RetrogeneDB ID: retro_etel_1565

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_279270:483..980(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSETEG00000002434
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RAC3
• Ensembl ID: ENSETEG00000012902
• Aliases: None
• Description: ras-related C3 botulinum toxin substrate 3 (rho family, small GTP binding protein Rac3) [Source:HGNC Symbol;Acc:9803]

Sequence

>retro_etel_1565
GCCATAGGTAAAACTTGCCTACTGATCAGCTACACCACCAATGCGTTTCCTGGAGAATACATCCCCACCGTCTTTGACAA
CTACTCTGCCAATGTATGGTAGATGGGAAACCGGTGAATCTGGGCCTGTGGGATACAGCTGGCCAGGTAGATTACGACAG
ATTACATCCTCTCTCCTATCCGCAAACAGAAGTGTTCTTAATCTGCTTCTCCCTGGTGAGTCCTGCATCATTTGAAAATG
TCCGGGCAAAGTGGTACCCAGAGGTTCGACACCACTGTCCCAACACTCCCATAATCCTCGTGGGCACCAAGCTTGACTTG
CAGGATGATAAGGACACCATCGAGAAGCTGAAGGAGAAGAAGCTGACGCCCATTACCTACCCCCAGGGCCTGGCGATGGC
CAAGGAGATTGGTGCTGTGAAATACCTGGAGTGCTTAGCGCTCACGCAGTGAGGCCTCAAGACAGTGTTTGATGAAGCCA
TCAGAGCCGTGCTCTGC

Alignment

ORF - retro_etel_1565 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.22 %
• Parental protein coverage: 92.22 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  AVGKTCLLISYTTNAFPGEYIPTVFDNYSANV-MVDGKPVNLGLWDTAGQEDYDRLRPLSYPQTDVFLIC
          A.GKTCLLISYTTNAFPGEYIPTVFDNYSANV.MVDGKPVNLGLWDTAGQ.DYDRL.PLSYPQT.VFLIC
Retrocopy AIGKTCLLISYTTNAFPGEYIPTVFDNYSANV<MVDGKPVNLGLWDTAGQVDYDRLHPLSYPQTEVFLIC

Parental  FSLVSPASFENVRAKWYPEVRHHCPHTPILLVGTKLDLRDDKDAVERLRDKKLAPITYPQGLAMAREIGS
          FSLVSPASFENVRAKWYPEVRHHCP.TPI.LVGTKLDL.DDKD..E.L..KKL.PITYPQGLAMA.EIG.
Retrocopy FSLVSPASFENVRAKWYPEVRHHCPNTPIILVGTKLDLQDDKDTIEKLKEKKLTPITYPQGLAMAKEIGA

Parental  VKYLECSALTQRGLKTVFDEAIRAVLC
          VKYLEC.ALTQ.GLKTVFDEAIRAVLC
Retrocopy VKYLECLALTQ*GLKTVFDEAIRAVLC

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_1565 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 15 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017364	1 retrocopy	retro_amel_1104,
Callithrix jacchus	ENSCJAG00000018194	1 retrocopy	retro_cjac_2687,
Cavia porcellus	ENSCPOG00000013861	1 retrocopy	retro_cpor_18,
Echinops telfairi	ENSETEG00000004443	1 retrocopy	retro_etel_2010,
Echinops telfairi	ENSETEG00000012902	3 retrocopies	retro_etel_1565 , retro_etel_1645, retro_etel_42,
Echinops telfairi	ENSETEG00000019234	3 retrocopies	retro_etel_1468, retro_etel_596, retro_etel_672,
Felis catus	ENSFCAG00000011671	1 retrocopy	retro_fcat_431,
Macropus eugenii	ENSMEUG00000006196	1 retrocopy	retro_meug_201,
Otolemur garnettii	ENSOGAG00000012467	1 retrocopy	retro_ogar_2140,
Oreochromis niloticus	ENSONIG00000017151	1 retrocopy	retro_onil_34,
Procavia capensis	ENSPCAG00000009949	1 retrocopy	retro_pcap_16,
Pongo abelii	ENSPPYG00000008763	2 retrocopies	retro_pabe_1047, retro_pabe_2546,
Tupaia belangeri	ENSTBEG00000007272	4 retrocopies	retro_tbel_1796, retro_tbel_2564, retro_tbel_4296, retro_tbel_9,
Takifugu rubripes	ENSTRUG00000004543	1 retrocopy	retro_trub_12,
Takifugu rubripes	ENSTRUG00000016201	1 retrocopy	retro_trub_15,