RetrogeneDB ID: retro_etel_1104

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_212241:7564..7856(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TRAPPC6B
• Ensembl ID: ENSETEG00000013828
• Aliases: None
• Description: trafficking protein particle complex 6B [Source:HGNC Symbol;Acc:23066]

Sequence

>retro_etel_1104
TTTACAAAAGATATTGTAAGGCTCAAGAATGAGTCAGATATCATGAGATTCATTTGTGAAGATTTTTGGACTAACACCCT
TCAAGAAACAAATCAACATTTAAGGACAAATCATCAGGTCACGATGTAATTCAGGACAACAAACTTGTCTGCTTACCCAG
ATGTCTACAGGAAAACCGTACTTAGAATATGCAGCAAGACATTTTGCATTTAGATGCGGCTTAATCTGAAGTGGCTTATC
ACATTTGGTAATGAAAAGTCTTGTGACAGCAGCAGTGTCTTCAATGCCTGCC

Alignment

ORF - retro_etel_1104 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.67 %
• Parental protein coverage: 66.22 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  FTKDTARFKDELDIMKFICKDFWT-TVFKKQID-NLRTNHQ-GIYVLQDNKFR-LLTQMSAGKQYLEHAS
          FTKD..R.K.E.DIM.FIC.DFWT.T.FKKQI...LRTNHQ.G..V.QDNK...LLTQMS.GK.YLE.A.
Retrocopy FTKDIVRLKNESDIMRFICEDFWT>TPFKKQIN<HLRTNHQ<GHDVIQDNKLV<LLTQMSTGKPYLEYAA

Parental  KYLAFTCGLIRGGLSNLGIKSIVTAEVSSMPA
          ...AF.CGLI..GLS.L..KS.VTA.VSSMPA
Retrocopy RHFAFRCGLI*SGLSHLVMKSLVTAAVSSMPA

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_1104 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 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000013828	1 retrocopy	retro_etel_1104 ,
Myotis lucifugus	ENSMLUG00000002627	2 retrocopies	retro_mluc_1179, retro_mluc_663,
Mus musculus	ENSMUSG00000020993	2 retrocopies	retro_mmus_1734, retro_mmus_2069,
Oryctolagus cuniculus	ENSOCUG00000002171	1 retrocopy	retro_ocun_813,
Sarcophilus harrisii	ENSSHAG00000001400	1 retrocopy	retro_shar_235,
Ictidomys tridecemlineatus	ENSSTOG00000002897	2 retrocopies	retro_itri_476, retro_itri_795,
Tupaia belangeri	ENSTBEG00000003331	1 retrocopy	retro_tbel_4529,