RetrogeneDB ID: retro_etel_1265

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_237659:9892..10380(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSETEG00000010002
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: GGPS1
• Ensembl ID: ENSETEG00000008916
• Aliases: None
• Description: geranylgeranyl diphosphate synthase 1 [Source:HGNC Symbol;Acc:4249]

Sequence

>retro_etel_1265
GTGGAGATTGCTCAAGAAACGGTCCAAAGAAATCTTCTAGAACCCTACAAGCAGTTATTTCAGTTACCAGGTAATCAAGT
AAAAACCAAGCTTTTACAAGCTGTTAATCATTGACTAAAAGTCCCAGAAGAAAAGCTACAGGTTGTCATTGAAGTGACAG
AAGAGTTGCATAAAGCCAGTTTGCTCATTGATATCAAAGAACTTCAATGTGATTTGACAGTGGCTCACGGTATCAACGAA
ATTCCATTTGTCATCACTTTGCTGATTATGTATATTTTATGGGTTTGGAAAAAGTCTTGACCCTTGATTACTCAGATACA
GTGAAACACTTTACCCACCATCTTTTAGAACTTCAATAGAGACAAGGCCCAGGCAATTACACTTAGTGGGACAATTGCAC
TTGTCCCACTGAAGAAGAATATAAAGCTATGGTCCCACAAAAGACCAGTGGGCGATTTGGATTAGCTGTACATCTCCTGC
ACCTGTTC

Alignment

ORF - retro_etel_1265 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.68 %
• Parental protein coverage: 55.33 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MEMAQETVQRILLEPYKYLLQLPGKQIRTKLSQAFNHWLKVPEDKLQVIIEVTEMLHNASLLIDDIEDNS
          .E.AQETVQR.LLEPYK.L.QLPG.Q..TKL.QA.NH.LKVPE.KLQV.IEVTE.LH.ASLLID..E...
Retrocopy VEIAQETVQRNLLEPYKQLFQLPGNQVKTKLLQAVNH*LKVPEEKLQVVIEVTEELHKASLLIDIKE---

Parental  KLRRGFPVAHSIYGIPSVI-NSANYVYFLGLEKVLTLDHPDAVKLFTRQLLEL--HQGQGLDIYWRDNYT
          .L.....VAH.I..IP.VI...A.YVYF.GLEKVLTLD..D.VK.FT..LLEL...QG.G....W.DN.T
Retrocopy -LQCDLTVAHGINEIPFVI<HFADYVYFMGLEKVLTLDYSDTVKHFTHHLLELQ*RQGPGNYT*W-DNCT

Parental  CPTEEDYKAMVLQKTGGLFGLAVGLMQLF
          CPTEE.YKAMV.QKT.G.FGLAV.L..LF
Retrocopy CPTEEEYKAMVPQKTSGRFGLAVHLLHLF

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_1265 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 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000011303	1 retrocopy	retro_cfam_1438,
Echinops telfairi	ENSETEG00000008916	1 retrocopy	retro_etel_1265 ,
Myotis lucifugus	ENSMLUG00000016813	1 retrocopy	retro_mluc_54,
Mus musculus	ENSMUSG00000021302	1 retrocopy	retro_mmus_1253,
Ictidomys tridecemlineatus	ENSSTOG00000004263	1 retrocopy	retro_itri_619,