RetrogeneDB ID: retro_etel_1446

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_267283:2047..2632(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSETEG00000004005
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: MPV17L2
• Ensembl ID: ENSETEG00000013840
• Aliases: None
• Description: MPV17 mitochondrial membrane protein-like 2 [Source:HGNC Symbol;Acc:28177]

Sequence

>retro_etel_1446
ATGGCATCCGGCGGCTGGCGCTGGGTGCGCAGGCTCTGCGCAGTGGAGAAGCCTGCTATTCCAGGACCCAGCGCTGCTGG
TCACTAACACGCTGGGCTGCAGGCACTTTCATGGCAGCCGGGGACAGCGCATGCCAGTCCTGCGAAATCCGCTCCAGGTC
TGGCCAGAGGTTCCACCTGTGGCGCTTTGCAAGCATTTTTGCCATGGGCTGCAGTGTGGGCCTCTTCCTGCACTACCCGT
ACCTCTGGCTGGACCGACTGCTCCCTGCCCCAGGCCTCCGCAGCCTTCCAACCGTCCTCAGAAAGGTCCTCGTGGGCCCG
CGGGTGGCCTCATCCTTGTTAGGTGTGTGGTACTTCCTGGGTCTTGGCTGGCTGGAGGGCCAGACGCTGGATGAGAGCCA
CCAGGAGCTTCGTGACAAGTTCTGGGAATTCTACAAGGCCGACTGGTGCGCTTGGCTCCCTGCCCACCTGGTGAACTTCC
TCTTCATACTCTCCCAGTTCCGGGTCATCTACATCAATGGGCAGTACTCTCGGCTGGGGCACTTAACTCTCTCATTTGAA
GTACTGGGGTGCCAGCCGTGACTGT

Alignment

ORF - retro_etel_1446 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.62 %
• Parental protein coverage: 96.04 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MVSGRWHWVRGLWAAGKP-LFQGRALLVTNTLGC-GALMAAGDGARQTWEIRARPGQRFNPLRSASMFAM
          M.SG.W.WVR.L.A..KP.LFQ..ALLVTNTLGC.G..MAAGD.A.Q..EIR.R.GQRF...R.AS.FAM
Retrocopy MASGGWRWVRRLCAVEKP>LFQDPALLVTNTLGC>GTFMAAGDSACQSCEIRSRSGQRFHLWRFASIFAM

Parental  GCSMGPFLHYWYLWLDRLLPASGLRSLPSVLRKVLVDQLVASPLLGVWYFLGLGWLEGQTLEESHQELRD
          GCS.G.FLHY.YLWLDRLLPA.GLRSLP.VLRKVLV...VAS.LLGVWYFLGLGWLEGQTL.ESHQELRD
Retrocopy GCSVGLFLHYPYLWLDRLLPAPGLRSLPTVLRKVLVGPRVASSLLGVWYFLGLGWLEGQTLDESHQELRD

Parental  KFWEFYKADWCVWPPAQLVNFLFVPSQFRVTYIN-GVTLGWDTYLSYLKYRGPPPGC
          KFWEFYKADWC.W.PA.LVNFLF..SQFRV.YIN.G.TLGW.T.LS.LKY.G....C
Retrocopy KFWEFYKADWCAWLPAHLVNFLFILSQFRVIYIN>GSTLGWGT*LSHLKYWGASRDC

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_1446 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 8 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000027644	1 retrocopy	retro_acar_180,
Bos taurus	ENSBTAG00000025788	1 retrocopy	retro_btau_306,
Callithrix jacchus	ENSCJAG00000014104	1 retrocopy	retro_cjac_4063,
Echinops telfairi	ENSETEG00000013840	1 retrocopy	retro_etel_1446 ,
Macropus eugenii	ENSMEUG00000016379	2 retrocopies	retro_meug_223, retro_meug_943,
Macaca mulatta	ENSMMUG00000005025	1 retrocopy	retro_mmul_2493,
Nomascus leucogenys	ENSNLEG00000005944	1 retrocopy	retro_nleu_2666,
Pteropus vampyrus	ENSPVAG00000002028	1 retrocopy	retro_pvam_1254,