RetrogeneDB ID: retro_etel_2037

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_37673:3068..3846(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSETEG00000005353
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: HMGCS2
• Ensembl ID: ENSETEG00000005380
• Aliases: None
• Description: 3-hydroxy-3-methylglutaryl-CoA synthase 2 (mitochondrial) [Source:HGNC Symbol;Acc:5008]

Sequence

>retro_etel_2037
TCTGAGTATCCTATAGTGGATGGCAAGCTCCCCACGCAGTGCTACCTCAGTGCCTTAGTTAGCTGCTATTCTATCTACCT
CATAAAGATCGGGGCCCAAGGGCAGAAGGAGGGAAACGATAAAGATTTCACTTTGAATGATTTTGGCTTCATGATCTTCC
ACTCACTGTATTGTAAACTGGTTCAGAAATTTCTAGTTAGGATGCTGTTGAATGACTTTCTGAATGACCAGAAAAGAGAT
AAAAATAGTTTCTATAGTGGCCTAGAAGCCTTTGGGGGTGTTAAATTAGAAGATACTTACTTTGATAGAGATGTGGAAAA
AGCATTTATGAAGGCTAGTTCTGAACTCCTTAATCAGAAAACGAAGGCATCTTTGCTTGTGTCAAATCAAAATGGAAATA
TGTGCACATCTTCAGTCTACGGTTCCCCTGCCTCTGTTCTAGCACAGGACTCACGTCAGCAGTTGGCAGCAAAAGGACTG
GTGTCTTCTCTGTGCTTCTAGTTTGGATGCCACCTTGTACTCCCTTAAAGTTACACAAGATGCTACACCAGGGTCTGCTC
TTGATCAAAGAACTGCAAGTTTCTGTGACCTTAAATCAAGGCTTGACTCAAGAACTCGTGTGGCACCAGATGTCTTTGCT
GAAAATATGATGCTCAGAAAGCACACTCATCACTTAGTCAGCCATATTCCCCAGGGTCCAATCGATTCACTCGTTGAAGG
AACATGGTACCTGGTTAGAGTGGATGAACTGCACTGAAGAACCTGTGCTCGGTGCCCC

Alignment

ORF - retro_etel_2037 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.33 %
• Parental protein coverage: 51.28 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SEYPVVDGKLSIQCYFRALDRCYSFYRQKIHNQIGKQAGIERPFTMDDFQFMIFHSPFCKLVQKSLGRLM
          SEYP.VDGKL..QCY..AL..CYS.Y..KI..Q.G...G....FT..DF.FMIFHS..CKLVQK.L.R..
Retrocopy SEYPIVDGKLPTQCYLSALVSCYSIYLIKIGAQ-GQKEGNDKDFTLNDFGFMIFHSLYCKLVQKFLVRML

Parental  FNDFLSASSDTRTSRYKGLEAFSGLNLEDTYTNRDVDAAFQKASLDMFNKKTKASLYLSAHNGNMYTSSL
          .NDFL........S.Y.GLEAF.G..LEDTY..RDV..AF.KAS....N.KTKASL..S..NGNM.TSS.
Retrocopy LNDFLNDQKRDKNSFYSGLEAFGGVKLEDTYFDRDVEKAFMKASSELLNQKTKASLLVSNQNGNMCTSSV

Parental  YGCLASLLSQHSAQDLA-GSRIGAFSY-GSGMAASLFSLRASKDASSGSPLEKLVSSVSDLPNRLASRKR
          YG..AS.L.Q.S.Q.LA...R.G.FS...S...A.L.SL....DA..GS.L.....S..DL..RL.SR.R
Retrocopy YGSPASVLAQDSRQQLA<SKRTGVFSV<ASSLDATLYSLKVTQDATPGSALDQRTASFCDLKSRLDSRTR

Parental  ASAEEFTEIMDQREHFHRKVNFSPPGDTNSLFPGTWYLEQVDEMYRRKYSRRP
          .....F.E.M..R.H.H..V...P.G...SL..GTWYL..VDE...R...R.P
Retrocopy VAPDVFAENMMLRKHTHHLVSHIPQGPIDSLVEGTWYLVRVDELH*RTCARCP

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_2037 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000010096	1 retrocopy	retro_cfam_1442,
Echinops telfairi	ENSETEG00000003583	1 retrocopy	retro_etel_526,
Echinops telfairi	ENSETEG00000005380	1 retrocopy	retro_etel_2037 ,