RetrogeneDB ID: retro_etel_1392

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_258681:1270..2155(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSETEG00000011471
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSETEG00000004855
• Aliases: None
• Description: None

Sequence

>retro_etel_1392
ATGCCAAAGCCTGGAAAAAAGGAAGCCGTGGCCAAAGACGGGGAAGAGCCCAAGACCGAGCCAGAGGCCAAGAAGAGTAA
GGCGGGGGCAAAGAAAACTGAGAAAGAGGCAGCGGGAGAGGGGCCAGCCCTTTGCTCCGACTCTCCGGATCAGAAAACAT
CTCCCAGTGGCAAATCTGCCACACTTAAGATCTGCTCGTGGAATGTGGATGGTCTTCGAGCCTGGATTAAGAAGAAAGGT
TTAGATTGGGTAAAGGAGGAAGCTCCAGATATCCTGTGCCTCCAAGAAACCAAGTGTTCGGAGAAAAAACTACCAGCTAA
ATTGCAAGACCTGCCTGGACTATCTCATCAGTACTGGTCAGCACCTTCGGACAAAGAAGGGGACAGTGGCGTGGGTCTAC
TCTCTCGCCAGTGCCCACTCAAAGTCTCCTAGGGCATTGGCGAAGAGGAGCATGATCAGGAAGGCCGGGTGATCGTAGCT
GAATATGCCGAGTTTGTGCTGGTAACAGTCTATGTACCTAATGCAGGCCGGGGTCTGGTGCGACTGGAGTACCGGCAGTG
CTGGGATGAAGCCTTCTGCAAATTCCTGAAGGACTTGACTGCCTGCAAGCCCCTAGTGCTATGTGGCGACCTCAACGTGG
CCCACGAAGAGATTGACCTTCGCAACCCAAAAGGCAACAAAAAGAATGCTGGCTTTACTCCACAGGAGCGCCAAGGCTTT
GGGGAATTGCTGCAGGCTGTGCCGTTGGCCGACAGCTTCCGCCACCTCTACCCAGATGTGGCCTATGCTTACACCTTTTG
GACCTACATGATGAATGCTCGATCCAAGAATGTTGGCTGGCGTCTTGATTATTTTTTGTTGTCTCATTCTCTGTTACCTG
CGCTT

Alignment

ORF - retro_etel_1392 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.92 %
• Parental protein coverage: 92.77 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MPKRGKKEAVAEDGEEPKTEPEAKKSKAGAKKNEKEAAGEGPALYSDPPDQKTSPSGKAATLKICSWNVD
          MPK.GKKEAVA.DGEEPKTEPEAKKSKAGAKK.EKEAAGEGPAL.SD.PDQKTSPSGK.ATLKICSWNVD
Retrocopy MPKPGKKEAVAKDGEEPKTEPEAKKSKAGAKKTEKEAAGEGPALCSDSPDQKTSPSGKSATLKICSWNVD

Parental  GLRAWIKKKGLDWVKEEAPDILCLQETKCSEKKLPAELQDLPGLSHQYWSAPSDKEGYSGVGLLSRQCPL
          GLRAWIKKKGLDWVKEEAPDILCLQETKCSEKKLPA.LQDLPGLSHQYWSAPSDKEG.SGVGLLSRQCPL
Retrocopy GLRAWIKKKGLDWVKEEAPDILCLQETKCSEKKLPAKLQDLPGLSHQYWSAPSDKEGDSGVGLLSRQCPL

Parental  KVSYGIGEEEHDQEGRVIVAEYDEFVLVTAYVPNAGRGLVRLEYRQRWDEAFRKFLKDLAARKPLVLCGD
          KVS.GIGEEEHDQEGRVIVAEY.EFVLVT.YVPNAGRGLVRLEYRQ.WDEAF.KFLKDL.A.KPLVLCGD
Retrocopy KVS*GIGEEEHDQEGRVIVAEYAEFVLVTVYVPNAGRGLVRLEYRQCWDEAFCKFLKDLTACKPLVLCGD

Parental  LNVAHEEIDLRNPKGNKKNAGFTPQERQGFGELLQAVPLADSFRHLYPDVAYAYTFWTYMMNARSKNVGW
          LNVAHEEIDLRNPKGNKKNAGFTPQERQGFGELLQAVPLADSFRHLYPDVAYAYTFWTYMMNARSKNVGW
Retrocopy LNVAHEEIDLRNPKGNKKNAGFTPQERQGFGELLQAVPLADSFRHLYPDVAYAYTFWTYMMNARSKNVGW

Parental  RLDYFLLSHSLLPAL
          RLDYFLLSHSLLPAL
Retrocopy RLDYFLLSHSLLPAL

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_1392 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 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000002745	1 retrocopy	retro_btau_1729,
Echinops telfairi	ENSETEG00000004855	1 retrocopy	retro_etel_1392 ,
Loxodonta africana	ENSLAFG00000021872	1 retrocopy	retro_lafr_948,
Mus musculus	ENSMUSG00000035960	2 retrocopies	retro_mmus_2027, retro_mmus_433,
Otolemur garnettii	ENSOGAG00000013335	3 retrocopies	retro_ogar_1284, retro_ogar_2145, retro_ogar_3243,
Rattus norvegicus	ENSRNOG00000009663	1 retrocopy	retro_rnor_2971,
Ictidomys tridecemlineatus	ENSSTOG00000010096	1 retrocopy	retro_itri_1560,
Tupaia belangeri	ENSTBEG00000006405	1 retrocopy	retro_tbel_3409,