RetrogeneDB ID: retro_etel_437

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: GeneScaffold_7151:100420..100697(+)
• Located in intron of: ENSETEG00000005577

Retrocopy information

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

Parental gene information

• Parental gene symbol: CDK2AP2
• Ensembl ID: ENSETEG00000006428
• Aliases: None
• Description: cyclin-dependent kinase 2 associated protein 2 [Source:HGNC Symbol;Acc:30833]

Sequence

>retro_etel_437
CCTGTTCCTACAGCAGGAAGCATCCCATCGCCATCCGGCTGCAAGCAGTGAGCTGCTGCCCCTTTCTGGCCACTGTTTAA
TGACTTTGGACTGCCATTCAGGGTCTATGTGCAGGCCATAAAGCTGCCCTGCACTCAGAGCTCCCAGAGCACCCACAGGA
ATCTGCTGTCAGTCGTAGAGGATTGGGCAAGGTGATCGGTCCACCTATGCCGGAAGCAAGAGTGCCATGAAGATAGGCAT
CATCCACGCCCAGGCCCTGGTCAGAGTGTACCTGGCG

Alignment

ORF - retro_etel_437 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.35 %
• Parental protein coverage: 75.4 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  PVPT-GSVPSPSGSGPGAAAPFRPLFNDFGPPSMGYVQAMKPPGTQGSQSTYTDLLSVIEE-MGKEIRP-
          PVPT.GS.PSPSG....AAAPF.PLFNDFG.P...YVQA.K.P.TQ.SQST...LLSV.E...GK.I.P.
Retrocopy PVPTAGSIPSPSGCKQ*AAAPFWPLFNDFGLPFRVYVQAIKLPCTQSSQSTHRNLLSVVED<LGKVIGP<

Parental  TYAGSKSAMERLKRGIIHARALVRECLA
          TYAGSKSAM...K.GIIHA.ALVR..LA
Retrocopy TYAGSKSAM---KIGIIHAQALVRVYLA

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_437 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 10 parental genes, and 31 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000011370	1 retrocopy	retro_cfam_55,
Equus caballus	ENSECAG00000020079	2 retrocopies	retro_ecab_180, retro_ecab_579,
Echinops telfairi	ENSETEG00000006428	3 retrocopies	retro_etel_257, retro_etel_334, retro_etel_437 ,
Homo sapiens	ENSG00000167797	4 retrocopies	retro_hsap_3699, retro_hsap_4172, retro_hsap_4176, retro_hsap_4268,
Gorilla gorilla	ENSGGOG00000010159	3 retrocopies	retro_ggor_2502, retro_ggor_2799, retro_ggor_2800,
Macaca mulatta	ENSMMUG00000011827	5 retrocopies	retro_mmul_1712, retro_mmul_640, retro_mmul_728, retro_mmul_730, retro_mmul_763,
Nomascus leucogenys	ENSNLEG00000006438	1 retrocopy	retro_nleu_176,
Otolemur garnettii	ENSOGAG00000008275	1 retrocopy	retro_ogar_1584,
Pan troglodytes	ENSPTRG00000003966	9 retrocopies	retro_ptro_2508, retro_ptro_2973, retro_ptro_2976, retro_ptro_3002, retro_ptro_3003, retro_ptro_3004, retro_ptro_3005, retro_ptro_3008, retro_ptro_3009,
Tupaia belangeri	ENSTBEG00000005476	2 retrocopies	retro_tbel_439, retro_tbel_612,