RetrogeneDB ID: retro_etel_1047

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_204051:3261..4405(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSETEG00000012610
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RCC1
• Ensembl ID: ENSETEG00000011999
• Aliases: None
• Description: regulator of chromosome condensation 1 [Source:HGNC Symbol;Acc:1913]

Sequence

>retro_etel_1047
CACAGAACCAAGCATGGTACTGCCACTGGGCAGGGAGCTGTGGGCCAGCTGGGGCTGGGGAAGAATGTGATCAAGAGGAA
GAGCCAGCGCTGGTGCCCATTCTTGAGGATGTCATCCAAGATGAGGCAGGGGCATGCACACCAGGTGTCAAAGAAAGACT
GGCCATATCTACTCCTTTTGCAGCAACTATGAGGTCGCTCTGGGAAGGACTACAACACTGGAAGGCTCGGAGAAGGTCCC
TGGGAACGTGGAACTGTAGGAGAAGGTGGTACAGGTATCAGCAGGAGGCAGCCACACAGAAACCCTCACCTAAGAGGGCC
GTGCCTTCCTCTGGGGCTCCTTCCGGGGCAATTACAGGGTCATTGGGCTCCTGCAGCCCTGCAGAAGAGCATGGTGCCGT
GCAAGTCCAGTTGGAGATGTCTGCGTTGCAAGGGCCCGCAGGGAATGACCACCTGGTCATGCTGACGGCTGGTGGTGACC
TCTAAACCTTGGCATGAGAAGAGGGCCAGTTCAGCTGAGTGCCTGAATTATTCGCTAACCGTGGTGTCTGGCCGGGTATT
GAACAGCTCCTCATCCTCAAGTCTGTGTTGCTGGAATCCAGGAGAATCCCGGGCTCCATGCACTTCCAGAATGTCTTCTG
CAGCACATACTTCACCTTCACTGTCTCCCAGGAAGCTCACATCTATGGCTTTGGTCTCTTTGGCTACCACCAACTTGGAA
CAGCAGACAAAGGCTCTTGTTTTGAACCCCAGTAACTGACATCGTCCCAGAACTCCACCATGTTCTGGGTGGGCTTCTCG
GGGGGCCAGCATCATATGCTCTGCGTGGATTTAGAAGAAGTATATCACCTGGCCCTGGCTGACTATGTGCGGCTGAGCCT
CAGGAGGGTGCTGAGGAAAAGAGCATGCCCTCCCTCATCCCCAGGCTGCCTGCTGTCTCCTCAGTGGCTTGCCGGGCCTC
TGTGGGGTATGCTATGACCAAGGAGGGCAGCGCTTTTGCCCAGGGCATGGGCACCAGCTACCAGCTGGGCACGGGGCAGA
ACGAGGACATCAGCAGCCGGGTGGAGATGACAGGCAACCAGTTGGAGAACCGAGTGGCCTTGTCTGTGCCAAGCAGGGGC
CAGCACACAGTCTTAGCAGTCAGA

Alignment

ORF - retro_etel_1047 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.36 %
• Parental protein coverage: 84.58 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  HNIELGKVLTLGGDVGLGLGENVMERK-KPALSSIPEDVIGAEAG-GMHTVCLSKTGQVYSFGCNDEGAL
          H....G.....G....LGLG.NV..RK..PAL..I.EDVI..EAG.GMHT.C..KTG..YSF..N.E.AL
Retrocopy HRTKHGTATGQGAVGQLGLGKNVIKRK<EPALVPILEDVIQDEAG<GMHTRCQRKTGHIYSFCSNYEVAL

Parental  GRDTSLEGLEMVPGKVDLQEKVVQVSAGDSHSAALTEDGRVFLWGSFRDNNGVIGLLEP-MKKSMVP-VQ
          GR.T.LEG.E.VPG.V.L.EKVVQVSAG.SH...LT..GR.FLWGSFR.N..VIGLL.P...KSMVP.VQ
Retrocopy GRTTTLEGSEKVPGNVEL*EKVVQVSAGGSHTETLT*EGRAFLWGSFRGNYRVIGLLQP<LQKSMVP<VQ

Parental  VQLDVSVVKVASGNDHLVMLTADGDLYTLGCGEQGQLGRVPELFANRGGRQGLERLLVPKRVLLKSRGSR
          VQL..S......GNDHLVMLTA.GDL.TL...E.GQ...VPELFANRG...G.E.LL..K.VLL.SR...
Retrocopy VQLEMSALQGPAGNDHLVMLTAGGDL*TLA*-EEGQFS*VPELFANRGVWPGIEQLLILKSVLLESRRIP

Parental  GHVRFQDVFCGAYFTFAVSQEGHIYGFGLSNYHQLGTPGTESCFVPQNLTSFKNSTKSWVGFSGGQHHTV
          G...FQ.VFC..YFTF.VSQE.HIYGFGL..YHQLGT....SCF.PQ.LTS..NST..WVGFSGGQHH..
Retrocopy GSMHFQNVFCSTYFTFTVSQEAHIYGFGLFGYHQLGTADKGSCFEPQ*LTSSQNSTMFWVGFSGGQHHML

Parental  CMDSEGKAYSLGRAEYGRLGL-GAGAEEKSIPTLIPRLPAVSSVACGASVGYAVTKDGRAFA-GMSTNYQ
          C.D.E...Y.L..A.Y.RL.L...GAEEKS.P.LIPRLPAVSSVAC.ASVGYA.TK.G.AFA.GM.T.YQ
Retrocopy CVDLE-EVYHLALADYVRLSL<QEGAEEKSMPSLIPRLPAVSSVACRASVGYAMTKEGSAFAQGMGTSYQ

Parental  LGTGQDEDVWSPVEMTGKQLENRVVLSVSSGGQHTVLLVK
          LGTGQ.ED..S.VEMTG.QLENRV.LSV.S.GQHTVL.V.
Retrocopy LGTGQNEDISSRVEMTGNQLENRVALSVPSRGQHTVLAVR

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_1047 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000011999	1 retrocopy	retro_etel_1047 ,