RetrogeneDB ID: retro_etel_101

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: GeneScaffold_1871:3003..3880(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: VPS72
• Ensembl ID: ENSETEG00000004257
• Aliases: None
• Description: vacuolar protein sorting 72 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:11644]

Sequence

>retro_etel_101
ACGACTTATGGGGGGTTTACAGAGGAAGCAGGCGATGATGAGTATCAAGGAGACCAGTCAGACACAGAGGATGAGGCGGA
CTCTGATTTTGACATCGGAGAAGCGAAGAGCCAAGAAGGAAGCGCCGGATAGTCACCAAGCCCTAAAAGGAACCTCTCAG
GGGTTTAAGGCCTCGAAAGGTTAGCACCCCAGCTGGTAGCTCTCAGAAGGCTCCAGAAGAGAAAGCACTGCTGCCGTTTG
AACTGCAGGATGATGGCTCTGACAGTCGGAAGTGTATGCGTCAGTCTACAGCGGAGCACACGCGACAAACATTCCCCCGG
GTACAGGAGAGGCAGGGCCAGTCACGGCGGCGAAAGGGGCCCCACTATGAGCGACCACTGACCCAGGAGGAGCTGCTTAG
GGAGGCCAAGATCACAGAGGGCTCAACCTCCGCTCACTGGAGACATATGAGCGACTTGAGGCTGACAAAAAGAAGCAGGT
TCACAAGAAACGGAAGGGCCCTGGGCCCATTATCACCCATCACTCTGTGACAGTGCCACTTGTTGGGGAGCCAGGCCCCA
AGCAAGAGAATGTGGATGTGGAAGGACTTGAACCTGGTCCCACAGCTTCAACACTGACTCCCCACGCTGGAACCGGACCT
GTCATCCCCGCTGCCCGCTGCTCACGCACCTTCATCACTTTTAGTGACGATGCGACATTTGAGGAATGGTTCCCCCAAGG
GCGGCCTCCAAAGGTCCCTGTTCGGGAAGTCTGCCCAGTGACACATCGCCCAGCCCTATACCGAGACCCGGTTACAGACA
TACCCTACGCTAGTGCCCGAGCCTTCAGGCTCATTCGTGAGGCCTACAAGAAGTACATCACTGCCCATGGACTGCCA

Alignment

ORF - retro_etel_101 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.24 %
• Parental protein coverage: 84.09 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  TEESGDDEYQGDQSDTEDEVDSDFDIDEGDEPSSDGEA-EEPRRKRRIVTKAYKEPLKSLRPRKVSTPAG
          T...G..E..GD.....D..D.....DE.D.....GEA.EEPRRKRRIVTK..KEPL..LRPRKVSTPAG
Retrocopy TTYGGFTEEAGDDEYQGDQSDTE---DEADSDFDIGEA<EEPRRKRRIVTKP*KEPLRGLRPRKVSTPAG

Parental  SSQKAREEKALLPLELQDDGSDSRKCMRQSTAEHTRQTFLRVQERQGQSRRRKGPHYERPLTQEELLREA
          SSQKA.EEKALLP.ELQDDGSDSRKCMRQSTAEHTRQTF.RVQERQGQSRRRKGPHYERPLTQEELLREA
Retrocopy SSQKAPEEKALLPFELQDDGSDSRKCMRQSTAEHTRQTFPRVQERQGQSRRRKGPHYERPLTQEELLREA

Parental  KITEE-LNLRSLETYERLEADKKKQVHKKRKCPGPIITYHSVTVPLVGEPGPKEENVDVEGLEPGPTAST
          KITE..LNLRSLETYERLEADKKKQVHKKRK.PGPIIT.HSVTVPLVGEPGPK.ENVDVEGLEPGPTAST
Retrocopy KITEG<LNLRSLETYERLEADKKKQVHKKRKGPGPIITHHSVTVPLVGEPGPKQENVDVEGLEPGPTAST

Parental  LTPHAGTGPVIPAARCSRTFITFSDDATFEEWFPQGRPPKVPVREVCPVTHRPALYRDPVTDIPYATARA
          LTPHAGTGPVIPAARCSRTFITFSDDATFEEWFPQGRPPKVPVREVCPVTHRPALYRDPVTDIPYA.ARA
Retrocopy LTPHAGTGPVIPAARCSRTFITFSDDATFEEWFPQGRPPKVPVREVCPVTHRPALYRDPVTDIPYASARA

Parental  FKIIREAYKKYITAHGLP
          F..IREAYKKYITAHGLP
Retrocopy FRLIREAYKKYITAHGLP

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_101 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 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000824	1 retrocopy	retro_amel_1768,
Canis familiaris	ENSCAFG00000012540	1 retrocopy	retro_cfam_807,
Equus caballus	ENSECAG00000017754	1 retrocopy	retro_ecab_13,
Echinops telfairi	ENSETEG00000004257	1 retrocopy	retro_etel_101 ,
Mustela putorius furo	ENSMPUG00000004027	1 retrocopy	retro_mputfur_1542,
Mus musculus	ENSMUSG00000008958	1 retrocopy	retro_mmus_1570,