RetrogeneDB ID: retro_etel_1952

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_319417:108749..109368(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSETEG00000013178
• Aliases: None
• Description: None

Sequence

>retro_etel_1952
GGAAGAGCTCCTGGATCCCGTGGAAGAGATAGTTACTGGGCTCACCATGAAGGGAACCCCTCCCCTCCCCAGAGATGTCT
ATTTGTCCCCGATAGACGATGAATATTCTACTAAAGACCATTATTTAAGCAGACATTACCCCAGTTCTTGTGATATAAGA
GATTATGCACCCCACCAGGAGATTATACGTATCGTGATTATGGAGATCCCAGTTCCCGTGATCGCTATCCATCCAGAGGT
TATAGTGATAGAGATGGGTATGGTCGTGATCAGACTATTCAACCATCCCAGTGGAGGCTCCCACAGCGATTTCTCTGCGA
GGTCTGGTCGTGCACGCACTGCACCACCCTGGCCAGGGCCCTGCCGTCTGAAGGGGAAGCAGTCACTCTGATGATGCAGC
AGCTCACAGGACAGATCTGGTGAAAGTCGAGACAGTTTCTCAAGCAGCCAAAGTGTTCTCTCTTCAAGGGATTGTGATCT
TGTCTTGTGGGCAGACAAGAAACAGGGCTTCCCCCTTTGATGGAGACGGGGTATCCTCTTCCGTGTGATTCCTACAGCAA
GCAGTTCAAGCCATGGAGCACCAAGAAATGTTGGCCGTGGAGGAAACCAGTCTGATAGA

Alignment

ORF - retro_etel_1952 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.3 %
• Parental protein coverage: 52.55 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 10

Retrocopy - Parental Gene Alignment:

Parental  GRAPVSRGRDSYG-GPPRREPLPSR-RDVYLSPRDDGYSTKDSYSSRDYPSSRDARDYAP-PPRDYTYRD
          GRAP.SRGRDSY..G.P.REPLPS..RDVYLSP.DD.YSTKD.Y.SR.YPSS.D.RDYAP.PP.DYTYRD
Retrocopy GRAPGSRGRDSYW<GSP*REPLPSP<RDVYLSPIDDEYSTKDHYLSRHYPSSCDIRDYAP<PPGDYTYRD

Parental  YGHSSSRDEYPSRGYSDRDGYGRDR-DYS-DHPSGGSYRDSYESYGNSRSAPPTRGP-PPSYG-GSSRYD
          YG..SSRD.YPSRGYSDRDGYGRD..DYS..HPSGGS..D.....G..R.APP..GP..PS.G.GSS..D
Retrocopy YGDPSSRDRYPSRGYSDRDGYGRDQ<DYS<NHPSGGSHSDFSARSGRARTAPPWPGP<LPSEG<GSSHSD

Parental  D-YSSSRDGYGGSRDSYSSSRSDLYSSGRDRV--GRQERGLP-PSMERGYPPPRDSYS-SS-SRGATRGG
          D..SSS.D..G.SRDS.SSS.S.L.S...D.V.......G.P.P.ME.GYP.P.DSYS.SS.S.GA.R..
Retrocopy D<CSSSQDRSGESRDSFSSSQSVLSSRDCDLVLWADKKQGFP<PLMETGYPLPCDSYS>SSSSHGAPRNV

Parental  GRGGSRSDR
          GRGG..SDR
Retrocopy GRGGNQSDR

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_1952 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 21 parental genes, and 45 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000018962	4 retrocopies	retro_cfam_1106, retro_cfam_1244, retro_cfam_1649, retro_cfam_1914,
Choloepus hoffmanni	ENSCHOG00000012369	3 retrocopies	retro_chof_1240, retro_chof_2596, retro_chof_880,
Dipodomys ordii	ENSDORG00000015481	1 retrocopy	retro_dord_793,
Echinops telfairi	ENSETEG00000007250	2 retrocopies	retro_etel_323, retro_etel_692,
Echinops telfairi	ENSETEG00000013178	1 retrocopy	retro_etel_1952 ,
Felis catus	ENSFCAG00000004779	1 retrocopy	retro_fcat_1903,
Homo sapiens	ENSG00000147274	7 retrocopies	retro_hsap_23, retro_hsap_3074, retro_hsap_3587, retro_hsap_4144, retro_hsap_4846, retro_hsap_800, retro_hsap_91,
Gorilla gorilla	ENSGGOG00000006944	1 retrocopy	retro_ggor_657,
Loxodonta africana	ENSLAFG00000005568	3 retrocopies	retro_lafr_1188, retro_lafr_276, retro_lafr_35,
Microcebus murinus	ENSMICG00000006856	2 retrocopies	retro_mmur_1252, retro_mmur_661,
Myotis lucifugus	ENSMLUG00000013209	5 retrocopies	retro_mluc_1630, retro_mluc_1746, retro_mluc_203, retro_mluc_2180, retro_mluc_80,
Mustela putorius furo	ENSMPUG00000001855	2 retrocopies	retro_mputfur_1539, retro_mputfur_956,
Mus musculus	ENSMUSG00000031134	2 retrocopies	retro_mmus_170, retro_mmus_187,
Oryctolagus cuniculus	ENSOCUG00000007220	1 retrocopy	retro_ocun_3,
Ochotona princeps	ENSOPRG00000016593	1 retrocopy	retro_opri_372,
Pongo abelii	ENSPPYG00000020771	3 retrocopies	retro_pabe_2548, retro_pabe_303, retro_pabe_766,
Rattus norvegicus	ENSRNOG00000000866	1 retrocopy	retro_rnor_268,
Sorex araneus	ENSSARG00000000397	1 retrocopy	retro_sara_169,
Ictidomys tridecemlineatus	ENSSTOG00000006211	2 retrocopies	retro_itri_1205, retro_itri_1346,
Tupaia belangeri	ENSTBEG00000001154	1 retrocopy	retro_tbel_1919,
Tursiops truncatus	ENSTTRG00000007322	1 retrocopy	retro_ttru_1450,