RetrogeneDB ID: retro_etel_358

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: GeneScaffold_5942:82820..83369(-)
• Located in intron of: ENSETEG00000007693

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: PTGR1
• Ensembl ID: ENSETEG00000006136
• Aliases: None
• Description: prostaglandin reductase 1 [Source:HGNC Symbol;Acc:18429]

Sequence

>retro_etel_358
ATGGTTCGTGCTAAGGACTTGGAATCCTGAAGAAGCATTTTGAAGGCTACCCGACTCATAGTAACTTTTGAGTTGCAGAC
AACGGAACTCCCAGCCTTAACAAATGGAGAGGTCCTGCTGGAAGCTTTGTTCCTCACGGTGGATCCTTATATGAGAGTGG
CAGCCGAGAGGTTGAAAGAGGGTGAGAAGATGATGGGCTAGCAAGTAGCCAGAGTTGTGGAAAGTAAAAACTCAGCCTTT
CCCGTGGGAACCACTGTGGTGGCTTCTTCTGGTTGGACAACACACTCCATTTCTGACAGGACAGGCCTGGAAACGCTGCC
TGCAGAATGGCCAGACACTTTACCCCTGTCTTTGGCTCTGGGGGCAGTCGGCATGACAGGCCTCACAGCGTACTTTGGCC
TGCTTGACATCTGTGGTGTGAAAGGAGGAGGAACCGTGATGGTCAATGCAGCTGCAGGAGCAGTGGGTGCTGTTGTGGGG
CAGAGAGCTAAGCTCAAGGTAGGAGGGGAGCTTTCAAATGTTGTTATCCCCCAAATGAAGAAATTTGGA

Alignment

ORF - retro_etel_358 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.66 %
• Parental protein coverage: 63.48 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MVRAK-TW-ILKKHFEGYPTHSNF-ELKTTELPALKNGELLLEALFLTVDPYMRVAAKKMKEGEKMMGQQ
          MVRAK.TW.ILKKHFEGYPTHSNF.EL.TTELPAL.NGE.LLEALFLTVDPYMRVAA...KEGEKMMG.Q
Retrocopy MVRAK>TW>ILKKHFEGYPTHSNF>ELQTTELPALTNGEVLLEALFLTVDPYMRVAAERLKEGEKMMG*Q

Parental  VARVVESKNSAFPVGTTVVASSGWTTHCISDGTGLETLPAEWPDTLPLSLALGAVGMTGLTAYFGLLDIC
          VARVVESKNSAFPVGTTVVASSGWTTH.ISD.TGLETLPAEWPDTLPLSLALGAVGMTGLTAYFGLLDIC
Retrocopy VARVVESKNSAFPVGTTVVASSGWTTHSISDRTGLETLPAEWPDTLPLSLALGAVGMTGLTAYFGLLDIC

Parental  GVKGGETVMVNAAAGAVGAVVGQIAKLKGCTVVGAAGSDDKVAYIKKLG
          GVKGG.TVMVNAAAGAVGAVVGQ.AKLK....VG...S.......KK.G
Retrocopy GVKGGGTVMVNAAAGAVGAVVGQRAKLK----VGGELSNVVIPQMKKFG

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_358 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 9 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000003000	2 retrocopies	retro_cfam_1290, retro_cfam_1876,
Callithrix jacchus	ENSCJAG00000017571	1 retrocopy	retro_cjac_1653,
Echinops telfairi	ENSETEG00000005782	1 retrocopy	retro_etel_216,
Echinops telfairi	ENSETEG00000006136	1 retrocopy	retro_etel_358 ,
Felis catus	ENSFCAG00000004339	1 retrocopy	retro_fcat_1898,
Homo sapiens	ENSG00000106853	1 retrocopy	retro_hsap_219,
Nomascus leucogenys	ENSNLEG00000017487	1 retrocopy	retro_nleu_2424,
Otolemur garnettii	ENSOGAG00000011144	1 retrocopy	retro_ogar_2834,
Pongo abelii	ENSPPYG00000019499	1 retrocopy	retro_pabe_283,