RetrogeneDB ID: retro_etel_1461

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_269670:265..1099(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSETEG00000014755
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: TOMM40L
• Ensembl ID: ENSETEG00000015755
• Aliases: None
• Description: translocase of outer mitochondrial membrane 40 homolog (yeast)-like [Source:HGNC Symbol;Acc:25756]

Sequence

>retro_etel_1461
AGTTTCGATGAGCTGCACAGGCTCTGCAAAGACGTATTTCCAGCCCAGATGGAAGGCGTGAAGCTGGTGTCAACAAGGTT
GTGAGCAGCCATTTCTAGGTGGCGCACAATGTGCACATGAGTGCCTTGGGCTTGCCGGGCTACCACCACGCCGTCTGTGC
CAGGGACTGTCAACTTAGCCCCAGTGAGGTGTTTCCCACCGTGGTCCGGGACATGGACAGCAGCAACAGCCTCAACGCCC
AGGTCCTGCTTCGCTTGGCCGAGCGGCTTCGCTCTGAGGCTGTCTCCCAGACGCAGCCGTCCAAGTTGCTGACTTGGCAA
TTTGACGGCAAGTATCGGGAGAAGACTACACAGCCACTCTGACCCTAGGGAATCCTGACCTGATTGGGGAGTCCGTGATC
ATGGTCAGACACTTCCTGCAGAGCCTGAGCCACCGGCTAGTCCTGTGGGGAGAGCTAGTGTACCACCGGTGGCCGGGCGA
AACGGTAGCCATCCTGACCCTGGCTGGGAAGTACTCGACCGTACACTGGCAAGCTACACTGAATGCAGGGCCAGGTGGGG
CCCACGCAAGTTATTACCACAAAGCAAATGAACAGGTTCAGGTTGGAGTGGAATTTGAGGCAAGCGCAAGGCTGCAGGAC
ACGACCTTCTCCATTGGTTACCACCTCATTCTGCCCCAGGCCAATATGGTCTTTGGAGGCTTGGTGGATCGTCACTGGTG
TGTGGGTGCTGTCCTGGAAAAGAAATGGCCCCCTTGCCGGTGACCCTAGCCCTCGGAGCATTCCTCAGTCACTGGCGGAA
TAGATCCCATTTTGGCTTCAGCATCACTGTGGGC

Alignment

ORF - retro_etel_1461 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.87 %
• Parental protein coverage: 90.91 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  SFDELHRLCKDVFPAQMEGVKLV-VNKVLSSHFQVAHSVHMSALGLPGYHLHAVYAGDCQLSPSEVFPTV
          SFDELHRLCKDVFPAQMEGVKLV.VNKV.SSHF.VAH.VHMSALGLPGYH.HAV.A.DCQLSPSEVFPTV
Retrocopy SFDELHRLCKDVFPAQMEGVKLV<VNKVVSSHF*VAHNVHMSALGLPGYH-HAVCARDCQLSPSEVFPTV

Parental  VGDMDSSGSLNAQVLLLLAERLRTKAVFQTQQAKFLTWQFDGEYR-GDDYTATLTLGNPDLIGESVIMVA
          V.DMDSS.SLNAQVLL.LAERLR..AV.QTQ..K.LTWQFDG.YR.G.DYTATLTLGNPDLIGESVIMV.
Retrocopy VRDMDSSNSLNAQVLLRLAERLRSEAVSQTQPSKLLTWQFDGKYR<GEDYTATLTLGNPDLIGESVIMVR

Parental  HFLQSLTHRLVLGGELVYHRRPGEEGAILTLAGKYSAVHWEATLNVGSGGAHASYYHKANEQVQVGVEFE
          HFLQSL.HRLVL.GELVYHR.PGE..AILTLAGKYS.VHW.ATLN.G.GGAHASYYHKANEQVQVGVEFE
Retrocopy HFLQSLSHRLVLWGELVYHRWPGETVAILTLAGKYSTVHWQATLNAGPGGAHASYYHKANEQVQVGVEFE

Parental  ANTRLQDTTFSFGYHLTLPQANMVFRGLVDSNWCVGAVLEKKMP-PLPVTLALGAFLSHWRNRFHCGFSI
          A..RLQDTTFS.GYHL.LPQANMVF.GLVD..WCVGAVLEKK.P.PLPVTLALGAFLSHWRNR.H.GFSI
Retrocopy ASARLQDTTFSIGYHLILPQANMVFGGLVDRHWCVGAVLEKKWP<PLPVTLALGAFLSHWRNRSHFGFSI

Parental  TVG
          TVG
Retrocopy TVG

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_1461 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 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Erinaceus europaeus	ENSEEUG00000004808	1 retrocopy	retro_eeur_472,
Echinops telfairi	ENSETEG00000015755	2 retrocopies	retro_etel_1124, retro_etel_1461 ,
Gorilla gorilla	ENSGGOG00000005720	2 retrocopies	retro_ggor_1075, retro_ggor_1761,
Otolemur garnettii	ENSOGAG00000013733	1 retrocopy	retro_ogar_2524,
Ictidomys tridecemlineatus	ENSSTOG00000003800	2 retrocopies	retro_itri_301, retro_itri_724,
Drosophila melanogaster	FBgn0016041	1 retrocopy	retro_dmel_74,