RetrogeneDB ID: retro_etel_2102

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_59030:336..1110(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NDRG3
• Ensembl ID: ENSETEG00000002250
• Aliases: None
• Description: NDRG family member 3 [Source:HGNC Symbol;Acc:14462]

Sequence

>retro_etel_2102
GCTCATGCTGTGGTAAGTGTCACTATAAGAGGCATACGCAAAGGAAACAGACTGGTCATTTCGACCTATCATGACATTGG
CCTCAACCACAAATCATATTTCAATGCCTTCTTTAACTTTGAGGATATGCAGGAGCTCACCCAATACTTGGCTGTCTGTC
ATGTGGATGCGCCGGGTCAACAGGAAGGTGCAGCCCCTTTCCCAACCCGGTACCAGTATCCTACAATGGATGAATGGACT
GAAATGCTGCCTTCTGTTCTTACCCACCTAAGTCTGCAAGGCGTCATTGGGATTGGAGTTGGAGCTGGGCAGGAGATTTG
CACTCAGTCATCCGGAGCTTGTGGAATGCCTGTGCTTATTAATGCTGACCCGTGTGTGAAAGACTGGATTGACTGGGCAG
CTTCCAAAATAATGTGCCTGACAGCTACTGTTGTGGACATTATTTTGGCTCATCACTTTGGGCAGGAGGAGTTGCAGGCC
AATGTGGACCTTATTCAAACCTATAGATTGCATATTGCCCAAGATGTCAACCAGGAGAACCTACAGCTCTTCGTCAGTTC
TTATAATGGATGCAGAGATCTTGAGATCGAAAGGCCCTTGCTGAGCCAAAATGATAACACAAAAACATTAAATTGTTGTA
TGTTATTGGTGGTAGGGGACAGTTCCCCTGCAGTTGCGGCTGTTGTTGAATGCAATTCGTGCCTGGACCTGATAAATATA
ACTTTGCTAAAGATGGCAGGCTGTGGGGGACTGCCTCAAGTACTTTTTGTAGGG

Alignment

ORF - retro_etel_2102 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.68 %
• Parental protein coverage: 67.7 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  AHGVVHVTIRGILKGNRPVILTYHDIGLNHKSCFNAFFNFEDMQEITQYFAVCHVDAPGQQEGAAPFPTG
          AH.VV.VTIRGI.KGNR.VI.TYHDIGLNHKS.FNAFFNFEDMQE.TQY.AVCHVDAPGQQEGAAPFPT.
Retrocopy AHAVVSVTIRGIRKGNRLVISTYHDIGLNHKSYFNAFFNFEDMQELTQYLAVCHVDAPGQQEGAAPFPTR

Parental  YQYPTMDELAEMLPSVLTHLSL-KGVIGIGVGAGAYILSRFALNHPELVEGL-VLINVDPCAKGWIDWAA
          YQYPTMDE..EMLPSVLTHLSL.K...G.....G.....RFAL.HPELVE.L.VLIN.DPC.K.WIDWAA
Retrocopy YQYPTMDEWTEMLPSVLTHLSL>KASLGLELELGR----RFALSHPELVECL<VLINADPCVKDWIDWAA

Parental  SKLFSLTTNVVDIILAHHFGQEELQANMDLIQTYRLHIAQDINQENLQLFLSSYNGRRDLEIERPLLGQN
          SK...LT..VVDIILAHHFGQEELQAN.DLIQTYRLHIAQD.NQENLQLF.SSYNG.RDLEIERPLL.QN
Retrocopy SKIMCLTATVVDIILAHHFGQEELQANVDLIQTYRLHIAQDVNQENLQLFVSSYNGCRDLEIERPLLSQN

Parental  DNTKTLKCCTLLVVGDSSPAVEAVVECNSRLDPINTTLLKMADCGGLPQVVQPG
          DNTKTL.CC.LLVVGDSSPAV.AVVECNS.LD.IN.TLLKMA.CGGLPQV...G
Retrocopy DNTKTLNCCMLLVVGDSSPAVAAVVECNSCLDLINITLLKMAGCGGLPQVLFVG

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_2102 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.

---

Parental genes homology:

Parental genes homology involve 6 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012562	1 retrocopy	retro_amel_378,
Echinops telfairi	ENSETEG00000002250	1 retrocopy	retro_etel_2102 ,
Myotis lucifugus	ENSMLUG00000009735	1 retrocopy	retro_mluc_1054,
Otolemur garnettii	ENSOGAG00000000895	1 retrocopy	retro_ogar_515,
Sus scrofa	ENSSSCG00000007322	5 retrocopies	retro_sscr_1116, retro_sscr_144, retro_sscr_519, retro_sscr_539, retro_sscr_937,
Ictidomys tridecemlineatus	ENSSTOG00000022531	1 retrocopy	retro_itri_1284,