RetrogeneDB ID: retro_etel_458

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: GeneScaffold_7598:244970..245441(+)
• Located in intron of: ENSETEG00000016352

Retrocopy information

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

Parental gene information

• Parental gene symbol: C19orf40
• Ensembl ID: ENSETEG00000002716
• Aliases: None
• Description: chromosome 19 open reading frame 40 [Source:HGNC Symbol;Acc:28467]

Sequence

>retro_etel_458
AGATGCTGTATTCTTTATGTTACCGAAGCTGAGTTGGTGGCAGGAAACGGCTACAGGAAGAGGCTTGTTCCATCAGAAAT
TCATCTCAAGGGATTGTACTAGTTGAGAAGACACAGATGAGCGTGCAGTACTTCCCCGGCCGCACAGAAGTTCACAGTAC
TGGACCTCGGCATGGTGTTGCTTCCAGTGTCCAGCCAGATGGAAGGAGCCAGCCTCATTATTCAGTTAGTCCACAAACAA
ACCAAAGAGCCCAGTAAGAACCCGTTTCTCAGGAAGAAGCGCGCTCAGCTCTCCGAGCCCTCCCTCCTCCAGACGATGCA
GCAGATCCTAGGAGTTGGAAAAGTGAAAGCCCCCTTTCTGCTCCTGAAATTCCCAAGTATCCAACACCTAAGTAACGCTT
CCACGCAAGAACTGGAGCACGTTGTTGGGCAAGCAGCGGCACAGCGGATTCACGCGTTTTTCACACAGTCC

Alignment

ORF - retro_etel_458 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.5 %
• Parental protein coverage: 74.3 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  RSCILYVTEADLVAGKGYRKRLV-QIRNSSHLQGIVLVEKTQMSEQYF-PAAQKFTVLDLGMVLLPVCSQ
          R.CILYVTEA.LVAG.GYRKRLV..IRNSS..QGIVLVEKTQMS.QYF.PAAQKFTVLDLGMVLLPV.SQ
Retrocopy RCCILYVTEAELVAGNGYRKRLV<SIRNSS--QGIVLVEKTQMSVQYF>PAAQKFTVLDLGMVLLPVSSQ

Parental  KEAASLIIQLXXEQAKEPSKKPVYQEKSAAQPEHSLLQPVQQIPGVGKVKAPLLLQKFPSIQHLSNASMQ
          .E.ASLIIQL...Q.KEPSK.P....K.A...E.SLLQ..QQI.GVGKVKAP.LL.KFPSIQHLSNAS.Q
Retrocopy MEGASLIIQLVHKQTKEPSKNPFLRKKRAQLSEPSLLQTMQQILGVGKVKAPFLLLKFPSIQHLSNASTQ

Parental  ELEHVVGQAAAQRIHTFFTQS
          ELEHVVGQAAAQRIH.FFTQS
Retrocopy ELEHVVGQAAAQRIHAFFTQS

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_458 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 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000000728	2 retrocopies	retro_cjac_1011, retro_cjac_3952,
Cavia porcellus	ENSCPOG00000011965	1 retrocopy	retro_cpor_1536,
Dasypus novemcinctus	ENSDNOG00000014134	4 retrocopies	retro_dnov_1817, retro_dnov_2382, retro_dnov_426, retro_dnov_942,
Echinops telfairi	ENSETEG00000002716	1 retrocopy	retro_etel_458 ,
Loxodonta africana	ENSLAFG00000006401	4 retrocopies	retro_lafr_165, retro_lafr_365, retro_lafr_415, retro_lafr_789,
Myotis lucifugus	ENSMLUG00000013287	1 retrocopy	retro_mluc_522,
Macaca mulatta	ENSMMUG00000017939	1 retrocopy	retro_mmul_788,
Procavia capensis	ENSPCAG00000009727	1 retrocopy	retro_pcap_444,
Sarcophilus harrisii	ENSSHAG00000016372	1 retrocopy	retro_shar_299,