RetrogeneDB ID: retro_etel_1231

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_232175:180..696(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSETEG00000019601
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: AASDHPPT
• Ensembl ID: ENSETEG00000004248
• Aliases: None
• Description: aminoadipate-semialdehyde dehydrogenase-phosphopantetheinyl transferase [Source:HGNC Symbol;Acc:14235]

Sequence

>retro_etel_1231
TTACCCTGCCAAGCGGTTCTGCTTAGTGCCAGAGCCATGGAGGGCGTGCACTGGGCCTTTTCCTGCGGCACTTAGCTGCC
GAGCAAGAGCCGAATGGCTGCTGGCGGTGCGGTCCATCCAGCCCGAGGAAAAGGAGCGTCTTGGCCAGTTTATCTTTGCC
CGGGAGGCAAAGGTAGCCATGGCTGGTCGTCTGACGATAAGGAAACTGGTTGCAGAGAAATTGAATATCCTTGGAATAAT
ATTCGTTTGCAGAGAACTGCAAAAGGAAAACCAGTTCTTGCAAAGGATTCACTGAATCCCTATCCCAATTTCAACTTTAA
CATTTCTCATCAAGGGGACTATGCGGTACTTGCTTCTGAACCTGAGCTGCGAGTTGGAATTGATATAATGAAGACTAGCT
TGCCAGGTCGCGGTTCAATTCCAGAGCTCTTCCATATTATGAAAAGAAAATTTACCAACAGAGTGGGGGAAACCATCAAA
AGCTTTAAGGACGAATGGACTCAACTGGATATGTTT

Alignment

ORF - retro_etel_1231 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.63 %
• Parental protein coverage: 55.34 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LPAKRVCL-VPAMEGVRWAFSCGTWLPS-RAEWLLAVRSIQPEEKERIGQFVFARDAKAAMAGRLMIRKL
          LP...V.L...AMEGV.WAFSCGT.LPS.RAEWLLAVRSIQPEEKER.GQF.FAR.AK.AMAGRL.IRKL
Retrocopy LPCQAVLLSARAMEGVHWAFSCGT*LPS>RAEWLLAVRSIQPEEKERLGQFIFAREAKVAMAGRLTIRKL

Parental  VAEKLNI-PWNNIRLQRTAKGKPVLAKDSSNPYPNFNFNISHQGDFAVLASEPELQVGIDIMKTSFPGRG
          VAEKLNI.PWNNIRLQRTAKGKPVLAKDS.NPYPNFNFNISHQGD.AVLASEPEL.VGIDIMKTS.PGRG
Retrocopy VAEKLNI<PWNNIRLQRTAKGKPVLAKDSLNPYPNFNFNISHQGDYAVLASEPELRVGIDIMKTSLPGRG

Parental  SIPEFFHIMKRKFTNKEWETIKSFKDEWTQLDMY
          SIPE.FHIMKRKFTN...ETIKSFKDEWTQLDM.
Retrocopy SIPELFHIMKRKFTNRVGETIKSFKDEWTQLDMF

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_1231 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 7 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000012279	1 retrocopy	retro_btau_134,
Echinops telfairi	ENSETEG00000004248	2 retrocopies	retro_etel_1231 , retro_etel_1503,
Myotis lucifugus	ENSMLUG00000016238	4 retrocopies	retro_mluc_1361, retro_mluc_1362, retro_mluc_1363, retro_mluc_479,
Mus musculus	ENSMUSG00000025894	1 retrocopy	retro_mmus_2827,
Oryctolagus cuniculus	ENSOCUG00000000231	1 retrocopy	retro_ocun_379,
Ictidomys tridecemlineatus	ENSSTOG00000000268	1 retrocopy	retro_itri_1438,
Tarsius syrichta	ENSTSYG00000005102	1 retrocopy	retro_tsyr_338,