATTTAATAATTGAAAAAATGATCTGTGATACTGA
CTCTGAGCTAGGAGGTGCTGTTCATTTAATGAGACTTCTTCGTGCTCTACTTGATCCAGACAACATGCTGCCAACACATA
GAAAATGTAAAAGAAGTGAATTTCTAAATTTCTTCTATAGACATTGTATACATAACTTCACAGCACCACTTTTGTCAGCT
ACTTCAGAAGATATATGTGAAGAG

Alignment

ORF - retro_ttru_1397 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.99 %
• Parental protein coverage: 58.28 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSDTRRRVKVYTLNEDRQWDDRGTGHVSSTYVEELKGMSLLVRAESDGSLLLESKINPNTAYQKQQDTLI
          M....R.VKVYTL....QW....TG..SSTY.E....M.LLVR..SD.SL.LESKINP...Y.K...TLI
Retrocopy MVGNQRYVKVYTLKDEQQWVILDTGYISSTYEEGAQAMFLLVRSKSDDSLILESKINPDMYYEKD-GTLI

Parental  VWSEAENYDLALSFQEKAGCDEIWEKICQVQGKDPSVEVTQDLIDESEEERFEEMPETSHLIDLPTCELN
          .W.EAEN...A..FQ..A.C...W..ICQV..K.P.VE...D..DESE.......P.TS.L.DLP.C.L.
Retrocopy FWFEAENRGTAIHFQDTAICHKVWKAICQVHSKVPCVETIHDIMDESEAKEGDDSPKTSELLDLPNCKLD

Parental  KLEEIADLVTSVLSSPIRREKLALALENEGYIKKLLQLFQACENLENTEGLHHLYEIIRGILFLNKATLF
          KL.EI.DLVT..L.SP...E.LAL.LE.E.YI.KLLQLF..CENLE.TEGL.HL.EII.GILFL....LF
Retrocopy KLGEIVDLVTLSLTSPMDKELLALLLEREDYIQKLLQLFHTCENLEYTEGLYHLHEIIKGILFLDNTSLF

Parental  EVMFSDECIMDVVGCLEYDPALAQPKRHREFLTKTAKFKEVIPITDSELRQKIHQTYRVQYIQDIILPTP
          E..FSDECIMDVVGCLEYDPALAQPKRHREFLT..A.F.EVIPITDSE.RQKIHQTYRVQYI.DI.LP.P
Retrocopy EILFSDECIMDVVGCLEYDPALAQPKRHREFLTQNAHFREVIPITDSEIRQKIHQTYRVQYIHDILLPIP

Parental  SVFEENFLSTLTSFIFFNKVEIVSMLQEDEKFLSEVFAQLTDEATDDDKRRELVNFFKEFCAFSQTLQPQ
          S.F..N.L..LT.....NKVE.V.MLQED...L.EVFAQ..DE.TDDDKRR.LV...KEFC.FS..L...
Retrocopy SKFQDNILPNLTXXXXXNKVELVNMLQEDDEYLAEVFAQMRDETTDDDKRRDLVXXXKEFCVFSHLLRSE

Parental  NRDAFFKTLAKLGILPALEIVMGMDDLQVRSAATDIFSYLVEFSPSMVREFVMQEAQQSDDDILLINVVI
          .R.A.F.TL..LGILPAL.IVMGMDDLQ.R.AATDI...LV...P..V..F.M.EAQQS.D..L..N..I
Retrocopy SRCALFTTLTELGILPALKIVMGMDDLQIRLAATDILGDLVKYTPFIVQRFMMDEAQQSEDGKLFTNLII

Parental  EQMICDTDPELGGAVQLMGLLRTLIDPENMLATTNKTEKSEFLNFFYNHCMHVLTAPLLTNTSEDKCEK
          E.MICDTD.ELGGAV.LM.LLR.L.DP.NML.T..K...SEFLNFFY.HC.H..TAPLL..TSED.CE.
Retrocopy EKMICDTDSELGGAVHLMRLLRALLDPDNMLPTHRKCKRSEFLNFFYRHCIHNFTAPLLSATSEDICEE

Legend:

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

Expression

RNA-Seq

Tursiops truncatus was not studied using RNA-Seq expression data.

ChIP-Seq

Tursiops truncatus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ttru_1397 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_1397 was not experimentally validated.

Homology

Retrocopy orthology:

Tursiops truncatus 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 19 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000003843	1 retrocopy	retro_amel_48,
Bos taurus	ENSBTAG00000000545	1 retrocopy	retro_btau_232,
Canis familiaris	ENSCAFG00000002860	1 retrocopy	retro_cfam_226,
Equus caballus	ENSECAG00000013819	1 retrocopy	retro_ecab_23,
Echinops telfairi	ENSETEG00000002420	1 retrocopy	retro_etel_1699,
Felis catus	ENSFCAG00000026457	1 retrocopy	retro_fcat_13,
Homo sapiens	ENSG00000138041	1 retrocopy	retro_hsap_4799,
Loxodonta africana	ENSLAFG00000017825	1 retrocopy	retro_lafr_791,
Myotis lucifugus	ENSMLUG00000003875	1 retrocopy	retro_mluc_994,
Macaca mulatta	ENSMMUG00000007001	1 retrocopy	retro_mmul_238,
Mustela putorius furo	ENSMPUG00000002435	1 retrocopy	retro_mputfur_92,
Nomascus leucogenys	ENSNLEG00000009338	1 retrocopy	retro_nleu_1112,
Oryctolagus cuniculus	ENSOCUG00000006880	1 retrocopy	retro_ocun_9,
Otolemur garnettii	ENSOGAG00000009837	1 retrocopy	retro_ogar_140,
Pan troglodytes	ENSPTRG00000011933	1 retrocopy	retro_ptro_3191,
Sus scrofa	ENSSSCG00000008398	1 retrocopy	retro_sscr_1187,
Ictidomys tridecemlineatus	ENSSTOG00000006276	1 retrocopy	retro_itri_63,
Tursiops truncatus	ENSTTRG00000000027	1 retrocopy	retro_ttru_1397 ,
Tursiops truncatus	ENSTTRG00000013598	1 retrocopy	retro_ttru_1398,