RetrogeneDB ID: retro_etel_1763

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_292556:132937..133212(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CDKN3
• Ensembl ID: ENSETEG00000018617
• Aliases: None
• Description: cyclin-dependent kinase inhibitor 3 [Source:HGNC Symbol;Acc:1791]

Sequence

>retro_etel_1763
GACATAATGGACGAGTTTACAATCTGCCTTAAACATACCCGGAAAACCTTAACACACTGTTCCTAAGAACGGGGGAGGTC
TTGTCTTGTAGTCTCTTTTCTCCTTCTATACTGTCTGACACAGAGTTGCCACAGCAAGCCATAGACACCCGGAAAGGCCT
CAGAGGATCAACGGTCATACAGACCATAAAACAATATAACTATCTTCATGAGTTCTGGTACACACTAGCTGCTCATCTGT
CATCAAGAGAGTCGCTATCAAGATCAGTATCTAGA

Alignment

ORF - retro_etel_1763 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.67 %
• Parental protein coverage: 58.97 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  DLKNELTNLSKMAGKTLIFCYGGLGRSCLVAACLLLY-LSDTVSPQQAIDSLRDLRGSGAIQTIKQYNYL
          D...E.T...K...KTL..C....GRSCLV...LLLY.LSDT..PQQAID....LRGS..IQTIKQYNYL
Retrocopy DIMDEFTICLKHTRKTLTHCS*ERGRSCLVVSFLLLY<LSDTELPQQAIDTRKGLRGSTVIQTIKQYNYL

Parental  HEFRDILAAHLSSRESLSRSVSR
          HEF...LAAHLSSRESLSRSVSR
Retrocopy HEFWYTLAAHLSSRESLSRSVSR

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_1763 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 8 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000012823	1 retrocopy	retro_chof_1806,
Echinops telfairi	ENSETEG00000018617	1 retrocopy	retro_etel_1763 ,
Felis catus	ENSFCAG00000015089	2 retrocopies	retro_fcat_135, retro_fcat_626,
Loxodonta africana	ENSLAFG00000014833	1 retrocopy	retro_lafr_637,
Macropus eugenii	ENSMEUG00000002497	3 retrocopies	retro_meug_1255, retro_meug_1768, retro_meug_1849,
Procavia capensis	ENSPCAG00000015559	1 retrocopy	retro_pcap_104,
Sarcophilus harrisii	ENSSHAG00000008977	1 retrocopy	retro_shar_502,
Tupaia belangeri	ENSTBEG00000010203	2 retrocopies	retro_tbel_1809, retro_tbel_4700,