RetrogeneDB ID: retro_etel_2162

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_81454:696..1496(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSETEG00000004534
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSETEG00000010208
• Aliases: None
• Description: None

Sequence

>retro_etel_2162
GCTGCCTCGGCCTTGCATGGACTCGGCCCTTCAACATCGCTGCACTAAGTCCAGCTTTTGCTGTGGGCCACCCAGCGGTG
CTCCAGCCCAGCAGAGACTACACTGCGCAAACTTCTCCTTCACCAAAGGCAGGCACTGCCACTGCGCGAATTGTGACAGC
CATCCGTGACGTGGTGGATGTCCAGTTTGATAATGGAGTACCCCCCACCCCCATCCTAACTGCCCTGGAAGTGAAATGCG
GATACACCAGGCTAGTTTTGGATGTGGCCCAGCATTTGGGTGAGAATAAGGACCACATTGCTATGGATGGTACTGAAGGC
TTGGTCAGAGGCCAGAAAATTCTGGATTCTGGTGCACCCATCAAAATTCCTGTTGGTCCTGAGACCTTAGGCAGAATCAT
GAGTGTCATTGGAGAACCCATTGATGAGAGAGGGCCCATCAAAACCAAACCATTTACTCCTCTTCATGCCGAGGCACCTG
AGTTCGTGGAGATGAGTGTTGAGCAGGAAATTCTGGTGACTGGCATCAAGGTTGTGGATCTGCTGGCTCCCTATGCCAAG
GGTGGCAACATCGGGCTTTTTGGTGGTGCTGCAGTTGGCAAGATGGTATTGATCATGGAATTAATCAACAATGTCACCAA
AGTCCATGGTGGTTACTCTGTTTTTGCCAGTGTTGGTAAGTGGATCCGTGAGGACAATGACTTATACCACGAAACGTCTG
AGTCTGGTGTTATCAACGTGAAAGATACTACCTCTAAGGTCGCGCTGGTGTATGGGCAAATGAATGAACCACCTGGTGCT

Alignment

ORF - retro_etel_2162 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.93 %
• Parental protein coverage: 50.38 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ASGALRGLSPSASLPQAQFLLRAA-PAALQPGRDYAAQTSPSPKAGTATGRIVAVIGAVVDVQFDEGLPP
          A..AL.GL.PS.SL...Q.LL.A..PA.LQP.RDY.AQTSPSPKAGTAT.RIV..I..VVDVQFD.G.PP
Retrocopy AASALHGLGPSTSLH*VQLLLWAT<PAVLQPSRDYTAQTSPSPKAGTATARIVTAIRDVVDVQFDNGVPP

Parental  --ILNALEVQGRDTRLVLEVAQHLGESTVRTIAMDGTEGLVRGQKVLDSGAPIKIPVGPETLGRIMNVIG
          ..IL.ALEV....TRLVL.VAQHLGE.....IAMDGTEGLVRGQK.LDSGAPIKIPVGPETLGRIM.VIG
Retrocopy TPILTALEVKCGYTRLVLDVAQHLGENKDH-IAMDGTEGLVRGQKILDSGAPIKIPVGPETLGRIMSVIG

Parental  EPIDERGPIKTKQFAPIHAEAPEFMEMSVEQEILVTGIKVVDLLAPYAKGGKIGLFGGAGVGKTVLIMEL
          EPIDERGPIKTK.F.P.HAEAPEF.EMSVEQEILVTGIKVVDLLAPYAKGG.IGLFGGA.VGK.VLIMEL
Retrocopy EPIDERGPIKTKPFTPLHAEAPEFVEMSVEQEILVTGIKVVDLLAPYAKGGNIGLFGGAAVGKMVLIMEL

Parental  INNVAKAHGGYSVFAGVGERTREGNDLYHEMIESGVINLKDTTSKVALVYGQMNEPPGA
          INNV.K.HGGYSVFA.VG...RE.NDLYHE..ESGVIN.KDTTSKVALVYGQMNEPPGA
Retrocopy INNVTKVHGGYSVFASVGKWIREDNDLYHETSESGVINVKDTTSKVALVYGQMNEPPGA

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_2162 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 19 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000016752	1 retrocopy	retro_acar_181,
Bos taurus	ENSBTAG00000013315	1 retrocopy	retro_btau_1264,
Choloepus hoffmanni	ENSCHOG00000005350	1 retrocopy	retro_chof_1544,
Callithrix jacchus	ENSCJAG00000033571	2 retrocopies	retro_cjac_1488, retro_cjac_928,
Dasypus novemcinctus	ENSDNOG00000011289	1 retrocopy	retro_dnov_361,
Echinops telfairi	ENSETEG00000010208	1 retrocopy	retro_etel_2162 ,
Homo sapiens	ENSG00000110955	1 retrocopy	retro_hsap_2128,
Gorilla gorilla	ENSGGOG00000011596	1 retrocopy	retro_ggor_1648,
Latimeria chalumnae	ENSLACG00000009340	1 retrocopy	retro_lcha_27,
Macropus eugenii	ENSMEUG00000002875	6 retrocopies	retro_meug_1416, retro_meug_1608, retro_meug_411, retro_meug_430, retro_meug_685, retro_meug_908,
Microcebus murinus	ENSMICG00000001084	1 retrocopy	retro_mmur_495,
Macaca mulatta	ENSMMUG00000001027	1 retrocopy	retro_mmul_103,
Pongo abelii	ENSPPYG00000004668	2 retrocopies	retro_pabe_1921, retro_pabe_2032,
Pan troglodytes	ENSPTRG00000005107	1 retrocopy	retro_ptro_1557,
Sus scrofa	ENSSSCG00000000405	1 retrocopy	retro_sscr_453,
Tarsius syrichta	ENSTSYG00000009962	1 retrocopy	retro_tsyr_644,
Tursiops truncatus	ENSTTRG00000002144	1 retrocopy	retro_ttru_371,
Vicugna pacos	ENSVPAG00000004025	2 retrocopies	retro_vpac_405, retro_vpac_562,
Xenopus tropicalis	ENSXETG00000024665	1 retrocopy	retro_xtro_68,