RetrogeneDB ID: retro_etel_252

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: GeneScaffold_4282:174428..174733(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSETEG00000008424
• Aliases: None
• Description: None

Sequence

>retro_etel_252
CCCCATCACCACGCTGCATCTGTCCACTGGACTGGTGAGAGGGTCGTCAAGGTTTTGCTCCTGGGCCTGCTCCCAGCTGC
TTATTTGAATCCCTGCTCGGCGATGGATTACTCCCTGGCAGCAGCTCTCACGCTTCACAGTCACTGGGGCATTGGACAGG
TTATTACTATGTCCACGGGGATGTTTCCCAGAAAGCTGCCAAGGCAGGCCCTGTTGGTACTCTCAGCGTGACCTTCGCTG
GTCTTTGTTATTTCAACTACCACGACGTCGGTATCTGCAAAGCTGTGGCCATGCTATGGAAGCTC

Alignment

ORF - retro_etel_252 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.85 %
• Parental protein coverage: 77.54 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PSHHAGSKAASVHWTGERVVSVLLLGLLPAAYLNPCSAVDYSLAAALTLHXXXGIGQVVTDYVHGDVSQK
          P.HH....AASVHWTGERVV.VLLLGLLPAAYLNPCSA.DYSLAAALTLH...GIGQV.T....G....K
Retrocopy PHHH----AASVHWTGERVVKVLLLGLLPAAYLNPCSAMDYSLAAALTLHSHWGIGQVIT-MSTGMFPRK

Parental  AAKAGLLVLSA-VTFAGLCYFNYHDVGICKAVAMLWKL
          .....LLVLSA.VTFAGLCYFNYHDVGICKAVAMLWKL
Retrocopy LPRQALLVLSA<VTFAGLCYFNYHDVGICKAVAMLWKL

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_252 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.

---

Parental genes homology:

Parental genes homology involve 15 parental genes, and 47 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000004066	3 retrocopies	retro_amel_1556, retro_amel_1588, retro_amel_998,
Callithrix jacchus	ENSCJAG00000010975	4 retrocopies	retro_cjac_1385, retro_cjac_1390, retro_cjac_1557, retro_cjac_3829,
Erinaceus europaeus	ENSEEUG00000013091	1 retrocopy	retro_eeur_336,
Echinops telfairi	ENSETEG00000008424	1 retrocopy	retro_etel_252 ,
Felis catus	ENSFCAG00000022580	3 retrocopies	retro_fcat_1371, retro_fcat_175, retro_fcat_492,
Homo sapiens	ENSG00000204370	8 retrocopies	retro_hsap_124, retro_hsap_1912, retro_hsap_2132, retro_hsap_2182, retro_hsap_2729, retro_hsap_2784, retro_hsap_355, retro_hsap_3791,
Gorilla gorilla	ENSGGOG00000026496	1 retrocopy	retro_ggor_50,
Loxodonta africana	ENSLAFG00000002763	1 retrocopy	retro_lafr_432,
Myotis lucifugus	ENSMLUG00000012228	3 retrocopies	retro_mluc_2418, retro_mluc_457, retro_mluc_756,
Macaca mulatta	ENSMMUG00000015247	1 retrocopy	retro_mmul_224,
Otolemur garnettii	ENSOGAG00000008568	5 retrocopies	retro_ogar_1651, retro_ogar_1795, retro_ogar_2087, retro_ogar_3122, retro_ogar_3147,
Pongo abelii	ENSPPYG00000003876	5 retrocopies	retro_pabe_1549, retro_pabe_1924, retro_pabe_2233, retro_pabe_2999, retro_pabe_3096,
Rattus norvegicus	ENSRNOG00000022980	3 retrocopies	retro_rnor_1529, retro_rnor_1686, retro_rnor_744,
Sus scrofa	ENSSSCG00000015034	3 retrocopies	retro_sscr_1060, retro_sscr_626, retro_sscr_627,
Tursiops truncatus	ENSTTRG00000010520	5 retrocopies	retro_ttru_1554, retro_ttru_238, retro_ttru_616, retro_ttru_633, retro_ttru_885,