RetrogeneDB ID: retro_etel_1069

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_206493:6163..6957(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSETEG00000005925
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: FH
• Ensembl ID: ENSETEG00000018721
• Aliases: None
• Description: fumarate hydratase [Source:HGNC Symbol;Acc:3700]

Sequence

>retro_etel_1069
GAATTTAGTGGTTGTGTTCAACAAGTAAATTATGCAATGATAAGAATAAAAGCTGCACTGCCAAGAATCTATGAGCTTGC
TGCTGGAGGCACTGTTGTTGGTACTGCTTTAAATACTAGAATTGGCTTTGCGGAAAAGGTTGTTTCAAAGGTGGTGGCTG
CACTTACAGGCTTGCCTTTTGTTACAGCTCCAAATAAATTTGAAGCTCTGGCTGCTCACGATGCCTTGGTTGAACTCAGT
GGAGCCCTGAATACTGCAGCATGTAGTCTGATGAAGATAGCAAATGACATTCGTTTTCTGGGTTCTGGTCCTCGATCAGG
TCTGGGAGAACTGATCTAGCCTGAAAATGAACCGGGAAGCAGTATCATGCCAGGAAAGGCGACCCCTACCCAGTGTGAAG
CTGTGACCATGGTTGCAGCCCAAGTTATGGGAAATCATGTTGCTGTTACTATTGGAGGTAACAATGGACCTTTTGAGTTG
AATGTTTTCAAGCCAATGATGATTAAAAATGTGTTACATTCAGCAAGGCTGCTCGGTGATGCTTCAGTTTCTTTCACAGA
AAACTGTGTGGTAGGAATCCAGGCCAACAGAGAAAGAATCACCAAGCTAATGAATGAGTCTTTAATGTTGGTAACAGCAC
TTAATCCTCATATAGGTTATGACAAGGCTGCAAAGATTGCTAAGACAGCACACAAAAATGGATCAACCTTAAAGGAAACT
GCCATTGAACTTGGCTATCTCACGCAGAGCAGTTTGATGAGTGGGTGACGCCTACAGATATGCTGGGTCCAAAG

Alignment

ORF - retro_etel_1069 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.35 %
• Parental protein coverage: 52.49 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EFSAYVQQVNYAMVRIKAALPRIYELAAGGTAVGTGLNTRIGFAEKVASKV-AALTALPFVTAPNKFETL
          EFS..VQQVNYAM.RIKAALPRIYELAAGGT.VGT.LNTRIGFAEKV.SKV.AALT.LPFVTAPNKFE.L
Retrocopy EFSGCVQQVNYAMIRIKAALPRIYELAAGGTVVGTALNTRIGFAEKVVSKVVAALTGLPFVTAPNKFEAL

Parental  AAHDALVELSGAMNTAACSLMKIANDIRFLSSGPRSSLRELILPENEPGSSIMPGKVNPTQCEALTMVAA
          AAHDALVELSGA.NTAACSLMKIANDIRFL.SGPRS.L.ELI.PENEPGSSIMPGK..PTQCEA.TMVAA
Retrocopy AAHDALVELSGALNTAACSLMKIANDIRFLGSGPRSGLGELI*PENEPGSSIMPGKATPTQCEAVTMVAA

Parental  QVMGNHVAVTIGGSNGHFELNVFKPMMIKNVLHSARLLGDASVSFTENCVVGIQANTERINKLMNESLML
          QVMGNHVAVTIGG.NG.FELNVFKPMMIKNVLHSARLLGDASVSFTENCVVGIQAN.ERI.KLMNESLML
Retrocopy QVMGNHVAVTIGGNNGPFELNVFKPMMIKNVLHSARLLGDASVSFTENCVVGIQANRERITKLMNESLML

Parental  VTALNPHIGYDKAAKIAKTAHKNGSTLKETAIELGYLT-AEQFDEWVKPTDMLGPK
          VTALNPHIGYDKAAKIAKTAHKNGSTLKETAIELGYLT.AEQFDEWV.PTDMLGPK
Retrocopy VTALNPHIGYDKAAKIAKTAHKNGSTLKETAIELGYLT<AEQFDEWVTPTDMLGPK

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_1069 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
Callithrix jacchus	ENSCJAG00000017359	1 retrocopy	retro_cjac_2339,
Echinops telfairi	ENSETEG00000018721	2 retrocopies	retro_etel_1069 , retro_etel_1457,
Microcebus murinus	ENSMICG00000003451	2 retrocopies	retro_mmur_1215, retro_mmur_720,
Mus musculus	ENSMUSG00000026526	1 retrocopy	retro_mmus_3600,
Oryctolagus cuniculus	ENSOCUG00000021494	1 retrocopy	retro_ocun_50,
Otolemur garnettii	ENSOGAG00000009936	1 retrocopy	retro_ogar_322,
Rattus norvegicus	ENSRNOG00000003653	1 retrocopy	retro_rnor_2979,
Xenopus tropicalis	ENSXETG00000032112	1 retrocopy	retro_xtro_55,