RetrogeneDB ID: retro_etel_2086

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_5256:204..836(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSETEG00000018594
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

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

Sequence

>retro_etel_2086
ATGAGATCAACTATGGCATTCCCCAGTATGCTCTGCGTGATCGCTCTCACTTTGTGAGTGACGTGGTCATCTCTTCTGAT
GGCCAGTTTGCGCTCTCAGGCTCCTGGGATGGAACACTAGGTCTCTGGGATCTGACAATGGGCACCACCACACGCCGCTT
TGTAGGCCAGACCAAGGATGTGCTGAGTGTGGCCTTCTCTGACAACCGGCAGATTGTCTCTGGCTCCCTAGATAAAACCT
CACGCTGTGGGTTTTACTCTGGGGGTTTGCAAGTACACCGTACAAGACGAGAGCCACTCTGAATGGGTGTCCTGTGTGCG
CTTTTCACCCAACAGCGGCAATCCCATCGTCGTCTCCTGTGGCTGGGACAAGCTGGTCAAGGTGTGAACTTGGCTAATTG
CAAACTGAAAACCAACTACATCAGCCACACAGGCTCCCTGAACACTGTGACGGTCTCTCCAGATGGATCCCTCTGTGCTT
CCGGAGGCAAGGATGGCCAAGCCATGCTGTGGGCCCTCAATGAAGGCAAGCACCTTTATACCCTTGATGGAGGGGACATC
ATCAATGCCCTCTGCTTCAGTCCCAACCACTACTGGCTCTGTGCTGCCACAGGCCCCAGCATCAAGATCTGG

Alignment

ORF - retro_etel_2086 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.51 %
• Parental protein coverage: 78.44 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MRPTMAFPNVLCVVTLTL-VTWSSLLMASLRSQAPGMEHYVSGIQR-KGTTTRRFVGHTKDVLSVAFSSD
          MR.TMAFP..LCV..LTL.VTWSSLLMASLRSQAPGMEH.VSGI....GTTTRRFVG.TKDVLSVAFS.D
Retrocopy MRSTMAFPSMLCVIALTL*VTWSSLLMASLRSQAPGMEH*VSGI*Q<MGTTTRRFVGQTKDVLSVAFS-D

Parental  NRQIVSGSRDKTIK-LWNTLGVCKYTVQDESHSEWVSCVRFSPNSSNPIIVSCGWDKLVKV-WNLANCKL
          NRQIVSGS.DKT......TLGVCKYTVQDESHSEWVSCVRFSPNS.NPI.VSCGWDKLVKV..NLANCKL
Retrocopy NRQIVSGSLDKTSR>VGFTLGVCKYTVQDESHSEWVSCVRFSPNSGNPIVVSCGWDKLVKV<VNLANCKL

Parental  KTNHIGHTGYLNTVTVSPDGSLCASGGKDGQAMLWDLNEGKHLYTLDGGDIINALCFSPNRYWLCAATGP
          KTN.I.HTG.LNTVTVSPDGSLCASGGKDGQAMLW.LNEGKHLYTLDGGDIINALCFSPN.YWLCAATGP
Retrocopy KTNYISHTGSLNTVTVSPDGSLCASGGKDGQAMLWALNEGKHLYTLDGGDIINALCFSPNHYWLCAATGP

Parental  SIKIW
          SIKIW
Retrocopy SIKIW

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_2086 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,