RetrogeneDB ID: retro_etel_681

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_14258:2006..2389(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSETEG00000003680
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RAB4A
• Ensembl ID: ENSETEG00000018042
• Aliases: None
• Description: RAB4A, member RAS oncogene family [Source:HGNC Symbol;Acc:9781]

Sequence

>retro_etel_681
ATATCCCAGATGGCTATGTCCGAGACCTACGATTTTTTAATTTAAATTCTTGGTTATTGGAAATGCAGGAACTGGCAAGT
CTTGCTTACTTCATCAGTTTATTGAAAAAAAATCAAAGATGACTCAAATCATACAAAAGGAGAGGAATTTGGTTCAAAGA
TAGTAAATGTTGGTGGTAAATATGTAAAGTTACAGATAGGGGACACAACAGGATAAGAGAGATTCAGGTCTGTGACACGA
AGCTATTACAGAGGTGCAGCTGGGCCCTCCTTGTCTAGGGCATTACCAGCCAAGAAACCTACAATGTGCTTACTAATTGG
TTAACAGGTGCCAAAATGCTAGCCAGTCAAAACATGGTGATCCTGCTGTGTGGAAACAAGAAG

Alignment

ORF - retro_etel_681 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.92 %
• Parental protein coverage: 58.45 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MSQTAMSETYDFL-FKFLVIGNAGTGKSCLLHQFIEKK-FKDDSNHTIAVEFGSKIINVGGKYVKLQIWH
          .SQ.AMSETYDFL.FKFLVIGNAGTGKSCLLHQFI.....KDDSNHT...EFGSKI.NVGGKYVKLQI..
Retrocopy ISQMAMSETYDFL>FKFLVIGNAGTGKSCLLHQFIXXX<XKDDSNHTKGEEFGSKIVNVGGKYVKLQIGD

Parental  TAGQERFRSVTRSYYRGAAG-ALLVYDITSRETYNALTNWLTDARMLASQNIVIILCGNKK
          T.G.ERFRSVTRSYYRGAAG.ALLV..ITS.ETYN.LTNWLT.A.MLASQN.VI.LCGNKK
Retrocopy TTG*ERFRSVTRSYYRGAAG<ALLV*GITSQETYNVLTNWLTGAKMLASQNMVILLCGNKK

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_681 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 7 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000013866	5 retrocopies	retro_chof_1017, retro_chof_1761, retro_chof_2377, retro_chof_64, retro_chof_703,
Echinops telfairi	ENSETEG00000004920	5 retrocopies	retro_etel_1150, retro_etel_2132, retro_etel_2214, retro_etel_694, retro_etel_837,
Echinops telfairi	ENSETEG00000010340	2 retrocopies	retro_etel_203, retro_etel_32,
Echinops telfairi	ENSETEG00000018042	3 retrocopies	retro_etel_1163, retro_etel_122, retro_etel_681 ,
Macaca mulatta	ENSMMUG00000017720	1 retrocopy	retro_mmul_2336,
Nomascus leucogenys	ENSNLEG00000014339	1 retrocopy	retro_nleu_2062,
Pongo abelii	ENSPPYG00000000128	1 retrocopy	retro_pabe_3321,