RetrogeneDB ID: retro_etel_313

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: GeneScaffold_5167:5058..5621(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CRLF3
• Ensembl ID: ENSETEG00000017897
• Aliases: None
• Description: cytokine receptor-like factor 3 [Source:HGNC Symbol;Acc:17177]

Sequence

>retro_etel_313
AAAGAGAGCTGGGAGGAATGGAGTCCTGGGAGTGCCCCCAGATAGGACATTCCACACTGGTGCCTCCCAAATGGCTTTCA
GGGATCGAGTCTGAACAGTCAAATAAATGTCACACTCCACAAGATACAGAATCGTGAGCAGTATCTACTCCAGTCATCCA
CCTTCTTTCTGTGGGAAGAACGAACCTTCAAGGTTGAAACTGTAGGATGACCAGAAAGAGGAGCCAATGTAAGAGTGTGT
GCAGGAAAGCAGAATGACTATGGCTCTTGGCAGCAGGATCAAGCAGTGTACGTTAGTGAAAATGGTGCACTTTTTGTAAA
GGGAAAAATATTAAAAAGACTAAGAAGTTACCTGCAGTCACTTCTAGGTCTACTGTCACGTTTGACGTTGAAGTTGTGAC
TCTAGGAACCATCAATAATAGCGAAAGCCAAAACTTCGAGTTTCAAGTCACTATTAGCACCAATAATAGAGATGTGGCTT
TTGATTGCCTGCTTGATCAATCCCGCAGTTCTTTTCACGTTGGATGCTCATTTTTCTATCCTGGCTGGAAAGTGTTGGTA
TTT

Alignment

ORF - retro_etel_313 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.09 %
• Parental protein coverage: 56.57 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  RQEWSPWSVPQTGHSTLVPHEWTP-GSEGYSLSSRRNIALRN-DTESPGV-LYSSAP-TYFCGQTLTF--
          ...W..WS.P........PH...P.G..G.SL.S..N..L...DTES..V..YSS.P.T.F.....TF..
Retrocopy KESWEEWS-PGSAPR*DIPHWCLPNGFQGSSLNSQINVTLHK<DTES*AV<IYSSHP<TFFLWEERTFKV

Parental  ETVGLPDRRDSLGVCAEKQDGCDSLQRDRAVCISTNGAVFVN-GKEM--TNQLPAVTSGSTVTFDIEAVT
          ETVG.P.R.....VCA.KQ....S.Q.D.AV..S.NGA.FV..GK....T..LPAVTS.STVTFD.E.VT
Retrocopy ETVG*PERGANVRVCAGKQNDYGSWQQDQAVYVSENGALFVK<GKNIKKTKKLPAVTSRSTVTFDVEVVT

Parental  LGALNNNEGGNIKLRVTISSNNREVVFDWLLDQSCGSLYFGCSFFYPGWKVLVF
          LG..NN.E..N....VTIS.NNR.V.FD.LLDQS..S...GCSFFYPGWKVLVF
Retrocopy LGTINNSESQNFEFQVTISTNNRDVAFDCLLDQSRSSFHVGCSFFYPGWKVLVF

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_313 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 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000017897	1 retrocopy	retro_etel_313 ,
Felis catus	ENSFCAG00000025986	1 retrocopy	retro_fcat_1916,
Macaca mulatta	ENSMMUG00000009069	2 retrocopies	retro_mmul_1002, retro_mmul_998,
Ictidomys tridecemlineatus	ENSSTOG00000012342	1 retrocopy	retro_itri_1384,