RetrogeneDB ID: retro_etel_323

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: GeneScaffold_5349:307127..307584(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TRA2A
• Ensembl ID: ENSETEG00000007250
• Aliases: None
• Description: transformer 2 alpha homolog (Drosophila) [Source:HGNC Symbol;Acc:16645]

Sequence

>retro_etel_323
TCTAGGTCTCGGTCTAGGTCCAGAAGAAGTTCACAAGATCACGGTCTCATTGCCATAGACGATCCTGCAGCAGGTGTTAC
CATTGATTATCACAGGTGGCCCAGCCGCGGTCCTTCTCCCACATCTACTCGTCTACTCGAGGCGTCATGTTGGGAATCGG
GCAAACCCTGATCCCAACTGCTGTCTTGGAGAGTTGGGGTTGAGCTTCCACACCACCGAAAGAGACCTTCGAGACGTGTT
CTCTAAATATGGCCCCATTGCTGATGAGTCTAGTGTGTATGACCAGCAGTCTATGCGTTCAAGAGGATGTGCCTTTGTAT
TTTTTGAAAATGTAGACGATGCCGAGGAAGCTAAAGAGCGTGCTAATGGAATGGAGCTCGATGGCTGTAGGATCAGAGTT
GATTTCTCCATTACAAAAAGACCACACACCCCAGCTCCTAGCGTTTGTATGGGGAGA

Alignment

ORF - retro_etel_323 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.66 %
• Parental protein coverage: 54.36 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SRSRRHSHR-RYTRSRSHSHSHRRRSRSRSYTPDYRRRRSRSRSHSPMSNR-RRHTGSRANPDPNTCLGV
          SRSR..S.R...TRSRSH.H...RRS.SR.Y.........RS.SH...S.R.RRH.G.RANPDPN.CLG.
Retrocopy SRSRSRSRR<KFTRSRSHCH---RRSCSRCYH*LSQVAQPRSFSHIYSSTR<RRHVGNRANPDPNCCLGE

Parental  FGLSLYTTERDLREVFSRYGPLSGVNVVYDQRTGRSRGFAFVYFERIDDSKEAMERANGMELDGRRIRVD
          .GLS..TTERDLR.VFS.YGP......VYDQ...RSRG.AFV.FE..DD..EA.ERANGMELDG.RIRVD
Retrocopy LGLSFHTTERDLRDVFSKYGPIADESSVYDQQSMRSRGCAFVFFENVDDAEEAKERANGMELDGCRIRVD

Parental  YSITKRAHTPTPGIYMGR
          .SITKR.HTP.P...MGR
Retrocopy FSITKRPHTPAPSVCMGR

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_323 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 12 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000001130	1 retrocopy	retro_chof_974,
Callithrix jacchus	ENSCJAG00000001509	1 retrocopy	retro_cjac_1759,
Echinops telfairi	ENSETEG00000007250	2 retrocopies	retro_etel_323 , retro_etel_692,
Echinops telfairi	ENSETEG00000013178	1 retrocopy	retro_etel_1952,
Homo sapiens	ENSG00000164548	1 retrocopy	retro_hsap_386,
Gorilla gorilla	ENSGGOG00000009053	1 retrocopy	retro_ggor_391,
Mustela putorius furo	ENSMPUG00000013480	1 retrocopy	retro_mputfur_1442,
Nomascus leucogenys	ENSNLEG00000014794	1 retrocopy	retro_nleu_1481,
Otolemur garnettii	ENSOGAG00000009733	3 retrocopies	retro_ogar_1966, retro_ogar_2558, retro_ogar_3027,
Pongo abelii	ENSPPYG00000017728	1 retrocopy	retro_pabe_324,
Pan troglodytes	ENSPTRG00000018988	1 retrocopy	retro_ptro_299,
Sorex araneus	ENSSARG00000012900	1 retrocopy	retro_sara_467,