RetrogeneDB ID: retro_etel_42

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: GeneScaffold_7539:163805..164378(+)
• Located in intron of: ENSETEG00000012806

Retrocopy information

• Ensembl ID: ENSETEG00000012818
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

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_42
ATGCAGACAATAAAGTGTGTTGTCGAAGGTGATGGTACCGGTAAAACATGTCTCCTGATATCCTATATAAAAAACAAATT
TCCATCTGAATATGTACGAACCGTTTTCGACAACTATGCAGTCACAGTTATGATTGGTGGAGAGCCATATGCTCTCGGAC
TTTTTGATACTGCAGGGCAAGAGGATTATGACAGATTACGGCCGCTGAGTTACCCACAAACAGATGTATCTCTAGTCTGT
TTTTCAGTGGTCTCTCCATCCTCATCTGAAAATGTGAAAGAAAAGTGGGTACCTGAGATAACACACCACTGTCCAAAGAC
TCCTTTCTTGCTTGTTGGAACCCAAGTTGATCTCAGAGATGACCCCTCTACTATTGAGAAACTTGCCAAGAACAAACAGA
AGCCTATCACCTCAGAGACTGCCGAAAAGCTGGCCCGTGACCTGAAGTCTGTCAAATATGTGGAGTGTTCTGCACTCACA
CAGAAAGGCCTAAAGAATGTGTTTGACGAAGCAGTATTGGCTGCCCTGGAGCCCCCAGAACCAAAGAAGAGCCGCAGGTG
TGTGCTGCTGTGA

Alignment

ORF - retro_etel_42 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.41 %
• Parental protein coverage: 98.33 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GKTCLLISYTTNAFPGEYIPTVFDNYSANVMVDGKPVNLGLWDTAGQEDYDRLRPLSYPQTDVFLICFSL
          GKTCLLISY..N.FP.EY..TVFDNY...VM..G.P..LGL.DTAGQEDYDRLRPLSYPQTDV.L.CFS.
Retrocopy GKTCLLISYIKNKFPSEYVRTVFDNYAVTVMIGGEPYALGLFDTAGQEDYDRLRPLSYPQTDVSLVCFSV

Parental  VSPASFENVRAKWYPEVRHHCPHTPILLVGTKLDLRDDKDAVERLRDKKLAPITYPQGLAMAREIGSVKY
          VSP.S.ENV..KW.PE..HHCP.TP.LLVGT..DLRDD....E.L...K..PIT.......AR...SVKY
Retrocopy VSPSSSENVKEKWVPEITHHCPKTPFLLVGTQVDLRDDPSTIEKLAKNKQKPITSETAEKLARDLKSVKY

Parental  LECSALTQRGLKTVFDEAIRAVLCPPPVKKPGKKCTL
          .ECSALTQ.GLK.VFDEA..A.L.PP..KK....C.L
Retrocopy VECSALTQKGLKNVFDEAVLAALEPPEPKK-SRRCVL

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_42 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,