RetrogeneDB ID: retro_etel_2181

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_9306:518..1293(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSETEG00000012393
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RIOK3
• Ensembl ID: ENSETEG00000003689
• Aliases: None
• Description: RIO kinase 3 [Source:HGNC Symbol;Acc:11451]

Sequence

>retro_etel_2181
AAATAGTATTTTACTGCTGAAAAAGCTGTTGATCCTAAGACACATTTACTTATGTATAAAATGGTCAACTCTGGAGTATT
GGAGACAATCACTGGCTGTATTAGTACAGGAAAGGAATCTCTTGTCTTTCATGCATATGGAGGGAGCATAGAAGATGAAA
AGGAAGATAGAAAAGTTGTACCTACAGAATGTGCCATCAAGGTATTTAAAACAACCCTTAATGAGTTTAAGAATCGTGAC
CAATATATTAAAGATGATTAGACATTTAAAGACCGCTTCAGTAAACTGAATCCAGGTAAGATCATCCACATGTGGGCAGA
AAAAGAAATGCACAATCTCTCAAGAATGCAGAGCACTGGAATTCCTTGTCCAACAGTTGTCATGCTCAAGAAACACAGTT
CAGTTATGTCTTTTATTGGCCACAGTCAAAGTTCCTGCTCCTAAATTAAAAGAAGTAAAGCTCAGTCAAGAAGAATTGAA
AGATGCCCACTGTCAAGCTCTTGATATTATTCAGCAGTTATATAATGAATGTACACTGGTCCATCCTGACATCCGTGAGT
ATAACATGCTGGAAAAGGTCTGGTTGATTGATGTCAGTCAGTCTGTAGAACCAACTCATCCTCATGGCCTGGAATTCCTG
TGCTGGGACTGTAGGAATGTCTCCCAGTTTTACCAGAAAGGAGGAGTTCTGGAAGCTCTCAGTGAATGAGAACTCTTTAA
TGCTGTTTTAGGCTTAAACATCTCGGCAGATAATGAAGGCGATTTCTTAGCTGAG

Alignment

ORF - retro_etel_2181 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.44 %
• Parental protein coverage: 53.83 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KEHSTAEKAVDPKTRLLMYKMVNSGLLETITGCISTGKESVVFHAYGGSMEDEKEDSKVVPTECAITVFK
          K...TAEKAVDPKT.LLMYKMVNSG.LETITGCISTGKES.VFHAYGGS.EDEKED.KVVPTECAI.VFK
Retrocopy K*YFTAEKAVDPKTHLLMYKMVNSGVLETITGCISTGKESLVFHAYGGSIEDEKEDRKVVPTECAIKVFK

Parental  TSVNEF-NRDKYIKDDYRFKDRFSKLNPRKIIRMWAEKEMHNLTRMQRAGIPCPTVVMLKKHILVMSFIG
          T..NEF.NRD.YIKDD..FKDRFSKLNP.KII.MWAEKEMHNL.RMQ..GIPCPTVVMLKKH..VMSFIG
Retrocopy TTLNEFKNRDQYIKDD*TFKDRFSKLNPGKIIHMWAEKEMHNLSRMQSTGIPCPTVVMLKKHSSVMSFIG

Parental  HDQ-VPAPKLKEVKLSSEEMKDAYYQTLDMMQRLYNECTLVHADLSEYNMLWHAGKVWLIDVSQSVEPTH
          H.Q.VPAPKLKEVKLS.EE.KDA..Q.LD..Q.LYNECTLVH.D..EYNML....KVWLIDVSQSVEPTH
Retrocopy HSQ>VPAPKLKEVKLSQEELKDAHCQALDIIQQLYNECTLVHPDIREYNML---EKVWLIDVSQSVEPTH

Parental  PHGLEFLFRDCRNVSQFFQKGGVMEALSERELFNAVSGLNISADNEADFLAE
          PHGLEFL..DCRNVSQF.QKGGV.EALSE.ELFNAV.GLNISADNE.DFLAE
Retrocopy PHGLEFLCWDCRNVSQFYQKGGVLEALSE*ELFNAVLGLNISADNEGDFLAE

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_2181 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 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000008343	1 retrocopy	retro_chof_1788,
Callithrix jacchus	ENSCJAG00000020556	1 retrocopy	retro_cjac_2617,
Echinops telfairi	ENSETEG00000003689	1 retrocopy	retro_etel_2181 ,
Macropus eugenii	ENSMEUG00000006292	1 retrocopy	retro_meug_1278,
Macaca mulatta	ENSMMUG00000021478	1 retrocopy	retro_mmul_1291,
Ochotona princeps	ENSOPRG00000004803	2 retrocopies	retro_opri_1034, retro_opri_946,
Pongo abelii	ENSPPYG00000009062	1 retrocopy	retro_pabe_1011,