RetrogeneDB ID: retro_etel_237

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: GeneScaffold_4022:3514..3956(-)
• Located in intron of: ENSETEG00000000386

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSETEG00000008408
• Aliases: None
• Description: None

Sequence

>retro_etel_237
CGTGGTCGTGGAATGAGAAGCCGTGGCAGAGGTTTCCAGTTTGTTTCCTCTTCTCTTCCAGACCTTTGTTATCATTGTGG
TGAGTCTGGTCACCTTGCCAAGGATTGTGATCTTCAGGAGGATGAAGCCTGCTCTAACTGCGATAGAGGTGGTCACATTG
CCAAGGACTGCAAGGAGCCCGAGCGAGAGAGCGAGCGCAGTGTTGCTACAACTGTGGCAAACCAGGCCGTCTGGCTCGTG
ACAGGGACCACGCTGATGAGCAGACGTGCTACTCTTGTGGAGAATTTGGACACATTCAAAAAGACTACACCAAAGTGAAG
TGCTACAGGTGTGGTGAGACTGGTCGGGTAGCCAGCAACTGCAGCAAGACAAGTGAAGTCAAGTCTACCGCCGTGGTGAA
TCAGGGCACCTTGCACAGGAATGCACAACTGAGACTTCAGCT

Alignment

ORF - retro_etel_237 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.0 %
• Parental protein coverage: 82.49 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  RGRGGFTSDRGFQFVSSSLPDICYRCGESGHLAKDCDLQED-ACYNCGRGGHIA-KDCKEPK-REREQCC
          RGRG.....RGFQFVSSSLPD.CY.CGESGHLAKDCDLQED.AC.NC.RGGHIA......P..RER.QCC
Retrocopy RGRGMRSRGRGFQFVSSSLPDLCYHCGESGHLAKDCDLQEDEACSNCDRGGHIA>RTARSPS>RERAQCC

Parental  YNCGKPGHLARDCDHADEQKCYSCGEFGHIQKDCTKVKCYRCGETGHVAINCSKTSEV-NCYRCGESGHL
          YNCGKPG.LARD.DHADEQ.CYSCGEFGHIQKD.TKVKCYRCGETG.VA.NCSKTSEV...YR.GESGHL
Retrocopy YNCGKPGRLARDRDHADEQTCYSCGEFGHIQKDYTKVKCYRCGETGRVASNCSKTSEV<QVYRRGESGHL

Parental  ARECTIEATA
          A.ECT.E..A
Retrocopy AQECTTETSA

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_237 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 30 parental genes, and 46 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000015334	2 retrocopies	retro_amel_1285, retro_amel_1773,
Bos taurus	ENSBTAG00000012159	1 retrocopy	retro_btau_19,
Canis familiaris	ENSCAFG00000004320	2 retrocopies	retro_cfam_1272, retro_cfam_23,
Callithrix jacchus	ENSCJAG00000017430	1 retrocopy	retro_cjac_4079,
Cavia porcellus	ENSCPOG00000012816	2 retrocopies	retro_cpor_424, retro_cpor_94,
Dipodomys ordii	ENSDORG00000002919	1 retrocopy	retro_dord_569,
Equus caballus	ENSECAG00000009512	1 retrocopy	retro_ecab_1072,
Echinops telfairi	ENSETEG00000008408	5 retrocopies	retro_etel_12, retro_etel_1791, retro_etel_2192, retro_etel_237 , retro_etel_583,
Felis catus	ENSFCAG00000028042	2 retrocopies	retro_fcat_1922, retro_fcat_2001,
Homo sapiens	ENSG00000169714	1 retrocopy	retro_hsap_50,
Gorilla gorilla	ENSGGOG00000010085	1 retrocopy	retro_ggor_2926,
Loxodonta africana	ENSLAFG00000002502	1 retrocopy	retro_lafr_49,
Macropus eugenii	ENSMEUG00000011699	1 retrocopy	retro_meug_55,
Myotis lucifugus	ENSMLUG00000012554	1 retrocopy	retro_mluc_141,
Macaca mulatta	ENSMMUG00000011585	1 retrocopy	retro_mmul_2505,
Mustela putorius furo	ENSMPUG00000017315	3 retrocopies	retro_mputfur_1465, retro_mputfur_1555, retro_mputfur_583,
Mus musculus	ENSMUSG00000030057	1 retrocopy	retro_mmus_230,
Nomascus leucogenys	ENSNLEG00000014482	1 retrocopy	retro_nleu_1986,
Oryctolagus cuniculus	ENSOCUG00000008696	2 retrocopies	retro_ocun_1626, retro_ocun_208,
Otolemur garnettii	ENSOGAG00000013898	1 retrocopy	retro_ogar_144,
Ochotona princeps	ENSOPRG00000005487	5 retrocopies	retro_opri_139, retro_opri_49, retro_opri_496, retro_opri_566, retro_opri_965,
Pongo abelii	ENSPPYG00000013423	1 retrocopy	retro_pabe_3658,
Pan troglodytes	ENSPTRG00000015369	1 retrocopy	retro_ptro_3131,
Pteropus vampyrus	ENSPVAG00000015070	1 retrocopy	retro_pvam_908,
Rattus norvegicus	ENSRNOG00000010239	2 retrocopies	retro_rnor_207, retro_rnor_727,
Sorex araneus	ENSSARG00000011874	1 retrocopy	retro_sara_397,
Sarcophilus harrisii	ENSSHAG00000017132	1 retrocopy	retro_shar_666,
Ictidomys tridecemlineatus	ENSSTOG00000000173	1 retrocopy	retro_itri_113,
Tarsius syrichta	ENSTSYG00000004344	1 retrocopy	retro_tsyr_1889,
Vicugna pacos	ENSVPAG00000007138	1 retrocopy	retro_vpac_548,