RetrogeneDB ID: retro_etel_267

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: GeneScaffold_4523:10134..10619(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PRPS1L1
• Ensembl ID: ENSETEG00000014736
• Aliases: None
• Description: phosphoribosyl pyrophosphate synthetase 1-like 1 [Source:HGNC Symbol;Acc:9463]

Sequence

>retro_etel_267
GATTTGTATGCCAAGGCAGCTGTCCTGAAGTGGATAGGGAGAGTACCTCTGAGTGGAGGAACTACACTATTATCCCCCTG
ATGCTGTTGGAGCTAGACAGCAGCTTCAATTGCAGACTGGTTGCATGTGGACTTGGTCTTGATTCACAAAGAACAGAAGA
CCAATGAAGTGGTCTGCATGGTGCTCATAGGAGATGTGACGTATCGTGTGGCGATCTTTGTGGATGACATGGCCGGTACC
TGCAGCTCAATCTGCCATGCAGCTGACATACTTCTCTCAGCTGAGCGGCCAGAGTTTATGCCATCGTGACTCATGGAATC
TTTTCTAGTCCTGCCGTTTTCTGCATCAACAATGCATGCTTCGAAGCAATAGTCGGCACCAATACCATACCTCAAGAGGA
TAAGAGGAAACAATCCTCTAAAACACAGGTGATTGACATCTCCATGAGCCTTGCAGAAGCCAGCAAGAGAACTCACAATG
AAGAG

Alignment

ORF - retro_etel_267 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.64 %
• Parental protein coverage: 51.57 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  NLYAEPAVLKWI-RENISEWRNCTIVS-PDAGGAKR-VTSIADRLNVDFALIHKERKKANEVDRMVLVGD
          .LYA..AVLKWI.RE..SEWRN.TI...PDA.GA.....SIAD.L.VD..LIHKE.K..NEV..MVL.GD
Retrocopy DLYAKAAVLKWI<RESTSEWRNYTIIP<PDAVGARQ<AASIADWLHVDLVLIHKEQK-TNEVVCMVLIGD

Parental  VKDRVAILVDDMADTCGTICHAADKLLSAG-ATRVYAILTHGIFSGPAISRINNACFEAVVVTNTIPQED
          V..RVAI.VDDMA.TC..ICHAAD.LLSA..A.RVYAI.THGIFS.PA...INNACFEA.V.TNTIPQED
Retrocopy VTYRVAIFVDDMAGTCSSICHAADILLSAE<AARVYAIVTHGIFSSPAVFCINNACFEAIVGTNTIPQED

Parental  KMKHCSKIQVIDISMILAEAIRRTHNGE
          K.K..SK.QVIDISM.LAEA..RTHN.E
Retrocopy KRKQSSKTQVIDISMSLAEASKRTHNEE

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_267 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 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000002028	2 retrocopies	retro_dnov_2677, retro_dnov_947,
Echinops telfairi	ENSETEG00000005166	2 retrocopies	retro_etel_1613, retro_etel_669,
Echinops telfairi	ENSETEG00000014736	1 retrocopy	retro_etel_267 ,
Macropus eugenii	ENSMEUG00000010071	2 retrocopies	retro_meug_1612, retro_meug_443,
Oryctolagus cuniculus	ENSOCUG00000012391	3 retrocopies	retro_ocun_430, retro_ocun_867, retro_ocun_912,
Ochotona princeps	ENSOPRG00000013140	1 retrocopy	retro_opri_704,