RetrogeneDB ID: retro_etel_2045

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_40103:3348..3764(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MGST1
• Ensembl ID: ENSETEG00000007466
• Aliases: None
• Description: microsomal glutathione S-transferase 1 [Source:HGNC Symbol;Acc:7061]

Sequence

>retro_etel_2045
ATGGTCGACCTCCCCCAACTAGCTGAGAATGAGCTCTTCGTGCACCTTGCCTCCTACATGACTGTTCTTTCGAAAATAAT
GCTCACAAGTGCTGCACGTGCGTGCTATGGAGTGACAGGCAAGGTTTGGCTAACCCAGGAGACTGCGCAATTTGGCAAAG
GGGAAAATGCTAGGAAACATCTTTGGACAGAGGACCAAGTAGAACATGTACGAAGAGCCCACTTGAATGACCTTGAAAGC
TGTGTGCCCTTGCTTGGCATCGGCCTCCTCTATTCCGTGAGCGATCGGATTTGTCTACAGCACTCCTGCATGTCAGACTC
TTTGGAGCATGGATCTACCACACGAGTGCAGATTATTTGACACCAGCCAAATAGAGGCTCGGGTTTTTTTTTTATATTGG
ATATGGGGTTACATTT

Alignment

ORF - retro_etel_2045 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.42 %
• Parental protein coverage: 91.61 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAGLTQLAENDVFMAFASYATIILSKMMLMSTVTAMHRVTKKAFANPEDCASFGKGEAAKKHLRTDDRVE
          M..L.QLAEN..F...ASY.T..LSK.ML.S...A...VT.K.....E..A.FGKGE.A.KHL.T.D.VE
Retrocopy MVDLPQLAENELFVHLASYMTV-LSKIMLTSAARACYGVTGKVWLTQET-AQFGKGENARKHLWTEDQVE

Parental  RVRRAHLNDLENIVPFLGIGLLYSLSD-PDLSTALLHFRLFVAARIYHTVA-YLTPLPQPNRGLAFFVGY
          .VRRAHLNDLE..VP.LGIGLLYS.SD..DLSTALLH.RLF..A.IYHT.A.YLTP......G.....GY
Retrocopy HVRRAHLNDLESCVPLLGIGLLYSVSD<SDLSTALLHVRLF-GAWIYHTSADYLTP-AK*RLGXXXXIGY

Parental  GVTF
          GVTF
Retrocopy GVTF

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_2045 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 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000013004	3 retrocopies	retro_chof_1564, retro_chof_1842, retro_chof_2298,
Callithrix jacchus	ENSCJAG00000021590	1 retrocopy	retro_cjac_745,
Echinops telfairi	ENSETEG00000007466	7 retrocopies	retro_etel_142, retro_etel_1541, retro_etel_1615, retro_etel_1727, retro_etel_2045 , retro_etel_789, retro_etel_989,
Loxodonta africana	ENSLAFG00000002693	1 retrocopy	retro_lafr_976,
Myotis lucifugus	ENSMLUG00000002358	1 retrocopy	retro_mluc_1078,
Tupaia belangeri	ENSTBEG00000016248	6 retrocopies	retro_tbel_1229, retro_tbel_2494, retro_tbel_3452, retro_tbel_3654, retro_tbel_366, retro_tbel_4500,