RetrogeneDB ID: retro_etel_641

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_121634:270..982(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TUBB
• Ensembl ID: ENSETEG00000013572
• Aliases: None
• Description: tubulin, beta class I [Source:HGNC Symbol;Acc:20778]

Sequence

>retro_etel_641
TTCTGGGAGGTGATCAGCGATGAACACGGCATCGACCCCACCGGCACCTACCACGGGGACAGCGCCCTGCAGCTGGACCG
CATCTCCGTGTACTACAACGAAGCCACAGGTGGCAATATGTTCCTCGTGCCATCTTGGTGGATCTAGAACCTGGAACCAT
GGACTCTGTTCGCTCAGGTCCTTTTGGCCAGATTTTCAGACTGGACAATTTTGGTGTTGGTCAGTGTGGGGCAGGCAACA
ACTGGGCCAAGGGCCACTACGCAGAGGGCGCTGAGCTGGTTGACTCCGTCCTGGACGTGGTGCGGAAGGAGGCCATGACC
AGTGACTGCCTGCAGGGCTTCCGGCTGACCCACTCACTGGGCGGAGGCACCGGCTCTGGAATGGGGACTTTGCTCATCAG
CAAGATCCGCGAAGCGTAGTACCCCACCGCATCATGAATACCTTCAGTGTGGTGCCCTCCCCCAAAGTCTCCAACATGGT
GGTCTAGCCCTACAATGCCACCCTCTCTGTCCACCAGCTGGTGGAGAACACTGACGAGACCTACTGCACCGATAACGAGG
CCCTCTATGATATCTGCTTCCGTACGCTGAAGCTGATTACGCCCACCTACGGAGACCTCAACCACCTGGTGTCGGCCACC
ATGAGCGGGGCCACCACCTGCCTCCGCTTCCCCCGCCAGCTCAATGCCGATCTCCGCAAACTAACCATCAAC

Alignment

ORF - retro_etel_641 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.58 %
• Parental protein coverage: 57.64 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  FWEVISDEHGIDPTGTYHGDSDLQLDRISVYYNEATGG-KYVPRAILVDLEPGTMDSVRSGPFGQIFRPD
          FWEVISDEHGIDPTGTYHGDS.LQLDRISVYYNEATGG..YVPRAILVDLEPGTMDSVRSGPFGQIFR.D
Retrocopy FWEVISDEHGIDPTGTYHGDSALQLDRISVYYNEATGG<QYVPRAILVDLEPGTMDSVRSGPFGQIFRLD

Parental  NFVFGQSGAGNNWAKGHYTEGAELVDSVLDVVRKEAESCDCLQGFQLTHSLGGGTGSGMGTLLISKIREE
          NF..GQ.GAGNNWAKGHY.EGAELVDSVLDVVRKEA...DCLQGF.LTHSLGGGTGSGMGTLLISKIRE.
Retrocopy NFGVGQCGAGNNWAKGHYAEGAELVDSVLDVVRKEAMTSDCLQGFRLTHSLGGGTGSGMGTLLISKIREA

Parental  -YP-DRIMNTFSVVPSPKVSDTVVEPYNATLSVHQL-ENTDETYCIDE--LYDICFRTLKLTTPTYGDLN
          .YP..RIMNTFSVVPSPKVS..VV.PYNATLSVHQL.ENTDETYC.D...LYDICFRTLKL.TPTYGDLN
Retrocopy *YP<HRIMNTFSVVPSPKVSNMVV*PYNATLSVHQLVENTDETYCTDNEALYDICFRTLKLITPTYGDLN

Parental  HLVSATMSGATTCLRFPRQLNADLRKLTIN
          HLVSATMSGATTCLRFPRQLNADLRKLTIN
Retrocopy HLVSATMSGATTCLRFPRQLNADLRKLTIN

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_641 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 7 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000006969	2 retrocopies	retro_btau_471, retro_btau_55,
Canis familiaris	ENSCAFG00000000443	1 retrocopy	retro_cfam_1860,
Echinops telfairi	ENSETEG00000013572	1 retrocopy	retro_etel_641 ,
Macaca mulatta	ENSMMUG00000023684	2 retrocopies	retro_mmul_2501, retro_mmul_375,
Nomascus leucogenys	ENSNLEG00000005348	1 retrocopy	retro_nleu_498,
Otolemur garnettii	ENSOGAG00000032213	1 retrocopy	retro_ogar_2391,
Ochotona princeps	ENSOPRG00000014770	4 retrocopies	retro_opri_1106, retro_opri_237, retro_opri_46, retro_opri_656,