RetrogeneDB ID: retro_etel_1135

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_216340:12785..13382(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSETEG00000016024
• Aliases: None
• Description: None

Sequence

>retro_etel_1135
CTCTGCGTGGTCACCCTCACTTTGTGAGTGACGTGGTCATCTCTTCCGATGGCCAGCATGCGCTCTCAGGCTCCTGGGAT
GGAACACTCCATCTCTGGGATCTCACAACGGGCACCACCACACGCCGCTGTGTAGGCCAGACCAAGGATGTGCTGAGTGT
GGCCTTCTCCTCTGACAACCGGCAGATTGTGTCTGGCTCCCGAGATAAAACCATCAAGCTGTGGAATACGCTGGGAGTTT
GCACGTACACCATACGGAGGAGAGCCACTCTGCATGGGTGTCTCGTGTGCGCTTTTCACCCAGCAGCAGCAACCCCGCCA
CTACCTCCCATGGATGGGACACGCTGGTCAAGGTGTGAACTTGGCTAATTGCAAACTGAAAACCAACTACATCAGCCACA
CAGGCTCCCTGAACACTGTGACGCTCTCTCCACATGGATTGCTCTGAGCTTCTGGAGGCAAGGATGGCCAAGCCATGCTG
TGGGCCCTCAATGAAGGCAAGCACCTTTATACCCTTGATGGAGGGGACATCATCAATGCCCTCTGCTTCAGTCCCAACCA
CTACTGGCTCTGTACTGCCACCAGCCCCAGCATCAAG

Alignment

ORF - retro_etel_1135 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.77 %
• Parental protein coverage: 73.98 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  LCVVTLTL-VTWSSLLMASLRSQAPGMEHYVSGIQRK-GTTTRRFVGHTKDVLSVAFSSDNRQIVSGSRD
          LCVVTLTL.VTWSSL.MAS.RSQAPGMEH..SGI....GTTTRR.VG.TKDVLSVAFSSDNRQIVSGSRD
Retrocopy LCVVTLTL*VTWSSLPMASMRSQAPGMEHSISGISQR<GTTTRRCVGQTKDVLSVAFSSDNRQIVSGSRD

Parental  KTIKLWNTLGVCKYTVQ-DESHSEWVSCVRFSPNSSNPIIVSCGWDKLVKV-WNLANCKLKTNHIGHTGY
          KTIKLWNTLGVC.YT....ESHS.WVS.VRFSP.SSNP...S.GWD.LVKV..NLANCKLKTN.I.HTG.
Retrocopy KTIKLWNTLGVCTYTIR<EESHSAWVSRVRFSPSSSNPATTSHGWDTLVKV<VNLANCKLKTNYISHTGS

Parental  LNTVTVSPDGSLCASGGKDGQAMLWDLNEGKHLYTLDGGDIINALCFSPNRYWLCAATGPSIK
          LNTVT.SP.G.L.ASGGKDGQAMLW.LNEGKHLYTLDGGDIINALCFSPN.YWLC.AT.PSIK
Retrocopy LNTVTLSPHGLL*ASGGKDGQAMLWALNEGKHLYTLDGGDIINALCFSPNHYWLCTATSPSIK

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_1135 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 26 parental genes, and 37 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000012008	1 retrocopy	retro_acar_185,
Ailuropoda melanoleuca	ENSAMEG00000000004	1 retrocopy	retro_amel_1627,
Bos taurus	ENSBTAG00000019648	1 retrocopy	retro_btau_1461,
Canis familiaris	ENSCAFG00000024818	1 retrocopy	retro_cfam_1824,
Callithrix jacchus	ENSCJAG00000018752	1 retrocopy	retro_cjac_2876,
Cavia porcellus	ENSCPOG00000008724	1 retrocopy	retro_cpor_687,
Dipodomys ordii	ENSDORG00000010735	1 retrocopy	retro_dord_117,
Equus caballus	ENSECAG00000022567	3 retrocopies	retro_ecab_172, retro_ecab_218, retro_ecab_986,
Erinaceus europaeus	ENSEEUG00000008729	1 retrocopy	retro_eeur_368,
Echinops telfairi	ENSETEG00000016024	3 retrocopies	retro_etel_1135 , retro_etel_114, retro_etel_2086,
Homo sapiens	ENSG00000204628	1 retrocopy	retro_hsap_3226,
Gorilla gorilla	ENSGGOG00000025367	1 retrocopy	retro_ggor_2194,
Macropus eugenii	ENSMEUG00000011055	3 retrocopies	retro_meug_1095, retro_meug_1109, retro_meug_1532,
Myotis lucifugus	ENSMLUG00000015507	1 retrocopy	retro_mluc_811,
Macaca mulatta	ENSMMUG00000003604	1 retrocopy	retro_mmul_1956,
Monodelphis domestica	ENSMODG00000004091	1 retrocopy	retro_mdom_1426,
Mustela putorius furo	ENSMPUG00000001148	2 retrocopies	retro_mputfur_1103, retro_mputfur_1111,
Mus musculus	ENSMUSG00000020372	1 retrocopy	retro_mmus_3282,
Nomascus leucogenys	ENSNLEG00000002604	1 retrocopy	retro_nleu_729,
Ornithorhynchus anatinus	ENSOANG00000002600	1 retrocopy	retro_oana_127,
Otolemur garnettii	ENSOGAG00000014924	2 retrocopies	retro_ogar_1257, retro_ogar_1591,
Pongo abelii	ENSPPYG00000019939	1 retrocopy	retro_pabe_149,
Pan troglodytes	ENSPTRG00000022734	1 retrocopy	retro_ptro_2178,
Rattus norvegicus	ENSRNOG00000002390	3 retrocopies	retro_rnor_1831, retro_rnor_2130, retro_rnor_895,
Ictidomys tridecemlineatus	ENSSTOG00000007063	1 retrocopy	retro_itri_1752,
Tupaia belangeri	ENSTBEG00000014661	2 retrocopies	retro_tbel_3897, retro_tbel_3899,