RetrogeneDB ID: retro_etel_341

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: GeneScaffold_5661:99643..100366(+)
• Located in intron of: ENSETEG00000017484

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: PAICS
• Ensembl ID: ENSETEG00000015242
• Aliases: None
• Description: phosphoribosylaminoimidazole carboxylase, phosphoribosylaminoimidazole succinocarboxamide synthetase [Source:HGNC Symbol;Acc:8587]

Sequence

>retro_etel_341
AGTCCAGCTTCTGTACATAACGCGGTCACAGCCCCCAGCCTACTCAAGATCATGGTGACCTCTGGGGTGGTGGTCCTTGG
TCCAAAGCTCTACGAGGAGGAAACAGAAGTCTCTGCATTGGTGCAGCACCCAGGGAAAGTCCTCCTGCCGCCCAAAGACC
AGACTACAGCAGGGGGTGAAGCTGGCAAGAGCCGCCTGGAAGGCAAAGCTGCGATTTCCAATAAAATCACCAGTTGTATT
TTTCAGTTGTTACAGGACGCAGGTATCAAAACTGCTTTCACCAAGACACAGGGGGAAACGGCTTTCATTGCCCCCAGTGT
GAAACGATTCCCATGGAGAGGAATAGCAACTGCTGCTTTTCTCAAAAGGAACCCTGGCGTCAAGGAAGGCTAAGAGTTGT
ACCCACCCAGAGTGGAACTGTTTTTCAAGGATGATGTCAATAAGGACCCACAGTGATCTGAAGAGCAGCTAATTGCTGCC
AAACTTTGCTTTGCTGGACTTGAGATAGGTCAAACTGAAGTGGATATCCTGAATCATGCCACACAGGCCATTTTTGAAAC
ACTGGAAAAGTCGTGGTTGCCCCAGGCCTGTACACTGGTTGGCATGAAGATTGAATTTGGTGCTGATGTCACCACCAAAG
AAAGTGTTCTTGCTGATGTTATTGATAACGATTCCTGGAGACTCTGGCCATCCAGAGATCGAACCCAACAGAAGGACAAG
CAG

Alignment

ORF - retro_etel_341 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.42 %
• Parental protein coverage: 54.81 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  NPASPLHAVAAPSLLEIMAASEVVS-GPKLYEGKTKEVYELVHHPGKVLLQSKDQITAGNAARKNHLEGK
          .PAS...AV.APSLL.IM..S.VV..GPKLYE..T.EV..LV.HPGKVLL..KDQ.TAG..A.K..LEGK
Retrocopy SPASVHNAVTAPSLLKIMVTSGVVVLGPKLYEEET-EVSALVQHPGKVLLPPKDQTTAGGEAGKSRLEGK

Parental  AAISNKITSCIFQLLQDAGIKTAFTKTWGETAFIAPQCEMIPIEWVCRRIATGSFLKRNPGVKEGYKFYP
          AAISNKITSCIFQLLQDAGIKTAFTKT.GETAFIAP.....P..W..R.IAT..FLKRNPGVKEG...YP
Retrocopy AAISNKITSCIFQLLQDAGIKTAFTKTQGETAFIAPSVKRFP--W--RGIATAAFLKRNPGVKEG*ELYP

Parental  PKVEMFFKDDANNDPQWSEEQLIAAKFCFAGLEIGQTEVDIMSHATQAIFEILEKCWLPQDCTLVDMKIE
          P.VE.FFKDD.N.DPQ.SEEQLIAAK.CFAGLEIGQTEVDI..HATQAIFE.LEK.WLPQ.CTLV.MKIE
Retrocopy PRVELFFKDDVNKDPQ*SEEQLIAAKLCFAGLEIGQTEVDILNHATQAIFETLEKSWLPQACTLVGMKIE

Parental  FGVDVTTKEIILADVIDNDSWRLWPSGDRSQQKDKQ
          FG.DVTTKE..LADVIDNDSWRLWPS.DR.QQKDKQ
Retrocopy FGADVTTKESVLADVIDNDSWRLWPSRDRTQQKDKQ

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_341 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 29 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000010577	1 retrocopy	retro_btau_508,
Cavia porcellus	ENSCPOG00000010749	1 retrocopy	retro_cpor_969,
Dasypus novemcinctus	ENSDNOG00000013413	1 retrocopy	retro_dnov_284,
Echinops telfairi	ENSETEG00000015242	2 retrocopies	retro_etel_1918, retro_etel_341 ,
Homo sapiens	ENSG00000128050	3 retrocopies	retro_hsap_3802, retro_hsap_3915, retro_hsap_3927,
Gorilla gorilla	ENSGGOG00000024392	1 retrocopy	retro_ggor_2643,
Mus musculus	ENSMUSG00000029247	6 retrocopies	retro_mmus_1748, retro_mmus_2750, retro_mmus_2858, retro_mmus_3126, retro_mmus_653, retro_mmus_971,
Nomascus leucogenys	ENSNLEG00000008786	2 retrocopies	retro_nleu_1274, retro_nleu_2156,
Otolemur garnettii	ENSOGAG00000003575	2 retrocopies	retro_ogar_2138, retro_ogar_865,
Procavia capensis	ENSPCAG00000008531	1 retrocopy	retro_pcap_172,
Pan troglodytes	ENSPTRG00000016081	2 retrocopies	retro_ptro_2662, retro_ptro_2670,
Rattus norvegicus	ENSRNOG00000002101	3 retrocopies	retro_rnor_1891, retro_rnor_2768, retro_rnor_804,
Tupaia belangeri	ENSTBEG00000006751	1 retrocopy	retro_tbel_3697,
Tarsius syrichta	ENSTSYG00000010497	2 retrocopies	retro_tsyr_2170, retro_tsyr_329,
Drosophila melanogaster	FBgn0020513	1 retrocopy	retro_dmel_82,