RetrogeneDB ID: retro_etel_1871

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_309864:118983..119728(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TRNT1
• Ensembl ID: ENSETEG00000018177
• Aliases: None
• Description: tRNA nucleotidyl transferase, CCA-adding, 1 [Source:HGNC Symbol;Acc:17341]

Sequence

>retro_etel_1871
AGACTGTGCCTTCTGAAGCAGTAACTCTTTACAAGGAAGTTACAGTCTCCTGAATTCCAATCACTCTTCCCAAAGGATTG
AAGAGTCTGACAGAAATATTTGTCAAAGAAAACCACAAGTTAAGAATAGCAGGAGGAGCCGGGAGGGATTTATTAAATGG
GGTGAAGCCTCAAGATGTGGATTTTGCAACCACAGCCACCCCTGCTCAGATGAAGGAGATGTTTCAGTCCGCTGGGATGC
GAATGATCAACAACAAAGGCGAAAACATGGAACAATCACTGTCAGGCTTCCTGAGGAAAAGTTTGAAATTACTACACTAT
GGATTGATATTCTCACAGATGGAAGACGTGCTGAGCTAGAATTTACCACTGACTGGCAGAAAGATGCTGAGCACAGAGAC
CTTAATATCAATTCTATGTTTCTAGGCTTTGATGGTACCTTGTTTGATTACTTCAATGGTTATGAAGATTTAAAAAACAA
GAAAATTTGATTTGTTGGACATGCTAAACAGAGAATACGAGAAGATTACCTTTGAATTTTAAGATAGTTCAGTTTTTATG
GAAGAATTGTTGAAAAACCTGATGACCATGATCCTAAAACATTGGAAGCAATTGCAGAAAATGGGAAAGGCCTGGCAGGA
ATATCAGGAGAGAGGATTTGGGTAGAATTGAAAAAAATTCTTGTTGGTCACCATGTAAAGCACCTGATTAATCTTATGTA
TGATCTTGATGTGGCCCCTTACATA

Alignment

ORF - retro_etel_1871 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.65 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  RLCLSKQYLFTMKLQSPESKSLFTE-GLKSLTEIFVKENHELRIAGGAVRDLLNGVKPQDVDFATTATPA
          RLCL.KQ.LFT.KLQSPE..SLF...GLKSLTEIFVKENH.LRIAGGA.RDLLNGVKPQDVDFATTATPA
Retrocopy RLCLLKQ*LFTRKLQSPEFQSLFPK<GLKSLTEIFVKENHKLRIAGGAGRDLLNGVKPQDVDFATTATPA

Parental  QMKEMFQSAGIRMINNKGE-KHGTITARLHEE-FEITTLRIDVLTDGGHAEVEFTTDWRKDAERRDLTIN
          QMKEMFQSAG.RMINNKGE.KHGTIT.RL.EE.FEITTL.ID.LTDG..AE.EFTTDW.KDAE.RDL.IN
Retrocopy QMKEMFQSAGMRMINNKGE<KHGTITVRLPEEKFEITTLWIDILTDGRRAELEFTTDWQKDAEHRDLNIN

Parental  SMFLGFDGTLFDYFNGYEDLKNKKVRFVGHAKERIREDYLRILRYFRFYGRIVEKPDDHDPKTLEAIAEN
          SMFLGFDGTLFDYFNGYEDLKNKK..FVGHAK.RIREDYL.ILR.F.FYGRIVEKPDDHDPKTLEAIAEN
Retrocopy SMFLGFDGTLFDYFNGYEDLKNKKI*FVGHAKQRIREDYL*ILR*FSFYGRIVEKPDDHDPKTLEAIAEN

Parental  GKGLAGISGERIWVEVKKILVGNHVKHLINLMYDLDVAPYI
          GKGLAGISGERIWVE.KKILVG.HVKHLINLMYDLDVAPYI
Retrocopy GKGLAGISGERIWVELKKILVGHHVKHLINLMYDLDVAPYI

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_1871 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 11 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000015466	1 retrocopy	retro_cjac_1512,
Dasypus novemcinctus	ENSDNOG00000008837	1 retrocopy	retro_dnov_1635,
Dipodomys ordii	ENSDORG00000014035	1 retrocopy	retro_dord_414,
Echinops telfairi	ENSETEG00000018177	2 retrocopies	retro_etel_1871 , retro_etel_905,
Homo sapiens	ENSG00000072756	2 retrocopies	retro_hsap_246, retro_hsap_2598,
Gorilla gorilla	ENSGGOG00000015286	1 retrocopy	retro_ggor_300,
Nomascus leucogenys	ENSNLEG00000003226	1 retrocopy	retro_nleu_856,
Petromyzon marinus	ENSPMAG00000002236	1 retrocopy	retro_pmar_17,
Pongo abelii	ENSPPYG00000013702	3 retrocopies	retro_pabe_1916, retro_pabe_2721, retro_pabe_412,
Pan troglodytes	ENSPTRG00000014564	1 retrocopy	retro_ptro_1522,
Rattus norvegicus	ENSRNOG00000006432	1 retrocopy	retro_rnor_512,