RetrogeneDB ID: retro_etel_1101

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_211645:8031..9001(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSETEG00000003593
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSETEG00000001922
• Aliases: None
• Description: None

Sequence

>retro_etel_1101
ATGTCCGGAGACGAGATGATCTTTGATCCTACTATGAGCAAGAAGAAGAAGAAGCCCTTTGTGCTGGATGAGGAAGGGGT
GCACAGACTGAAGAAACCAACTCTCAGAAACAAAGGAAGTGGAGCCAGAGCCAACCGAGGACAAAGCTGTGGGAGCTGAT
GAGGAGGACAGCAGGGAAAAGATGCTTCAGATGATCTAGAAGACTTGAACTGTTTTAATTAAAAGAAAAAGAAGAAAAAA
ACTAAAAAGATATTTGATATCGATGAAGCTGAAGAAGGTGTAAAGGATCTTAAACTTGAAGGTGATGTTCAAGAGCCGGC
TGAGTCAGAGGATGACCTGGACATTATGCTTGGCAATAAAAAGAAGGTCAAGTTCCCAGACAAGGATGCAATCCTAGAGA
AAGACGAAGCTTTAGAAGAAGAAGACAGCAAAAAAGGTGACGGCATAGCATTCACTAACGAGACAGGCCCTGCCTGGGCC
GGCTCAGAATGAGACTACACGTATGAGGAGCTACGGAATCGAGTGTTCAACCTCATGGGGGAAAGAATCCGATATGGTTG
CCAGAGAGAAGAGGAAATTAGTCGTGAAACCTCCACAGGTCATCTGTTTTCCAAGAAAAACATCTTTAGTCAACTTTACA
GATATCTGTAAACTATTGCATCGTCGGCCTAAACATCTCCTTGCATTTTTATTGGCTGAGCTGGGAACAATTGGTTCTAT
AGATGGTAATAACCAACTTGTAATCAAAGGATGATTCCAACAGAAACAGATAGAAAATGTCTTGAGAAGATATATCAAGG
AATACGTCACCTGCCACACGTGCCGATCACCGGACACGATCCTGTAGAAGGACACCCGACTTTATTTCTTACAGTGCGAA
GCTTGTCACTCTCCATGCTCTGTTGCCAGCATCAAAACCGGCTTCCCGGCTGTCATGGGCAAGCGAGCACAGCTCCATGC
CAAAGCTAAC

Alignment

ORF - retro_etel_1101 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.29 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  MSGDEMIFDPTMSKKKKKKKKPFMLDEEG-DAQTEET-QLSETKEVEPEPTEDKDVEADEEDSRKK-DAS
          MSGDEMIFDPTMS...KKKKKPF.LDEEG..AQTEET.QLSETKEVEPEPTEDK.V.ADEEDSR.K.DAS
Retrocopy MSGDEMIFDPTMS---KKKKKPFVLDEEG<GAQTEET<QLSETKEVEPEPTEDKAVGADEEDSREK<DAS

Parental  DDLDDLNFFNQKKKKKKTKKIFDIDEAEEGIKDLKLEGDVQEPAEPEDDLDIMLGNKKKKKKNVKFPDED
          DDL.DLN.FN...........FDIDEAEEG.KDLKLEGDVQEPAE.EDDLDIMLGNKKK....VKFPD.D
Retrocopy DDLEDLNCFNXXXXXXXXXXXFDIDEAEEGVKDLKLEGDVQEPAESEDDLDIMLGNKKK----VKFPDKD

Parental  EILEKDEALEDEDSKKDDGISFSNQIGPAWAGSERDYTYEELLNRVFNIMRE-KNP-DMVAGEM-KFVMN
          .ILEKDEALE.EDSKK.DGI.F.N..GPAWAGSE.DYTYEEL.NRVFN.M.E.KNP.DMVA.E..K.V..
Retrocopy AILEKDEALEEEDSKKGDGIAFTNETGPAWAGSE*DYTYEELRNRVFNLMGE<KNP<DMVAREKRKLVVK

Parental  PPQVVXXXXXXXXXXNFTDICKLLHRQPKHLLAFLLAELGTSGSIDGNNQLVIKGRFQQKQIENVLRRYI
          PPQ.V..........NFTDICKLLHR.PKHLLAFLLAELGT.GSIDGNNQLVIKG.FQQKQIENVLRRYI
Retrocopy PPQ-VICFPRKTSLVNFTDICKLLHRRPKHLLAFLLAELGTIGSIDGNNQLVIKG*FQQKQIENVLRRYI

Parental  KEYVTCHTCRSPDTILQKDTRLYFLQCETCHSRCSVASIKTGFQAVTGKRAQLRAKAN
          KEYVTCHTCRSPDTIL.KDTRLYFLQCE.CHS.CSVASIKTGF.AV.GKRAQL.AKAN
Retrocopy KEYVTCHTCRSPDTIL*KDTRLYFLQCEACHSPCSVASIKTGFPAVMGKRAQLHAKAN

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_1101 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 18 parental genes, and 33 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000007498	1 retrocopy	retro_cfam_2070,
Choloepus hoffmanni	ENSCHOG00000006521	1 retrocopy	retro_chof_271,
Callithrix jacchus	ENSCJAG00000018334	2 retrocopies	retro_cjac_4196, retro_cjac_697,
Cavia porcellus	ENSCPOG00000015439	1 retrocopy	retro_cpor_1143,
Echinops telfairi	ENSETEG00000001922	1 retrocopy	retro_etel_1101 ,
Homo sapiens	ENSG00000125977	3 retrocopies	retro_hsap_2176, retro_hsap_2260, retro_hsap_713,
Gorilla gorilla	ENSGGOG00000015546	5 retrocopies	retro_ggor_1683, retro_ggor_1726, retro_ggor_2007, retro_ggor_280, retro_ggor_604,
Microcebus murinus	ENSMICG00000006944	1 retrocopy	retro_mmur_1583,
Myotis lucifugus	ENSMLUG00000005335	1 retrocopy	retro_mluc_604,
Macaca mulatta	ENSMMUG00000018095	1 retrocopy	retro_mmul_1483,
Monodelphis domestica	ENSMODG00000002805	5 retrocopies	retro_mdom_1981, retro_mdom_365, retro_mdom_368, retro_mdom_370, retro_mdom_837,
Mus musculus	ENSMUSG00000074656	1 retrocopy	retro_mmus_3200,
Nomascus leucogenys	ENSNLEG00000010034	2 retrocopies	retro_nleu_2242, retro_nleu_466,
Otolemur garnettii	ENSOGAG00000001417	1 retrocopy	retro_ogar_196,
Pongo abelii	ENSPPYG00000010933	2 retrocopies	retro_pabe_1955, retro_pabe_2421,
Pan troglodytes	ENSPTRG00000013412	2 retrocopies	retro_ptro_1600, retro_ptro_508,
Rattus norvegicus	ENSRNOG00000017447	1 retrocopy	retro_rnor_2395,
Tupaia belangeri	ENSTBEG00000009970	2 retrocopies	retro_tbel_1505, retro_tbel_2508,