RetrogeneDB ID: retro_etel_161

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: GeneScaffold_2780:135787..136204(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DNAJC24
• Ensembl ID: ENSETEG00000003054
• Aliases: None
• Description: DnaJ (Hsp40) homolog, subfamily C, member 24 [Source:HGNC Symbol;Acc:26979]

Sequence

>retro_etel_161
TCCATGGATGATATACCCAGAAAGGATTGCTACAGCATTCTGGGCCCAGACGCATTTGCAAGTGTGTCAGGCCTAAAACA
AAAGTATCAAAAACTCATTTTAATGTATCATCCAGACCAACAAAGTGCAGACACGCCAGCAGGAGCAGTGGAGGACTGCA
TACAAAAGTTCATCGCAGTTGATCAGGCGTGGATGATTCTAGAGGCAGAAAGGGAATATGACCTGCAGTGGCAGGCAGAT
GACCTGAGAAATATCGGACCAGTGGAGGCGCAAATATATCTTGAAGACATGTTCTGAAATAAAGCTGATTGCTCTTTCTT
TCTGAGCTGCGGCTATGGTGGAAAATACAGTGTTTCCAAGGAGGAAGCAGAAGTTAACCTGATTTCTTTTGATAGGCCTT
CACTAATTAAAGAACTT

Alignment

ORF - retro_etel_161 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.93 %
• Parental protein coverage: 96.62 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AFEQIPRKDWYSILGADPFTSVSDLKEKYQKLILMYHPDKQSADVPAGAVEECIQKFIEIDQAWKILGNE
          ....IPRKD.YSILG.D.F.SVS.LK.KYQKLILMYHPD.QSAD.PAGAVE.CIQKFI..DQAW.IL...
Retrocopy SMDDIPRKDCYSILGPDAFASVSGLKQKYQKLILMYHPDQQSADTPAGAVEDCIQKFIAVDQAWMIL---

Parental  QTKKEYDLQRHEDDLRNIGPVDARICLEDMSWNKDDCSYFLSCRCGGKYSVSKDEAKDVNLISCDTCSLV
          ....EYDLQ...DDLRNIGPV.A.I.LEDM..NK.DCS.FLSC..GGKYSVSK.EA..VNLIS.D..SL.
Retrocopy EAEREYDLQWQADDLRNIGPVEAQIYLEDMF*NKADCSFFLSCGYGGKYSVSKEEA-EVNLISFDRPSLI

Parental  IEL
          .EL
Retrocopy KEL

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_161 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 11 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000013512	1 retrocopy	retro_dnov_2247,
Dipodomys ordii	ENSDORG00000000248	3 retrocopies	retro_dord_221, retro_dord_395, retro_dord_77,
Echinops telfairi	ENSETEG00000003054	1 retrocopy	retro_etel_161 ,
Microcebus murinus	ENSMICG00000007553	3 retrocopies	retro_mmur_1052, retro_mmur_1150, retro_mmur_973,
Macaca mulatta	ENSMMUG00000006845	1 retrocopy	retro_mmul_2112,
Nomascus leucogenys	ENSNLEG00000017878	1 retrocopy	retro_nleu_3029,
Otolemur garnettii	ENSOGAG00000007848	1 retrocopy	retro_ogar_1542,
Ochotona princeps	ENSOPRG00000001638	1 retrocopy	retro_opri_881,
Pongo abelii	ENSPPYG00000003390	2 retrocopies	retro_pabe_2783, retro_pabe_2788,
Pan troglodytes	ENSPTRG00000003471	1 retrocopy	retro_ptro_2301,
Tarsius syrichta	ENSTSYG00000009243	1 retrocopy	retro_tsyr_623,