RetrogeneDB ID: retro_etel_526

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: GeneScaffold_8799:5948..7003(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSETEG00000011339
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: HMGCS1
• Ensembl ID: ENSETEG00000003583
• Aliases: None
• Description: 3-hydroxy-3-methylglutaryl-CoA synthase 1 (soluble) [Source:HGNC Symbol;Acc:5007]

Sequence

>retro_etel_526
CCTGGGCCACTTCCTTTGACTATGGAAGCCTGCTGGCCAAAAGATGTAGAATTTTTTGCCCTGGAAATCTACTTTCCTTC
TCAGTAAGTTGATCAATCATAACTGTAAAAATATGATGGAAAGTATACCGCTGGCTTGGGCCAGGCCAAGATGGGTTTCT
GCACAGAGAAGATATCAACTCTATTTGCTTGACTGTGGTTCAGTTTCTTATGGAGAGAAATGACCTATCATATGACTGCA
TTGGGCAACTGGAGGTTGGAAAACAGACAATCAACATCAAATCAAAGTCAGTGAAGATTTATTTGACGCAGCTATTTGAG
GAACCTGGGAATTCAAATATACAAGGAATAGATGCAACAAATGCATGCTGTAGAGGCACAGCTATTATCTTTAATGCAAT
TAACTGGATTGAATGGAGCTCCTGGAATGAACGGTATACCCTGATAATTATAGGAGATATTGCTGTATATTCCACAGGAA
ATGCTAGGCCAACTAGTGGAGTGAGAGCTATTGATTTGCTCATTGGAGCAAATGCTCCTTTAATTTTTAAAGGAGGGATT
CGTGCAACCCATATGCAGCATGCCTATGACTTTTAAAAGCCTAATATGCTCTTGGAGTATCATATGGTGAATGGCAAACT
CTCCATACAGTGCTGTCCCAGTGTCTTAGGCTGCTTCTATTTTGTCTACCACAAAAGATCCAGGCCCAGTGGCAGAAGAA
GGGACAGGATAAAGATTTCACTTTGAATGATTTGGGCTTCATGATCTTCCACTCACAGTATTGTAAACTGGCTCAGAAAT
CTCTAGCTCAGATGCAGCTGAATGACTTTCTGAATGACCAGAGCAGAGATAAAAATAGTGTCTGTAGTGTCCTAGAAGCC
TTTGGGACTGTTAAATTAGAAGATACCTACTCTGATAGAGATGTGGAAAAGGCATTTATGAAGGCGAGTTCTGAACTCTT
GGATCAGAAAACAAAGGGCATGTTTTTTGTATCAAATGAAAATGGAAATATGTACACATCCTTCAATCCGTGTTTGACTT
GCTTCTGTTCTAGCA

Alignment

ORF - retro_etel_526 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.94 %
• Parental protein coverage: 72.51 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  PGSLPLNAEACWPKDVGIVALEIYFPSQYVDQSELEKYDGVDAGKYTIGLGQAKM-GFCTDREDINSLCL
          PG.LPL..EACWPKDV...ALEIYFPSQ.VDQS.L.KYD....GKYT.GLGQAKM.GF...REDINS.CL
Retrocopy PGPLPLTMEACWPKDVEFFALEIYFPSQ*VDQS*L*KYD----GKYTAGLGQAKM<GFL-HREDINSICL

Parental  TAVQNLMERNNLSYDCIGRLEVGTETIIDKSKSVKTNLMQLFEESGNTDIEGIDTTNACYGGTAAVFNAI
          T.VQ.LMERN.LSYDCIG.LEVG..TI..KSKSVK..L.QLFEE.GN..I.GID.TNAC..GTA..FNAI
Retrocopy TVVQFLMERNDLSYDCIGQLEVGKQTINIKSKSVKIYLTQLFEEPGNSNIQGIDATNACCRGTAIIFNAI

Parental  NWIESSSWDGRYALVVAGDIAVYATGNARPTGGVGAVALLIGPNAPLIFERGLRGTHMQHAYDFYKPDML
          NWIE.SSW..RY.L...GDIAVY.TGNARPT.GV.A..LLIG.NAPLIF..G.R.THMQHAYDF.KP.ML
Retrocopy NWIEWSSWNERYTLIIIGDIAVYSTGNARPTSGVRAIDLLIGANAPLIFKGGIRATHMQHAYDF*KPNML

Parental  SEYPIVDGKLSIQCYLSALDRCYYVYRK-KIRAQ-QKEGNDKDFTLNDFGFMIFHSPYCKLVQKSLARML
          .EY..V.GKLSIQC..S.L...Y.VY.K.KI.AQ.QK.G.DKDFTLND.GFMIFHS.YCKL.QKSLA.M.
Retrocopy LEYHMVNGKLSIQCCPSVLGCFYFVYHK<KIQAQWQKKGQDKDFTLNDLGFMIFHSQYCKLAQKSLAQMQ

Parental  LNDFLNDQNRDKNSVYSGLEXXXDVKLEDTYFDRDVEKAFMKASSELFNQKTKASLLVSNQIGNMYTS-S
          LNDFLNDQ.RDKNSV.S.LE....VKLEDTY.DRDVEKAFMKASSEL..QKTK....VSN..GNMYTS.S
Retrocopy LNDFLNDQSRDKNSVCSVLEAFGTVKLEDTYSDRDVEKAFMKASSELLDQKTKGMFFVSNENGNMYTS>S

Parental  VYGSLASVLA
          ....LASVLA
Retrocopy IRV*LASVLA

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_526 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 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000001303	1 retrocopy	retro_cjac_1754,
Echinops telfairi	ENSETEG00000003583	1 retrocopy	retro_etel_526 ,
Echinops telfairi	ENSETEG00000005380	1 retrocopy	retro_etel_2037,
Homo sapiens	ENSG00000112972	1 retrocopy	retro_hsap_328,
Pongo abelii	ENSPPYG00000015439	1 retrocopy	retro_pabe_361,
Pan troglodytes	ENSPTRG00000016845	1 retrocopy	retro_ptro_265,