RetrogeneDB ID: retro_etel_966

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_192661:917..1576(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSETEG00000016338
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: USP14
• Ensembl ID: ENSETEG00000004949
• Aliases: None
• Description: ubiquitin specific peptidase 14 (tRNA-guanine transglycosylase) [Source:HGNC Symbol;Acc:12612]

Sequence

>retro_etel_966
ATGAAATGTACAGAATCTGACGAACAAGAAGTTACTAAAGGAAAGGAAAATCAGCTTCAACTTAGCTGCTTCATTAATCA
AGAAGTCAAGTATCTTTTTACAGGACTGAAATTGCGACTACAGGAAGAAATCACCAGCAGTCTCCAACATTGCAAAGAGA
TGCTTTGTACATCAAATCTTCCAAGATTAGCCGTTTGCCTGCTTACTTGACAATTCAGATGGTTCGATTTTTTTTATAAA
GAGAAGGAATCTGTGAATGCCAAAGTTCTTAAGGATGTTAAATTTCCTCTTATGTTGGATGTGTATGAACTATGTACACC
AGAACTGCAAGAGAAAATGGTCTCTTTTCGATCAAAGTTCAAGGATCTGGAAGATAAAACAGTGAATCAGCAACCAAAGA
TAAGTGATCAAAAAAGTAGTCCCCAGAAGGAGGCTAAATATGAACCCTTTTCTTTTGTTGATGATATTGGCTCCAATAAC
TGTGGATACTATGACTTACAAGCAGTGCTAACTCTCCAGGGAAGGTCTAGTTCTTCAGGTCATTATGTATCTTGGGTGAA
AAGGAAAAAAGATGAATTAAAGTTTGATGATGATAAAGTCAGCATCGTCACACCAGAAGATATCTTGAGGCTTTCTGGTG
TGGAGACTGGCATATAGCT

Alignment

ORF - retro_etel_966 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.86 %
• Parental protein coverage: 50.46 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MKCTESDEEEVTKGKENQLQLSCFINQEVKYLFTGLKLRLQEEIT-KQSPTLQRDALYTKSSKISRLPAY
          MKCTESDE.EVTKGKENQLQLSCFINQEVKYLFTGLKLRLQEEIT..QSPTLQRDALY.KSSKISRLPAY
Retrocopy MKCTESDEQEVTKGKENQLQLSCFINQEVKYLFTGLKLRLQEEIT<QQSPTLQRDALYIKSSKISRLPAY

Parental  LTIQMVR-FFYKEKESVNAKVLKDVKFPLMLDVYELCTPELQEKMVSFRSKFKDLEDKKVNQQPKISDQK
          LTIQMVR....KEKESVNAKVLKDVKFPLMLDVYELCTPELQEKMVSFRSKFKDLEDK.VNQQPKISDQK
Retrocopy LTIQMVR>XXXKEKESVNAKVLKDVKFPLMLDVYELCTPELQEKMVSFRSKFKDLEDKTVNQQPKISDQK

Parental  SSPQKETKYEPFSFVDDIGSNNCGYYDLQAVLTHQGRSSSSGHYVSWVKRKQDEWIKFDDDKVSIVTPED
          SSPQKE.KYEPFSFVDDIGSNNCGYYDLQAVLT.QGRSSSSGHYVSWVKRK.DE..KFDDDKVSIVTPED
Retrocopy SSPQKEAKYEPFSFVDDIGSNNCGYYDLQAVLTLQGRSSSSGHYVSWVKRKKDE-LKFDDDKVSIVTPED

Parental  ILRLSG-GGDWHIA
          ILRLSG..GDWHIA
Retrocopy ILRLSG<CGDWHIA

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_966 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 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000008213	1 retrocopy	retro_acar_108,
Choloepus hoffmanni	ENSCHOG00000010588	4 retrocopies	retro_chof_1736, retro_chof_2406, retro_chof_2529, retro_chof_2603,
Echinops telfairi	ENSETEG00000004949	1 retrocopy	retro_etel_966 ,