RetrogeneDB ID: retro_etel_1040

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_203154:7590..8173(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: POLR3G
• Ensembl ID: ENSETEG00000008379
• Aliases: None
• Description: polymerase (RNA) III (DNA directed) polypeptide G (32kD) [Source:HGNC Symbol;Acc:30075]

Sequence

>retro_etel_1040
GATACAGATCATAAACCAGTGCCGTTGCTAACAGGAGAAGGTGGGGAGTATATGCTGGCCCTGAAACAGAAGCTGAGAGA
AACTATGAAAAGAATGCTTAATTTAATAGAAACATTTGAAAAAAGAAAAAGATATAGAAGGGTATATTTATAACCAAGTG
AAAATATACAAAGAAGATTGGGTACCATATTGGTGGAGATTCCCACGAGAGATGATGTCAGGAGGGAGGGGGGATGCAAA
AAAGCACATCCCAAATCCAAAAATGCAGCAAATTCTAGCAAAGCAACTTCAGTCACAAATAGTATTAATGTATTAAAAAA
TATCAAGGAATTGGAAAAAAGAGGTGATGGTGAAAAATCAGACGAGGGGATTGAAGGGATAGAAGAAAGCAAATAGAACA
ATAAAGAAGGCAGGCAACAATGAAGAAGATGCTTTTGTAGAACATGAACATGATAAAGAGGAACAAAAGAGAAAAATGAT
TACATTCATTCTTACTTTAACAATGGAGATTAATTTGGTGCAGACAGTGATAACATGGATGAAGCAAACCATTACTAGTC
ACAAGGCTCAAAACATTTTAGGA

Alignment

ORF - retro_etel_1040 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63. %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  DTDYKPVPLRTGEGEEYMLALKQELRETMKRMPYFIEPHEEK-QDIERYSKNHMKIYKEEWVPDWRRLPR
          DTD.KPVPL.TGEG.EYMLALKQ.LRETMKRM...IE..E....DIE.Y..N..KIYKE.WVP.W.R.PR
Retrocopy DTDHKPVPLLTGEGGEYMLALKQKLRETMKRMLNLIETFEKR>KDIEGYIYNQVKIYKEDWVPYWWRFPR

Parental  EMMP--RKKCKRAAP-KSKKAEDASKAASVTNSMDVLKKIEELEKRGDGEKSDEETEEKEGGKEKNKEG-
          EMM...R...K...P.KSK.A...SKA.SVTNS..VLK.I.ELEKRGDGEKSDE..E..E..K..NKEG.
Retrocopy EMMSGGRGDAKKHIP<KSKNAANSSKATSVTNSINVLKNIKELEKRGDGEKSDEGIEGIEESK*NNKEG>

Parental  DDDEEDAAAEQEEYDEEEQ-EEENDYINSYFDNGDDFGAD-MTTWMKQPISHDMAQNISG
          ...EEDA..E..E.D.EEQ..E.NDYI.SYF.NGD.FGAD...TWMKQ.I....AQNI.G
Retrocopy GNNEEDAFVE-HEHDKEEQ<KEKNDYIHSYFNNGD*FGAD>VITWMKQTITSHKAQNILG

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_1040 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 14 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000006306	1 retrocopy	retro_chof_125,
Callithrix jacchus	ENSCJAG00000010747	1 retrocopy	retro_cjac_2691,
Echinops telfairi	ENSETEG00000008379	1 retrocopy	retro_etel_1040 ,
Homo sapiens	ENSG00000113356	2 retrocopies	retro_hsap_1454, retro_hsap_1885,
Gorilla gorilla	ENSGGOG00000000266	2 retrocopies	retro_ggor_1119, retro_ggor_1382,
Myotis lucifugus	ENSMLUG00000014954	1 retrocopy	retro_mluc_2233,
Macaca mulatta	ENSMMUG00000018972	1 retrocopy	retro_mmul_1332,
Nomascus leucogenys	ENSNLEG00000013749	1 retrocopy	retro_nleu_1807,
Otolemur garnettii	ENSOGAG00000005560	1 retrocopy	retro_ogar_3512,
Pongo abelii	ENSPPYG00000015624	1 retrocopy	retro_pabe_1564,
Pan troglodytes	ENSPTRG00000017068	2 retrocopies	retro_ptro_1266, retro_ptro_989,
Rattus norvegicus	ENSRNOG00000016260	2 retrocopies	retro_rnor_458, retro_rnor_503,
Ictidomys tridecemlineatus	ENSSTOG00000008664	1 retrocopy	retro_itri_18,
Tupaia belangeri	ENSTBEG00000002278	2 retrocopies	retro_tbel_2495, retro_tbel_3069,