RetrogeneDB ID: retro_etel_1416

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_262522:7785..8307(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSETEG00000011536
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: COMMD8
• Ensembl ID: ENSETEG00000020257
• Aliases: None
• Description: COMM domain containing 8 [Source:HGNC Symbol;Acc:26036]

Sequence

>retro_etel_1416
TGGCAGCTGCAGCAGTTACCGGCTGAGCTTGGCCCGCACCTTCTTCACAAACTAAACCGATGGCATGTGTGGCCTGGCCG
CTCCTCTCTACCCGCATTATCAGAGCATTTGGGGTTCAACAGAATGGATTCACGTTCTAGAAGCTAGTGCCCCGTTTTTC
AAAGCTGCCTTGGGTAGAAATGTCTCTGATGAAAAGCTCTCTCCGAAGTGGAACCAGCTGAATTCTTTGCATCAGGAGGC
GATCGTGACATGCTTGAAAAGCAAAACAGATGAAATCAAGGGGCCTCGGCTGGGAGAAATAGTTGGTATTTCCTCTGCCC
AGGTTCCGGATTTTGATTGGCAGCTAAAGCTTGCACTGTCTAGTGTCAAGATTGTTACCTGACAGATGCCACTTTTAAAC
CTCCACCTCCATTTAAAGGACGTTGGAGCAGTGAAGTGTGTTCTGCTGAGGTGCGTCAAGAAGGGCTGCAGGGTCCACTG
AAGTCCTTGGCAGCAGCTAGCCTGGTGGCCCTGCAGGTGAAA

Alignment

ORF - retro_etel_1416 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.66 %
• Parental protein coverage: 94.57 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  WRLQKVPAELGPQLLHKM-IDGMCGRAYPLYQDYQSVWDSTEWIHVREDITTFFKDAVGKSLSDEEISQQ
          W.LQ..PAELGP.LLHK...DGMCG.A.PLY..YQS.W.STEWIHV.E....FFK.A.G...SDE..S..
Retrocopy WQLQQLPAELGPHLLHKL>TDGMCGLAAPLYPHYQSIWGSTEWIHVLEASAPFFKAALGRNVSDEKLSPK

Parental  LNQLHSFHQEAIMKCLRSRKDEIKQALLGEIAAISSAQLQDFDWQLKLALSSDKIAALQMPLLTLHLDVK
          .NQL.S.HQEAI..CL.S..DEIK...LGEI..ISSAQ..DFDWQLKLALSS.KI...QMPLL.LHL..K
Retrocopy WNQLNSLHQEAIVTCLKSKTDEIKGPRLGEIVGISSAQVPDFDWQLKLALSSVKIVT*QMPLLNLHLHLK

Parental  EKGA-ATPCCVEMSREELQSLIESLEAANKEVLQVQ
          ..GA....C..E...E.LQ....SL.AA....LQV.
Retrocopy DVGA<SEVCSAEVRQEGLQGPLKSLAAASLVALQVK

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_1416 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 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000001348	1 retrocopy	retro_btau_579,
Echinops telfairi	ENSETEG00000020257	3 retrocopies	retro_etel_1416 , retro_etel_182, retro_etel_210,
Felis catus	ENSFCAG00000023811	1 retrocopy	retro_fcat_421,
Myotis lucifugus	ENSMLUG00000011376	1 retrocopy	retro_mluc_1158,
Macaca mulatta	ENSMMUG00000021777	1 retrocopy	retro_mmul_434,
Ochotona princeps	ENSOPRG00000000739	1 retrocopy	retro_opri_805,
Ictidomys tridecemlineatus	ENSSTOG00000001221	1 retrocopy	retro_itri_1566,