RetrogeneDB ID: retro_etel_905

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_182532:3125..3797(+)
• 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_905
AGATTGTGACTTCTGAAACAATCTCTATTTACAGGGACGTTAAAGTCCCCAGGACTCCAGTCCCTCTTCATCAAAGGATT
CAAGAGTCTGACAGAATCATTTGTCAAAGGAAAATCATGAGTTACGATTACCAGGAGGAGCCACGAGGGCTTTATTAAAT
GGAGTAAAGTCTCAAGATATGGATCTTGCAACAGTGACCACCACCACTCAAACGAAGGAGCTATTTCAATCTGCCCAGAA
TCGTATGAGCAACAACAAAGGAGAAAACCAGAGAACAGTCACTGCCAGGTTTCATGAAGAAAAATTTGAAATTACTACAC
TACAGATGGATGTCCTCACAGATGGAAGACATGCTGAGGTAGAATTCACCACTGACTGGCAGAAAGATTCTGTGCACAGG
GACTTTATTATTAATTTTACATTTCTATGCTTTCATAGTACTTTATTTAACTAGCTTAATGCTTATGAAGAATTAAAAAT
ATGAAAGTTTGATGTGTCAGACATGCTAAATAAAGAGCACAGGGAGATTATCTTCAGTATTCTAGATATTTCATGTTTTA
TGGGAAAATTGCTGAAAAACCGGGAGACCATGATCCTGAAACTTTGGAATCAATGCCAGAAAATAGAAAAGGCTTGGCTG
GGATATCAAGAGAGAGGATTTGAGTCGAATTG

Alignment

ORF - retro_etel_905 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.04 %
• Parental protein coverage: 89.92 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  RLCLSKQYLFTMKLQSPESKSLFTEGLKSLTEIFV-KENHELRIAGGAVRDLLNGVKPQDVDFATTATPA
          RL.L.KQ.LFT..L.SP...SLF..G.KSLTE.FV.KENHELR..GGA.R.LLNGVK.QD.D.AT..T..
Retrocopy RL*LLKQSLFTGTLKSPGLQSLFIKGFKSLTESFV>KENHELRLPGGATRALLNGVKSQDMDLATVTTTT

Parental  QMKEMFQSAGIRMINNKGEKHGTITARLHEE-FEITTLRIDVLTDGGHAEVEFTTDWRKDAERRDLTINS
          Q.KE.FQSA..RM.NNKGE...T.TAR.HEE.FEITTL..DVLTDG.HAEVEFTTDW.KD...RD..IN.
Retrocopy QTKELFQSAQNRMSNNKGENQRTVTARFHEEKFEITTLQMDVLTDGRHAEVEFTTDWQKDSVHRDFIINF

Parental  MFLGFDGTLFDYFNGYEDL-KNKKVRFVGHAKERIREDYLRILRYFRFYGRIVEKPDDHDPKTLEAIAEN
          .FL.F..TLF...N.YE.L.KN.KV..V.HAK.R...DYL...RYF.FYG.I.EKP.DHDP.TLE...EN
Retrocopy TFLCFHSTLFN*LNAYEEL<KNMKV*CVRHAK*RAQGDYLQYSRYFMFYGKIAEKPGDHDPETLESMPEN

Parental  GKGLAGISGERIWVEV
          .KGLAGIS.ERI.VE.
Retrocopy RKGLAGISRERI*VEL

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_905 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,