RetrogeneDB ID: retro_etel_1694

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_288023:40880..41617(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: HADH
• Ensembl ID: ENSETEG00000013807
• Aliases: None
• Description: hydroxyacyl-CoA dehydrogenase [Source:HGNC Symbol;Acc:4799]

Sequence

>retro_etel_1694
CGGACTTGCCGCCACTGCTGCTCCGTGGCTTTCGTGACCAGGCAGTTCATGCGCTCTGTGTCCTCCCGGTCCGCCGCCTT
GGCCACGGCGAAGAAAATCGTCCTCAAACACGTGACAGTCATCGCGGTGGACTGATGGGGGCCGGCATCACCCAGGTTGC
TGCAGCAACTGGCCACACAGTAGTGCTGGTAGACAGGCAGGCAGAGGGCATCCCGGCAAAATCTAAAAAGGGGATTGAGG
AAAGCCTTAAGAAAGTGGCCAAGAAGAAGTTTGCAGACAACCCAAAGGCCACCGAGGAGTTGGTTGGGAAGACCCTGAAC
AGCATCTCGACCAGCATGGACGCTGCGTCTGTGGTCCACAGCGCAGACCTGGTGGTGGAGGCCATCGTGGAGAACCTGAC
GGGGAAGAATGAGCTCTTCGGCAGGCTGGACAAGTTCGCTGCTGAACATACAATTTTTGCCAGCAACACTTCCTCTTTGC
AAATCACAAGCATAGCCAGTGCCACCACCAGACAAGACCGATTTGCCGGGCTCCACTTCTTCAACCCAGTGCCCCTCATG
AAGCTTGTGGAGGTCATTAAAACCCCCATGACCAGCCAGAAGACATTTGAATCTCTGATAGACTTTAGCAAAACCCTAGG
AAAGCATCCTATTTCTTGCAAGGACACTCCGGGGTTTATTGTCAACCGTCTGCTGGTGCGGTACCTCATGGAAGCAATCA
GCCTGTATGAACGAGGG

Alignment

ORF - retro_etel_1694 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.66 %
• Parental protein coverage: 66.22 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RRRRRLCTMAFVTRQFVRSVSSSSTASATAKKIVLKHVTVIG-GGLMGAGIAQVAAATGHTVVLVD-QAE
          R..R..C..AFVTRQF.RSVSS.S.A.ATAKKIVLKHVTVI..GGLMGAGI.QVAAATGHTVVLVD.QAE
Retrocopy RTCRHCCSVAFVTRQFMRSVSSRSAALATAKKIVLKHVTVIA<GGLMGAGITQVAAATGHTVVLVDRQAE

Parental  DILAKSKKGIEESLKKMAKKKFADNPQAAEEFVGKTLNSISTSMDAASVVHSTDLVVEAIVENLKVKNEL
          .I.AKSKKGIEESLKK.AKKKFADNP.A.EE.VGKTLNSISTSMDAASVVHS.DLVVEAIVENL..KNEL
Retrocopy GIPAKSKKGIEESLKKVAKKKFADNPKATEELVGKTLNSISTSMDAASVVHSADLVVEAIVENLTGKNEL

Parental  FARLDKFAAEHTIFASNTSSLQITSIANATTRQDRFAGLHFFNPVPLMKLVEVIKTPMTSQKTFESLIDF
          F.RLDKFAAEHTIFASNTSSLQITSIA.ATTRQDRFAGLHFFNPVPLMKLVEVIKTPMTSQKTFESLIDF
Retrocopy FGRLDKFAAEHTIFASNTSSLQITSIASATTRQDRFAGLHFFNPVPLMKLVEVIKTPMTSQKTFESLIDF

Parental  SKTLGKHPVSCKDTPGFIVNRLLVPYLMEAIKLYERG
          SKTLGKHP.SCKDTPGFIVNRLLV.YLMEAI.LYERG
Retrocopy SKTLGKHPISCKDTPGFIVNRLLVRYLMEAISLYERG

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_1694 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 10 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000002049	2 retrocopies	retro_btau_1111, retro_btau_1685,
Callithrix jacchus	ENSCJAG00000015938	1 retrocopy	retro_cjac_772,
Echinops telfairi	ENSETEG00000013807	1 retrocopy	retro_etel_1694 ,
Felis catus	ENSFCAG00000022260	1 retrocopy	retro_fcat_1225,
Homo sapiens	ENSG00000138796	1 retrocopy	retro_hsap_1571,
Gorilla gorilla	ENSGGOG00000004423	1 retrocopy	retro_ggor_1196,
Macaca mulatta	ENSMMUG00000023254	1 retrocopy	retro_mmul_2217,
Nomascus leucogenys	ENSNLEG00000012951	1 retrocopy	retro_nleu_1738,
Pongo abelii	ENSPPYG00000014986	1 retrocopy	retro_pabe_1296,
Pan troglodytes	ENSPTRG00000016351	1 retrocopy	retro_ptro_1058,