RetrogeneDB ID: retro_etel_1829

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_304525:7075..7674(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSETEG00000015880
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: UPP1
• Ensembl ID: ENSETEG00000013986
• Aliases: None
• Description: uridine phosphorylase 1 [Source:HGNC Symbol;Acc:12576]

Sequence

>retro_etel_1829
GAAAAACTAGGCATGGAACCTCTCAATATCTTTGCCGGAACTGACTGCTTTGCCATCTATAAAGCAGGGCCAGTGCTGTG
CGTCAACCATGGTATGGGCACACCTCCCATTGGAAGCATGCAGTATGAGCTCACCAAGCTACTGTACCATGCCAGGAGCT
TCCAAGTCACCATCAGCACATCAGGTCTGGAGCCTGGCTCTGTGGTTATCACCCAACAAATGGTGCGTGCCTGCTTCAAG
CCTGAGTTTGAGCAGATTGCCCTGGGGAAGTGAGTTGTTCAAAGCACACACCTCAATAACCAGCTAGTTCAGGAGCTGAT
GCAGTAGTCCCAACAGCTAGACAAACTCCCCGTGGTTGTGGGGAACACCATGTACACCTTGGATTTCTCTGAAGGGCAAG
GCCATTTGCAGGGTGCTCCTGTTCGTATACCGAAAAGGCCAAGCAACAGTGCTTGAGGGCAGCCTGCGCCGTTGGCATCC
GGAGCATTGAGGTGGAGTCCTCAGTCTTTGCTGCCATGTGTGGTGCTTGTGACCTCTGAGCGGCTGTGGTGTGTGCCACC
CTTCTCAATTGGTTAGATGGAGACCAGATCAATAGCACC

Alignment

ORF - retro_etel_1829 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.57 %
• Parental protein coverage: 71.03 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EEPGVEPVNICAGTDRYAMYKVGPVLSVSHGMGIPSIAIMLHELIKLLYHARCSNITIIRIGTSGGIGLE
          E..G.EP.NI.AGTD..A.YK.GPVL.V.HGMG.P.I..M..EL.KLLYHAR....TI....TSG...LE
Retrocopy EKLGMEPLNIFAGTDCFAIYKAGPVLCVNHGMGTPPIGSMQYELTKLLYHARSFQVTI---STSG---LE

Parental  PGSVVISQQAVDACFKPEFEQIILGKRVVRSTHLNNQLVQELLLCSTELDEFPVVVGNTMCTLDFYEGQG
          PGSVVI.QQ.V.ACFKPEFEQI.LGK.VV.STHLNNQLVQEL...S..LD..PVVVGNTM.TLDF.EGQG
Retrocopy PGSVVITQQMVRACFKPEFEQIALGK*VVQSTHLNNQLVQELMQ*SQQLDKLPVVVGNTMYTLDFSEGQG

Parental  RLDGA-LCSYTEKDKQQYLKAAYAVGIRNIEMESSVFAAMCASSNLRAAVVCVTLLNRLDGDQITSS
          .L.GA..CSYTEK.KQQ.L.AA.AVGIR.IE.ESSVFAAMC....L.AAVVC.TLLN.LDGDQI.S.
Retrocopy HLQGA<SCSYTEKAKQQCLRAACAVGIRSIEVESSVFAAMCGACDL*AAVVCATLLNWLDGDQINST

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_1829 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000013986	1 retrocopy	retro_etel_1829 ,
Monodelphis domestica	ENSMODG00000009417	1 retrocopy	retro_mdom_1539,