RetrogeneDB ID: retro_etel_2065

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_4561:1978..2700(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSETEG00000005646
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSETEG00000015721
• Aliases: None
• Description: None

Sequence

>retro_etel_2065
GACATCCATGGCCAGTACTATGATCAGTAGCTGTTTGTGTATGGCGGCTTCCCCCGAGAGAGCAGATCCCTTTTCCTGGG
TGACTACATGGAACAGGGCAATCAGTCACTGGAGACCACCTGCCTGCTGCTGGCCTTCAAGATCAAGTATCCAGAGAGCT
TCTTCCCATTTGGGGGGGAGAGCATCGACGAGTGTGCCAGCATCAACCACATCTAAGGCGTCTACGATGAGTGCAAGAGG
CCCTACAACATCAAACTCTGCAAAACTTTCACAGATTGCTCAACAGTCTGCCCATCGCAGCCATTGTAGACAAGGAGACA
TGCTGCTGCCAAGGAGGTATGTCCCATGACCTGCAGTCCATGAAAGGAATATGGTGCATCATGTTGCCCACAGACGGGTC
CAACCAGGGCCTGGTGTGCAACCCACTGTGGTAGGACCCTGACAAGGATGTGCAGAGCTGAGATGAGAACAACTATGGCG
ACTCCTTCACCTTCAGGGCAGAGGTGGTGGCCGAGTTTCTGCACAAGCATGACCTGGAACTCACCTGCTGAGCCCAACAG
GTGGTGGAAGATGGCTATGAGTTCACTGGCAAGTGGCAGCTGCTTATGCTTTTCTTAGCACTCAATTACTGCAGCAAGTT
TGACGAGGCTGGAGTCATTTTGCGTGCAGATGAGACACTCACGTGCGCCTTCCAGATCCTCAGGCTCACCGACAAAAACA
AG

Alignment

ORF - retro_etel_2065 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.84 %
• Parental protein coverage: 71.22 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  DIHGQYYDLLRLFEYGGFPPESNYLFLGDYVDRGKQSLETICLLLAYKIKYPENFFLLRGNH--ECASIN
          DIHGQYYD...LF.YGGFP.ES..LFLGDY...G.QSLET.CLLLA.KIKYPE.FF...G....ECASIN
Retrocopy DIHGQYYDQ*-LFVYGGFPRESRSLFLGDYMEQGNQSLETTCLLLAFKIKYPESFFPFGGESIDECASIN

Parental  RIYGFYDECKRRYNIKLWKTFTDC-FNCLPIAAIVDEKIFCCHGGLSPDLQSMEQIRRIMRPTDVPDQGL
          .I.G.YDECKR.YNIKL.KTFTDC..N.LPIAAIVD....CC.GG.S.DLQSM..I..IM.PTD...QGL
Retrocopy HI*GVYDECKRPYNIKLCKTFTDC<LNSLPIAAIVDKETCCCQGGMSHDLQSMKGIWCIMLPTDGSNQGL

Parental  LCDLLWSDPDKDVLGWGENDRGVSFTFGAEVVAKFLHKHDLDLICRAHQVVEDGYEFFAKRQLVTLFSAP
          .C..LW.DPDKDV....EN..G.SFTF.AEVVA.FLHKHDL.L.C.A.QVVEDGYEF..K.QL..LF.A.
Retrocopy VCNPLW*DPDKDVQS*DENNYGDSFTFRAEVVAEFLHKHDLELTC*AQQVVEDGYEFTGKWQLLMLFLAL

Parental  NYCGEFDNAGAMMSVDETLMCSFQILKPAEKKK
          NYC..FD.AG.....DETL.C.FQIL....K.K
Retrocopy NYCSKFDEAGVILRADETLTCAFQILRLTDKNK

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_2065 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 16 parental genes, and 38 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000013861	1 retrocopy	retro_amel_1721,
Bos taurus	ENSBTAG00000011198	2 retrocopies	retro_btau_6, retro_btau_960,
Ciona intestinalis	ENSCING00000004542	1 retrocopy	retro_cint_3,
Callithrix jacchus	ENSCJAG00000009147	7 retrocopies	retro_cjac_1062, retro_cjac_1165, retro_cjac_1408, retro_cjac_2304, retro_cjac_2535, retro_cjac_3288, retro_cjac_822,
Dipodomys ordii	ENSDORG00000010484	2 retrocopies	retro_dord_260, retro_dord_261,
Equus caballus	ENSECAG00000017228	1 retrocopy	retro_ecab_853,
Echinops telfairi	ENSETEG00000015038	2 retrocopies	retro_etel_1223, retro_etel_1364,
Echinops telfairi	ENSETEG00000015721	1 retrocopy	retro_etel_2065 ,
Myotis lucifugus	ENSMLUG00000010661	2 retrocopies	retro_mluc_15, retro_mluc_2217,
Mus musculus	ENSMUSG00000004455	5 retrocopies	retro_mmus_2274, retro_mmus_2968, retro_mmus_3418, retro_mmus_851, retro_mmus_925,
Oryctolagus cuniculus	ENSOCUG00000009275	2 retrocopies	retro_ocun_1232, retro_ocun_665,
Pan troglodytes	ENSPTRG00000005448	1 retrocopy	retro_ptro_2435,
Sorex araneus	ENSSARG00000000571	1 retrocopy	retro_sara_700,
Tupaia belangeri	ENSTBEG00000013852	4 retrocopies	retro_tbel_1710, retro_tbel_2116, retro_tbel_2311, retro_tbel_4450,
Vicugna pacos	ENSVPAG00000008411	1 retrocopy	retro_vpac_540,
Drosophila melanogaster	FBgn0003134	5 retrocopies	retro_dmel_21, retro_dmel_37, retro_dmel_42, retro_dmel_48, retro_dmel_81,