RetrogeneDB ID: retro_etel_1699

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_288185:50722..52175(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSETEG00000003821
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SMEK2
• Ensembl ID: ENSETEG00000002420
• Aliases: None
• Description: SMEK homolog 2, suppressor of mek1 (Dictyostelium) [Source:HGNC Symbol;Acc:29267]

Sequence

>retro_etel_1699
TCTTTGATTGTTTGGTGTAAAGCCGAGGGCCAAGGAGTGGCTATCAGTTTCCATGAGTCCGCATGCTGTGAGGCAGTCTG
GGAAGACACTTGCCATGCTCAGGGCAAAGATGCTTCTCTCCACACCACACAAGACCCGTCAGACAACTCAGAACAGCAAC
TTCTATGATGTGCCAGATACTAGTTGCTTGAGTAGATCTGCCCAACTGTGAAATCTCCAAACTTGAGCACATTGCGCAAA
TAGCTCACTCGGCTCTTGACTCACCTGCCCTTAAGGAAAAGCTAGCTCTGGCCTCGGAAAAAGAAAACTATATTAAAAAA
TTACTGCAGCTGTTCCATGTTTGCGAGCTTCTTGGTAACCCTAAAAACTTACACCATATGTATGACATTTTTAAAGCAAT
CTTATTCCTCAACAAGACATCTCTGTTTGAGATCATGTTTTCCGATGCTTGCATCATGGATGTAGTGGGATGCCTTGAAT
ACGACCCTACCGTGCGTGAGCCCATAAGGCATAGGGAATTTTTGTTTCAAACAGCACATTTCAGGGAAGTTGTACCAATC
TCAGACTCTGAATTAAGAAAAAAATACATCAGACCTACAGGGCCCAGTATATTTATGATCTCCTATTGCCTCTACCACCC
ATGTTTGAAGCGAATGTTCTTTCTACTATTAGTAGTTTTATTTTCTTCAACAAGATTGAGATAGTCAGCTTACTGCAGGA
AGATGAAAAGTTTTTGTGTGAAGTTTTTGCACAGTTAACAGATAAGGGTACCGCTGATATTAAGCGGTGCGAATTGTTGT
TTTTCCTTAAGGAATTCTGTGCCTTTTCTAAGACATTACAAAATCAAAGCAGAGATGAATTATTGGCAACGATGGCAAAG
TTGGGAATTCTTCCTGCTCTTAAAATTGCAATGGGCATGAATCATTTGAAGATAAGATCTGCTGCTGCAGATATATTTGC
TTATCTAGTAGAGTACAGCCCATCCATAATACGAAAATATACAATCCAAGAAGCCAAGCACGTTGAACAAGGGAACCTTT
TTATTAATATAATAATTAAACAAATGATCTATGATCCTGATCCTGAGCTAGGAGGTGCTCTTCAATTAATGGGACTTCTC
TGTTCTATTCTTGATCCAAGCAACATGCTGGCTGTACCTAGTGAATATGGAAGAGGTGCGTTTCTAAATTTCTTTTACAA
GCACTGCATGCATGTCTTGATAGGGCCACTTTGCACCACCATATCAGAAGATAAATGTGAGAACACTATAGTTATATCTA
ATGAAAATTGTGCCACTGATTATCAAACAGCACAAATGCTTTCCATAATTGTAGAGCTGCTCACCTTTTGTGTACAACAC
CATGCCCATTACATTAATAATTATATTTTGAACAAAGACTTGCTAAGGCAAGTCTTGACCTTGATGAAGTCAAAGCACAC
TTTCCTGATCTTG

Alignment

ORF - retro_etel_1699 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.37 %
• Parental protein coverage: 61.65 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  TLIVWSEAENYDLALSFQEKAGCDQIWEKICQVQGKDPSVEVTQDLIDESEEER-FEEMPETSHL-IDLP
          .LIVW..AE....A.SF.E.A.C...WE..C..QGKD.S...TQD..D.S.E...F...P.TS.L..DLP
Retrocopy SLIVWCKAEGQGVAISFHESACCEAVWEDTCHAQGKDASLHTTQDPSDNS-EQQ>FYDVPDTSCL>VDLP

Parental  TCELNKLEEIADLVTSVLSSPIRREKLALALENEGYIKNLLRLFQACENLENTEGLHHLYEIMRGILFLN
          .CE..KLE.IA....S.L.SP...EKLALA.E.E.YIK.LL.LF..CE.L.N...LHH.Y.I...ILFLN
Retrocopy NCEISKLEHIAQIAHSALDSPALKEKLALASEKENYIKKLLQLFHVCELLGNPKNLHHMYDIFKAILFLN

Parental  KATLFEVMFSDECIMDVVGCLEYDPALAQPKRHREFLTKTAKFKEVIPITDSELRQK-IHQTYRVQYIQD
          K..LFE.MFSD.CIMDVVGCLEYDP....P.RHREFL..TA.F.EV.PI.DSELR.K.IHQTYR.QYI.D
Retrocopy KTSLFEIMFSDACIMDVVGCLEYDPTVREPIRHREFLFQTAHFREVVPISDSELRKK<IHQTYRAQYIYD

Parental  IILPTPSVFEENFLSTLTSFIFFNKVEIVSMLQEDEKFLSEIFAQLTDEATDDDKRRELVNFFKEFCAFS
          ..LP.P..FE.N.LST..SFIFFNK.EIVS.LQEDEKFL.E.FAQLTD..T.D.KR.EL..F.KEFCAFS
Retrocopy LLLPLPPMFEANVLSTISSFIFFNKIEIVSLLQEDEKFLCEVFAQLTDKGTADIKRCELLFFLKEFCAFS

Parental  QTLQPQNRDAFFKTLAKLGILPALEIVMGMDDLQVRSAATDIFSYLVEFSPSMVREFVMQEAQQSDDDIL
          .TLQ.Q.RD....T.AKLGILPAL.I.MGM..L..RSAA.DIF.YLVE.SPS..R....QEA........
Retrocopy KTLQNQSRDELLATMAKLGILPALKIAMGMNHLKIRSAAADIFAYLVEYSPSIIRKYTIQEAKHVEQGNX

Parental  LINVIIEQMICDTDPELGGAVQLMGLLRTLIDPENMLATNNKTEKSEFL-FFY-HCMHVLTAPLLANTSE
          .......QMI.D.DPELGGA.QLMGLL....DP.NMLA.........FL.FFY.HCMHVL..PL....SE
Retrocopy XXXXXXXQMIYDPDPELGGALQLMGLLCSILDPSNMLAVPSEYGRGAFLNFFYKHCMHVLIGPLCTTISE

Parental  DKCEKDNIVGANKNNTICPDNYQTAQLLALILELLTFCVEHHTYHIKNYIMNKDLLRRVLVLMNSKHTFL
          DKCE...IV..N.N...C...YQTAQ.L..I.ELLTFCV.HH...I.NYI.NKDLLR.VL.LM.SKHTFL
Retrocopy DKCE-NTIVISNEN---CATDYQTAQMLSIIVELLTFCVQHHAHYINNYILNKDLLRQVLTLMKSKHTFL

Parental  AL
          .L
Retrocopy IL

Legend:

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

Expression

RNA-Seq

Echinops telfairi was not studied using RNA-Seq expression data.

ChIP-Seq

Echinops telfairi was not studied using ChIP-Seq data.

EST

Echinops telfairi was not studied using EST data.

TSS

Echinops telfairi was not studied using FANTOM5 data.

Lab

retro_etel_1699 was not experimentally validated.

Homology

Retrocopy orthology:

Echinops telfairi 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,