RetrogeneDB ID: retro_etel_1503

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_275351:1766..2293(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSETEG00000003480
• 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_1503
ATGGTTTACCCTGCCAAACGATTCTGCTTAGTGCCAGCAATGAGGGTGTGCACTGGGCCTTTTCCTGCGGCACTTGGCTG
CTGAGCAGAGCCAAATGGCTGCTGATGGTGTGATCAATCCAGCCTGAGGAGAAGGCGCATATTGACCAGTTTGTCTTAGC
CCAGGACACAAAGGCAGCCATGGCTGGTTGTCTGATGATAGGGAAATTGGTTGCAGAAAAATTGAATATCCCTTGGAATA
ATATTCATTTGCGAAGAACTGCAAAAGGAAAACCAGTTCTTGCAAAGGACTCATTGAATCCTTATCCCAATTTCAACTTT
AATATCTCTCATTAAGGGGACTATGCGGCACTTGTTTCTGAACCTGAGCTGCAAGTTGGAATTGATATAATGAAGACTAG
CTTTCCAGGTCGTGGTTCAGTTCCAGAGTTCTTCCATATTACGAAAAGAAAACTTACCAACAAAGAGTGGGAAACCACCA
AAAGCTTTAAGGATGAATGGACTCAACTGGATCTGTTTTATAGAAAT

Alignment

ORF - retro_etel_1503 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.24 %
• Parental protein coverage: 57.28 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MVYPLPAKRVCLVPAM-EGVRWAFSCGTWLPSRAEWLLAVRSIQPEEKERIGQFVFARDAKAAMAGRLMI
          MVYP..AKR.CLVPAM.EGV.WAFSCGTWL.SRA.WLL.V.SIQPEEK..I.QFV.A.D.KAAMAG.LMI
Retrocopy MVYP--AKRFCLVPAM<EGVHWAFSCGTWLLSRAKWLLMV*SIQPEEKAHIDQFVLAQDTKAAMAGCLMI

Parental  RKLVAEKLNIPWNNIRLQRTAKGKPVLAKDSSNPYPNFNFNISHQGDFAVLASEPELQVGIDIMKTSFPG
          .KLVAEKLNIPWNNI.L.RTAKGKPVLAKDS.NPYPNFNFNISH.GD.A.L.SEPELQVGIDIMKTSFPG
Retrocopy GKLVAEKLNIPWNNIHLRRTAKGKPVLAKDSLNPYPNFNFNISH*GDYAALVSEPELQVGIDIMKTSFPG

Parental  RGSIPEFFHIMKRKFTNKEWETIKSFKDEWTQLDM-YRN
          RGS.PEFFHI.KRK.TNKEWET.KSFKDEWTQLD..YRN
Retrocopy RGSVPEFFHITKRKLTNKEWETTKSFKDEWTQLDLFYRN

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_1503 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,