RetrogeneDB ID: retro_itri_63

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393363.1:3783765..3786117(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSTOG00000025431
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: SMEK2
• Ensembl ID: ENSSTOG00000006276
• Aliases: None
• Description: SMEK homolog 2, suppressor of mek1 (Dictyostelium) [Source:HGNC Symbol;Acc:29267]

Sequence

>retro_itri_63
ATGGCGAGTAAGCGGAATTGTGTAAAGGTCTATGTGCTGAAAGAAGATCAACAATGGGGCCAGCTGGGCATGGGACAAAT
CTCCTCAAGTTACATAGAGCGCCTCCAAAGCGTGTGTCTGCTTGTTCGGTCAGAGTCTGATGGCTCACTGATTTTACAGT
CCAAGATACACCCAAACGTGCCCTATCAGAAACAACAGGGTGTGTTAATTGTTTGGTCTGAAGATGAGAACCATGGTGTG
GCACTAAGTTTCCAGGATCCAGCAGGCTGTCGAGAGATCTGGGAAGACATATGCCAAGTCCAAGGTAAAGACCCAACTGT
TGAAATCACACAAGATCTTTTGGATGGACCAGACCAATTTGATGAAATGCCATCAACCAGTAGTCTGGTTGAGCTGCCGA
ACTGTGAACTCCATACACTTGAAGAAATAGCTGATCTGTTTACTTCTGTCCTTGCTTCACCTATACGTAAAGAAAGGTTG
GCACTGATCTTGGAAAATGAAGATTATATTAAAAAACTACTGCAAATATTTCACATTTGTGAGAACCTAAAGAACATTGA
AGGCTTACATAACTTGCACAAAATTATTAAAGGCATCTTATTCCTCAACAAAACTCCTCTGTTTGAGATCATGTTTTCTG
ATGAGTGTATCATGGATGTGGTGGGATGCCTTGAATATGACCCTGCCTTGACTCAGCCAAAAAGGTATAGGGAATTCTTG
ACCCAAAATGTAAAGTTCAAGGAAGTTATGCCAATAAAAGACTCTAAACTTAGGCAAAAAATACATCAGACCTACAGAGT
GCAGTACATTCATGATATTCTTTTTCCTATACCATCCATATTTGAAGAGAATCTTCTCTCTACTCTTACAACTTTTATTT
TCTTCAACAAGGTTGAGATAGTCAGCATGCTGCTGGAAGATGATGTGTTTTTGTTTGAAGTTCTTGCACAGTTAAGGGAT
AAGACTACAGATGAAAATAAACGACGTGAATTATTATTTTTTTTCAAGGAATTCTGTGGGTTTTCCCAGACACTGCAGCC
TCAAAGCAAGGATGCTTTATTCACAACATTGTTACAACTGGGAATTCTTTCTGCTCTTAAAATTTTAATGAGCATGGATG
ATTTCCAAGTAAAGATAACAGCTACAGATATTTTTGCTTATCTGGTAGAGTATAGTCCATCTATGATCCGAATATTTGTA
ATGGAGGAAGCTCAGGATGGTGAAGATGATGAACTTTTTATTAATGTAGTAATTGAACAAATGATCAGTGATACTGATCC
TGAACTTGGAGGTGCCATTAATTTGATGGGACTTCTTCGTTCTCTACTTGATGTGGACAACATGCTGCTAGTACCCAATG
AATGTGAAAAAAGTGAATTTCTAAATTTCTTCTATAGACGTTGCATGCATAATTTGATAGCACCAATTTTGTCTACCACT
TCAGAAGACAGAGATGAAGAGGATTATTTATTTGGACCTGACAAAAACAAAAATTGTCTCAATAATTATCAAACAGTACA
GCTGCTTAGTTTAATTATAGAACTACTCACATTTTGTGTACAACATCACACATATCACATTAAAAACTACATATTGAGCA
AAGACTTGCTAAGAAGAGTCTTGATGTTGATGAATTCAAAGCACACGTTCCTGATCTTATCTGCTGTTCGTTTTATGAGA
AGGATGATTGGTCTTAAAGATGAACTTTATAATCGTTACATCATCAAGGGAAATCTTTTTGATCCAGTTGTAAATGCATT
TCTGATTAATGGAACTCGGTACAATATGCTAAATTCGGCTATTATTGAGCTATTTGAATATATACGAGTGGAAAATATCA
AGTCTCTTGTTGCACATATAGTTGAAAAGTTTTACAAGGCTTTTGAATTGATTGAATATGTTCAGACATTCAAAGGATTG
AAGATTAAATATGAACAAGAGAAAGACAGACAAAATCAAATAAGGAAGAATTTACATTCTATACTATATATTAAAATTTT
TTGCAGAGATGCCAATGGCATGGAGGAGGTGAAGGCTGATATGTATTTTAAGGAAAATACCACAGATGTACTTATGCCAC
CAATGGAAAATGAATTTCCAGATCATTATGATACATCTATAGATACTAAAATACCAAAAGAAAATGGAGAAAAGGTAGAC
CTTCTCAAAAGAACATCTTCCAGTGAATTCAGAATTTCTTCATCTAGCTCTCCTGATTCTGAGGATGAAATGAGTACACC
ATCCAGTAGCAGTTTGGTTGGTTTAGTGGATTATCCAGATGATGATAATGAAGAAGAAGATAAGGAAGAAGATAAAGCAT
CCCCCAGAAAGAGACCTCATCTTGACTTATAA

Alignment

ORF - retro_itri_63 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.25 %
• Parental protein coverage: 86.13 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSDTRRRVKVYTLNEDRQWDDRGTGHVSSTYVEELKGMSLLVRAESDGSLLLESKINPNTAYQKQQANDT
          M...R..VKVY.L.ED.QW...G.G..SS.Y.E.L....LLVR.ESDGSL.L.SKI.PN..YQKQQ....
Retrocopy MASKRNCVKVYVLKEDQQWGQLGMGQISSSYIERLQSVCLLVRSESDGSLILQSKIHPNVPYQKQQG--V

Parental  LIVWSEAENYDLALSFQEKAGCDEIWEKICQVQGKDPSVEVTQDLIDESEEERFEEMPETSHLIDLPTCE
          LIVWSE.EN...ALSFQ..AGC.EIWE.ICQVQGKDP.VE.TQDL.D......F.EMP.TS.L..LP.CE
Retrocopy LIVWSEDENHGVALSFQDPAGCREIWEDICQVQGKDPTVEITQDLLDGPDQ--FDEMPSTSSLVELPNCE

Parental  LNKLEEIADLVTSVLSSPIRREKLALALENEGYIKKLLQLFQACENLENTEGLHHLYEIIRGILFLNKAT
          L..LEEIADL.TSVL.SPIR.E.LAL.LENE.YIKKLLQ.F..CENL.N.EGLH.L..II.GILFLNK..
Retrocopy LHTLEEIADLFTSVLASPIRKERLALILENEDYIKKLLQIFHICENLKNIEGLHNLHKIIKGILFLNKTP

Parental  LFEVMFSDECIMDVVGCLEYDPALAQPKRHREFLTKTAKFKEVIPITDSELRQKIHQTYRVQYIQDIILP
          LFE.MFSDECIMDVVGCLEYDPAL.QPKR.REFLT...KFKEV.PI.DS.LRQKIHQTYRVQYI.DI..P
Retrocopy LFEIMFSDECIMDVVGCLEYDPALTQPKRYREFLTQNVKFKEVMPIKDSKLRQKIHQTYRVQYIHDILFP

Parental  TPSVFEENFLSTLTSFIFFNKVEIVSMLQEDEKFLSEVFAQLTDEATDDDKRRELVNFFKEFCAFSQTLQ
          .PS.FEEN.LSTLT.FIFFNKVEIVSML.ED..FL.EV.AQL.D..TD..KRREL..FFKEFC.FSQTLQ
Retrocopy IPSIFEENLLSTLTTFIFFNKVEIVSMLLEDDVFLFEVLAQLRDKTTDENKRRELLFFFKEFCGFSQTLQ

Parental  PQNRDAFFKTLAKLGILPALEIVMGMDDLQVRSAATDIFSYLVEFSPSMVREFVMQEAQQSDDDILLINV
          PQ..DA.F.TL..LGIL.AL.I.M.MDD.QV...ATDIF.YLVE.SPSM.R.FVM.EAQ...DD.L.INV
Retrocopy PQSKDALFTTLLQLGILSALKILMSMDDFQVKITATDIFAYLVEYSPSMIRIFVMEEAQDGEDDELFINV

Parental  VIEQMICDTDPELGGAVQLMGLLRTLIDPENMLATTNKTEKSEFLNFFYNHCMHVLTAPLLTNTSEDKCE
          VIEQMI.DTDPELGGA..LMGLLR.L.D..NML...N..EKSEFLNFFY..CMH.L.AP.L..TSED..E
Retrocopy VIEQMISDTDPELGGAINLMGLLRSLLDVDNMLLVPNECEKSEFLNFFYRRCMHNLIAPILSTTSEDRDE

Parental  KDNIVGSNKNNTICPDNYQTAQLLALILELLTFCVEHHTYHIKNYIMNKDLLRRVLVLMNSKHTFLALCA
          .D...G..KN...C..NYQT.QLL.LI.ELLTFCV.HHTYHIKNYI..KDLLRRVL.LMNSKHTFL.L.A
Retrocopy EDYLFGPDKNKN-CLNNYQTVQLLSLIIELLTFCVQHHTYHIKNYILSKDLLRRVLMLMNSKHTFLILSA

Parental  LRFMRRIIGLKDEFYNRYITKGNLFEPVINALLDNGTRYNLLNSAVIELFEFIRVEDIKSLTAHIVENFY
          .RFMRR.IGLKDE.YNRYI.KGNLF.PV.NA.L.NGTRYN.LNSA.IELFE.IRVE.IKSL.AHIVE.FY
Retrocopy VRFMRRMIGLKDELYNRYIIKGNLFDPVVNAFLINGTRYNMLNSAIIELFEYIRVENIKSLVAHIVEKFY

Parental  KALESIEYVQTFKGLKTKYEQEKDRQNQKLNSVPSILRSNRFRRDAKALEE-DEEMWFNEDEEDEGKAVV
          KA.E.IEYVQTFKGLK.KYEQEKDRQNQ......SIL....F.RDA...EE....M.F.E...D......
Retrocopy KAFELIEYVQTFKGLKIKYEQEKDRQNQIRKNLHSILYIKIFCRDANGMEEVKADMYFKENTTD---VLM

Parental  APVEKSKPD
          .P.E...PD
Retrocopy PPMENEFPD

Legend:

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

Expression

RNA-Seq

Ictidomys tridecemlineatus was not studied using RNA-Seq expression data.

ChIP-Seq

Ictidomys tridecemlineatus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_itri_63 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_63 was not experimentally validated.

Homology

Retrocopy orthology:

Ictidomys tridecemlineatus 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 18 parental genes, and 18 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,