RetrogeneDB ID: retro_etel_120

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: GeneScaffold_2245:94820..95667(+)
• Located in intron of: ENSETEG00000005181

Retrocopy information

• Ensembl ID: ENSETEG00000005187
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: EIF3M
• Ensembl ID: ENSETEG00000013437
• Aliases: None
• Description: eukaryotic translation initiation factor 3, subunit M [Source:HGNC Symbol;Acc:24460]

Sequence

>retro_etel_120
ATGAGCGTCCCTGCCTTCATCAATATCAGTGAGGAAGATCAGGCTGCTGAGCTTTGAGCTTACCTAAAATCGAAAGGAGC
TGAAATTTCCGAAGAAAACTCAGAAGGTGATCTTCATATAGATTTAGCTCAGATTATAGAAGCCTGCGATGTGTGTCTGA
AGGAAGATGACAAAGATGTGGAAAGTGTGATGAACAGTGTGGTGTCCCTCCTCTTGATCTTGGAACCAGACAAGCAAGAA
GCTCTGACTGAAAGCCTGTGTGAAAAGCTAGTCAAATTTCGAGAAGGAGAACGCCCATCTCTGAGGCTGCAGTTGCTAAG
CAACCTTTTCCATGGGATGGATAAGAATACTCCTGTACGATACACAGTGTATGTAGCCTCATTAAAGTAGCAGCATCCGG
TGGAGCTATCCAGTACATCCCAACTGAGCTGGATCCAGTCTGAAAATGAATTTCTGACTGGAACCTCACCACTGAGAAGA
AGCACACCCTTTTAAGGCTGCTTTACGAGGCACTAGTAGATTGCAAGAAAAGTGAAGCTGCTTCGAAGGTCATGGTGGAG
TTGCTGGGAAGTTACACAGAAGATAATGCTTCTCAAGCTGGAGTTGATGCCCACAGGTGTATTGTCCGTGCATTGAAAGA
TCCAAGTGCATTTCTTTTTGACCATCTTCTTACTTTAAAACCAGTGAAGCTTTTAGAAGGCGAGCTTATTCTTGATTTGT
TAACCATTTTTGTGAGTGCTAAATTGGCATCATATGTCAAGTTTTATCAGAATAATAAAGACTTCATTGACTCACTTGCC
TCTTACATGAGCAGAACATGGCAAAAATGAGACTGCTTACTTTTATG

Alignment

ORF - retro_etel_120 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.63 %
• Parental protein coverage: 75.54 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MSVPAFIDISEEDQAAELRAYLKSKGAEISEENSEGGLHIDLAQIIEACDVCLKEDDKDVESVMNSVVSL
          MSVPAFI.ISEEDQAAEL.AYLKSKGAEISEENSEG.LHIDLAQIIEACDVCLKEDDKDVESVMNSVVSL
Retrocopy MSVPAFINISEEDQAAEL*AYLKSKGAEISEENSEGDLHIDLAQIIEACDVCLKEDDKDVESVMNSVVSL

Parental  LLILEPDKQEALIESLCEKLVKFREGERPSLRLQLLSNLFHGMDKNTPVRYTVY-CSLIKVAASCGAIQY
          LLILEPDKQEAL.ESLCEKLVKFREGERPSLRLQLLSNLFHGMDKNTPVRYTVY.CSLIKVAAS.GAIQY
Retrocopy LLILEPDKQEALTESLCEKLVKFREGERPSLRLQLLSNLFHGMDKNTPVRYTVY<CSLIKVAASGGAIQY

Parental  IPTELDQVRKWISDWNLTTEKKHTLLRLLYEALVDCKKSEAASKVMVELLGSYTEDNASQARVDAHRCIV
          IPTELD.V.K.ISDWNLTTEKKHTLLRLLYEALVDCKKSEAASKVMVELLGSYTEDNASQA.VDAHRCIV
Retrocopy IPTELDPV*K*ISDWNLTTEKKHTLLRLLYEALVDCKKSEAASKVMVELLGSYTEDNASQAGVDAHRCIV

Parental  RALKDPSAFLFDHLLTLKPVKFLEGELIHDLLTIFVSAKLASYVKFYQNNKDFIDSLG--LSQNMAK-MR
          RALKDPSAFLFDHLLTLKPVK.LEGELI.DLLTIFVSAKLASYVKFYQNNKDFIDSL....S....K.MR
Retrocopy RALKDPSAFLFDHLLTLKPVKLLEGELILDLLTIFVSAKLASYVKFYQNNKDFIDSLASYMSRTWQK<MR

Parental  LLTFM
          LLTFM
Retrocopy LLTFM

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_120 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 8 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000005338	2 retrocopies	retro_btau_1736, retro_btau_812,
Echinops telfairi	ENSETEG00000013437	1 retrocopy	retro_etel_120 ,
Myotis lucifugus	ENSMLUG00000014727	2 retrocopies	retro_mluc_1982, retro_mluc_431,
Mus musculus	ENSMUSG00000027170	1 retrocopy	retro_mmus_421,
Oryctolagus cuniculus	ENSOCUG00000004483	1 retrocopy	retro_ocun_282,
Otolemur garnettii	ENSOGAG00000015913	1 retrocopy	retro_ogar_1783,
Pteropus vampyrus	ENSPVAG00000015083	1 retrocopy	retro_pvam_1134,
Vicugna pacos	ENSVPAG00000007791	1 retrocopy	retro_vpac_342,