RetrogeneDB ID: retro_etel_200

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: GeneScaffold_3511:46152..46767(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMEM126B
• Ensembl ID: ENSETEG00000008939
• Aliases: None
• Description: transmembrane protein 126B [Source:HGNC Symbol;Acc:30883]

Sequence

>retro_etel_200
GACATCAAGTTGGCAACATATACTCATGGCCAACCCAGTTCTTCTCCAGAAGATGCAACATTCAGAAGACCAATGGTGAC
GGAAATTATAGGGAACAAATTGAATATCTTAGAAAAGAAAATATAACCTTAAATATACAAGGATCTGTTTTCATGGGAAC
AACAGCTGGTTTCTCTGGAATAATGGCAAACTTTATTTTCAGGTACTGCTTCAAGGTTCAACATGATGCTTTGAAGACAT
ATTCATCATTGGCCACCCTTCCGTTTTTATCTACTGTAGTTACTTACAAACTCTTTGTAACTGATACTTTGTATTAAGGT
AACATCAGCCAGGAGAACTGTGCTGTGAGACGGTCACTGGCGGGGTTATTGGGCAGTGTTTCATTCCAGTGCTTCGGCTT
TTTCTAAAACCAGACGTCTGGCAGGCAAGTATCATACGGTCCCGTTGCCACCCAAAGGAAGGCTTTTACTCCTCTGGTTT
CCACTTTGCCAAAGGGAGGTGAAAGCAATGGCCATTCCCCTGACCCTGCTAATGCTCACTGGAATCGTGAATGGTCTGCA
GCATTATGAAGTATTTGAAAGTATTCAGAACAGGAAGGAGACTCTACATGAAGAT

Alignment

ORF - retro_etel_200 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.37 %
• Parental protein coverage: 88.21 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  DIKLATYTHGQPSSSPEDAKFKRPMVMEIIEKK-IEYLRKEK-TLNLYGSV-LGTTAGFSGILANFIFRY
          DIKLATYTHGQPSSSPEDA.F.RPMV.EII..K.IEYLRKE..TLN..GSV..GTTAGFSGI.ANFIFRY
Retrocopy DIKLATYTHGQPSSSPEDATFRRPMVTEIIGNK<IEYLRKENITLNIQGSVFMGTTAGFSGIMANFIFRY

Parental  CFKVQHDALKTYSSLATLPFLSTIVTYKLFVTDALYSGDISQENCVVRSSLVGVLCG-VLYPSGLAFSKN
          CFKVQHDALKTYSSLATLPFLST.VTYKLFVTD.LY.G.ISQENC.VR.SL.G.L.G.V...S..AFSK.
Retrocopy CFKVQHDALKTYSSLATLPFLSTVVTYKLFVTDTLY*GNISQENCAVRRSLAG-LLG>VFHSSASAFSKT

Parental  GRLAVKYHTVPLPPKGRVLLHWSLLCHREVKAMAIPLTLQMLLGIMNGLQHYEVFESIIGK--TVHED
          .RLA.KYHTVPLPPKGR.LL.W..LC.REVKAMAIPLTL.ML.GI.NGLQHYEVFESI.....T.HED
Retrocopy RRLAGKYHTVPLPPKGRLLLLWFPLCQREVKAMAIPLTLLMLTGIVNGLQHYEVFESIQNRKETLHED

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_200 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 6 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000020596	1 retrocopy	retro_btau_420,
Echinops telfairi	ENSETEG00000007180	2 retrocopies	retro_etel_1693, retro_etel_667,
Echinops telfairi	ENSETEG00000008939	1 retrocopy	retro_etel_200 ,
Mus musculus	ENSMUSG00000030614	1 retrocopy	retro_mmus_1618,
Oryctolagus cuniculus	ENSOCUG00000016529	3 retrocopies	retro_ocun_1656, retro_ocun_1671, retro_ocun_607,
Sus scrofa	ENSSSCG00000014905	1 retrocopy	retro_sscr_452,