RetrogeneDB ID: retro_etel_2090

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_53173:506..927(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSETEG00000003538
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: TAF10
• Ensembl ID: ENSETEG00000008886
• Aliases: None
• Description: TAF10 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 30kDa [Source:HGNC Symbol;Acc:11543]

Sequence

>retro_etel_2090
CGAGTGCCGGGGAGCCGGCTGGCCGGCGCTGCACCCGCAGAAGGGGCCAAGTCTAACGGGAGTTCATGGCTGCCCAGCGC
GGCCAGCGGAGAAGGGACGCCGGTGATGGCCAGCACGCCTCTGTGGACTTTCTGCTGCAGCTGGAGGTTACACGACTACG
ATCCCCGATCCCGGACGCAGTGACTGGTTACTGCCTAAACCCTGCGGGCTCTGCGGCCTCGGACCCTCGCATAATTCGCC
TCATCTCCCTAGCTGCCCAGAAATTCATCTCAGATACGGCCAACGGTGCCCTGCAGCACCGCAAATGAAGGGCGCGGCCT
CTGGCAGCTCCCGAAGCAAGAGCAAGGACCGCAAGGACGCTCTGACCATGGAGGAGGTGACTCTGCCCTCAGAGTGCGGC
ATCAGTGTCAAGAAGACCTAC

Alignment

ORF - retro_etel_2090 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.59 %
• Parental protein coverage: 64.68 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  RVPAPVTAGGAAPPEGVMSNGVYVLPSAANGEVKPVVSSTPLVDFLM--QLEDYTPT-IPDAVTGYYLNR
          RVP....AG.AAP.EG..SNG...LPSAA.GE..PV..STPL..F.....L.DY.P..IPDAVTGY.LN.
Retrocopy RVPGSRLAG-AAPAEGAKSNGSSWLPSAASGEGTPVMASTPLWTFCCSWRLHDYDPR<IPDAVTGYCLNP

Parental  AGFEASDPRIIRLISLAAQKFISDIANDALQHCK-MKGTASGSSRSKSKDRKYTLTMEDLTPALSEYGIN
          AG..ASDPRIIRLISLAAQKFISD.AN.ALQH.K.MKG.ASGSSRSKSKDRK..LTME..T...SE.GI.
Retrocopy AGSAASDPRIIRLISLAAQKFISDTANGALQHRK<MKGAASGSSRSKSKDRKDALTMEEVT-LPSECGIS

Parental  VKKPH
          VKK..
Retrocopy VKKTY

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_2090 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 13 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016278	2 retrocopies	retro_amel_1088, retro_amel_297,
Canis familiaris	ENSCAFG00000006498	2 retrocopies	retro_cfam_1041, retro_cfam_992,
Dasypus novemcinctus	ENSDNOG00000000814	1 retrocopy	retro_dnov_592,
Equus caballus	ENSECAG00000007794	1 retrocopy	retro_ecab_525,
Erinaceus europaeus	ENSEEUG00000008412	3 retrocopies	retro_eeur_542, retro_eeur_692, retro_eeur_709,
Echinops telfairi	ENSETEG00000008886	1 retrocopy	retro_etel_2090 ,
Felis catus	ENSFCAG00000015390	1 retrocopy	retro_fcat_1458,
Loxodonta africana	ENSLAFG00000029330	1 retrocopy	retro_lafr_750,
Macropus eugenii	ENSMEUG00000008216	2 retrocopies	retro_meug_1645, retro_meug_992,
Myotis lucifugus	ENSMLUG00000024459	1 retrocopy	retro_mluc_1960,
Macaca mulatta	ENSMMUG00000007743	1 retrocopy	retro_mmul_1144,
Mus musculus	ENSMUSG00000043866	1 retrocopy	retro_mmus_35,
Tursiops truncatus	ENSTTRG00000004894	1 retrocopy	retro_ttru_1113,