RetrogeneDB ID: retro_etel_2077

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_49479:89..1253(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSETEG00000013196
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSETEG00000019380
• Aliases: None
• Description: None

Sequence

>retro_etel_2077
TTTTCACCTCTCAACCCCTTTGCCTGGGCAGATCATTTGAAAGCCCACGAAGAGGCTCAGGTCTCATACAGCACTGCAGG
GCAACAGAAGTTACCTTACCTCAGAGGCTGCAGGATCCCAGGCTTGCCGCTGGGCTCCGGTGGGCCTTCCAGCAGAGTCT
TGTCTATTGGCTCCACCCTTCTTTGCCCTGGCTGCCACTGTTCCCTCGAATCGGAACAGACAGAAGAATGGCCGGAAAGA
CAAGCCCACGGTCAAATGATGATGCCCTGCAACACGTTTTAATGAGTGACTGGTCAGTAAGCTTTACTTCTCTATATAGT
CTGCTGAAAACAAAGCTTTGCCCCTATTTCTACATTCGTCCCTATCAGTTTACAGTACTGTTCCGGGCAGCAGGGTTTCC
TGGAAGTGCTGTCATCACGGTTCTCATCTCCCCCACAACTAGAGGTTTAAGAGAAGCTATGAAAAATGAAGGTATTGACT
TTTCTCTGCCTTTAATAAAAGAAACTGCCCATAAGAAGAAAGGATCGGGAACAAGCTTGGGACACGGAGAGGAGCAAGCC
ATCAGTGATGAGGATGAAGAGGAAACTTTTTCCTGGTTGAAGGAGATGGGTGTGCAAGATAAAATTAAAAAGCCAGACAT
ACCCTCTATCGAGCTGCGGAAAGAAAAACATGCAGTGCAGATGGATCATAAGCTTGAGTCTGTTGTATTGGTGAAAGGAA
TCAACGCTTTTACCTTGCTCAATTTTTTGATCAACTCTTAAGAGTCTAGTGGCCACCTCTGGTCCACAGGCAGGACTTCC
ACCAGCCCTGTTATCCCCTGGAGCTTTCAGAGGCGCCACCATGCAAACGCTTAGGGCACGAAGCGTCAACGTGAAGACAG
AAGCTCCTTCTGGATGCAAAGATCAGTTTAGTTTGGAGATCGCAGGTCCGGTGATGCCTCATTCGCTACACTCTGTGCTA
ATGCTCCTCCAATCTTCTCAGAGCGGGTCTTTTTCAGCAGGACCGTACACACATGAGTCAACTGCTGTATTTTATAGCAG
CCCGCCAGTGGATAAAGTACTGGACAAGGAAATTGTTCATAAGGAACTTGCCAACTGTGGGTTGCACCCTAAAACTCTGG
AGCACCTAAGTCAGATACCATTACTGGGGAAATCATCCTTCCAG

Alignment

ORF - retro_etel_2077 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.21 %
• Parental protein coverage: 71.22 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  FTSSQPFAWADHLKAHEEAQ-GLVQHCRATEVTLPQRIQDPRLSTELRCAFQQSLVYWLHPSLPWLPLFP
          F....PFAWADHLKAHEEAQ.GL.QHCRATEVTLPQR.QDPRL...LR.AFQQSLVYWLHPSLPWLPLFP
Retrocopy FSPLNPFAWADHLKAHEEAQ<GLIQHCRATEVTLPQRLQDPRLAAGLRWAFQQSLVYWLHPSLPWLPLFP

Parental  RIGADRRMAGKTSPWSNDDALQHVLMSDWSVSFTSLYNLLKTKLCPYFYICTYQFTVLFRAAGFAGSDVI
          RIG.DRRMAGKTSP.SNDDALQHVLMSDWSVSFTSLY.LLKTKLCPYFYI..YQFTVLFRAAGF.GS.VI
Retrocopy RIGTDRRMAGKTSPRSNDDALQHVLMSDWSVSFTSLYSLLKTKLCPYFYIRPYQFTVLFRAAGFPGSAVI

Parental  TALISPTTRGLREAMKNEGIDFSLPLIKETAHKKKRSGTSLGHGEEQAISDEDEEETFSWLKEMGVQDKI
          T.LISPTTRGLREAMKNEGIDFSLPLIKETAHKKK.SGTSLGHGEEQAISDEDEEETFSWLKEMGVQDKI
Retrocopy TVLISPTTRGLREAMKNEGIDFSLPLIKETAHKKKGSGTSLGHGEEQAISDEDEEETFSWLKEMGVQDKI

Parental  KKPDILSIKLRK-KHEVQMDHKPES-VLVKGINTFTLLNFLIN-CKSLVATSGPQAGLPPTLLSPVAFRG
          KKPDI.SI.LRK.KH.VQMDHK.ES.VLVKGIN.FTLLNFLIN..KSLVATSGPQAGLPP.LLSP.AFRG
Retrocopy KKPDIPSIELRKEKHAVQMDHKLESVVLVKGINAFTLLNFLIN>LKSLVATSGPQAGLPPALLSPGAFRG

Parental  ATMQMLKARSVSVKTQAPSGYREQFSLEITGPVMPHSLHSVLTLLQSSQSGSFSAGLYTHEPTAVFNSSP
          ATMQ.L.ARSV.VKT.APSG...QFSLEI.GPVMPHSLHSVL.LLQSSQSGSFSAG.YTHE.TAVF.SSP
Retrocopy ATMQTLRARSVNVKTEAPSGCKDQFSLEIAGPVMPHSLHSVLMLLQSSQSGSFSAGPYTHESTAVFYSSP

Parental  PVDKVLDKDIVHKELANCGLHPKTLEQLSQIPLLGKSSLQ
          PVDKVLDK.IVHKELANCGLHPKTLE.LSQIPLLGKSS.Q
Retrocopy PVDKVLDKEIVHKELANCGLHPKTLEHLSQIPLLGKSSFQ

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_2077 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000007826	1 retrocopy	retro_ecab_657,
Echinops telfairi	ENSETEG00000019380	1 retrocopy	retro_etel_2077 ,
Macaca mulatta	ENSMMUG00000003701	1 retrocopy	retro_mmul_711,