RetrogeneDB ID: retro_etel_2160

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_80855:432..1662(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSETEG00000000178
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: COPS2
• Ensembl ID: ENSETEG00000019523
• Aliases: None
• Description: COP9 signalosome subunit 2 [Source:HGNC Symbol;Acc:30747]

Sequence

>retro_etel_2160
GAAGACTCTGAAGACAGTAACTCTGAACCAAATGTGGATTTGGAAAATCAGTACTGTAATTCCAAAGCATTAAAAGAATA
TGACCCAAAAGCAGCGTTAAGCACTTTCCAAAAGGTCTTGGAACTTGAAGGTGAACAAGGAGAATGGGGATTTAAAGCAC
TGAAACAAATGATTAAGATTAACTTCAAATTGACAAATTTTCCAGAAATGATGAACAGATATAAACAACTATTGACCTAT
ATTCAGAGTGCAGTCACAAGAAATTATTCTGAAAAATCTATTAATTCTATTCTTGATTATATCTCCTCTTCTAACCAGAA
TTCTCATTTTTTATGTCAGATGGATTTACTGCAGGAATTCTATTACACACCACTGGAAGCTTTGAAAGATGCTAAGAATG
ATGGACTATGGTTCAAGACAAACACAAAGCTTGGAAAATTATACTTAGAGCGAGAGGAATATGGAAAATCTCAAAACAAT
TTTACGCCAACTACACCAGTCCTGCCAGGCTGATGATGGCGAAAATGACCTGGAAAAAGGTACACGGTTATTAGAAATAC
ACGCTTTGGAAATTCAAATGTATACAGCACAGAAAGATAACAGAAAACGTAAAGCACTCTATGAACAGTCACTTCACATC
AAGGCTGCCATCCCTCATCCACTGATCATGGGAGTCATCAGAGAATGTGGAGGTAAAATGCACTTGGGAGAAGGTGAATT
TGAAAAGGAGCACACTGATTTTTTTGAAGCCTTCAAGAATTATGATGAATCAGGAAATCCCAGATGAACTACTTGCTTAA
AATATTTGGTCTTGGAAAATATGTTAATGAATTGGGAATAAATCCATTTGACTCCCAGGAAGCCAAGCTGTACAAAAATG
ATCCAGAAATTCTATCAATGACAAATTTAGTAAGTGCCTATCAGAATAATAACATTACTGAATTTGAAAAGATTCTAAAC
ACAAATCGCAGCAACATCATGGATGACCCTTTCATAAGAAAACACATTGAAGAGATTTTGAGAAACATCAGAACACAAGT
GCTCATAAAATTAATAACGCCTTACACAAGAATACATGTTCCTTTTATTTCTAAGGAGTTAAACATAGATGTAGCTGACG
TGGAGAGCTTGCTGGTGCAGTGCATATTGGTTAACACTATTCATGGCCGAATTGATCAAGTCGACCAGCCCCTGGAACTG
GATCATCAGAAGAGGAGTGGTGCACGATAT

Alignment

ORF - retro_etel_2160 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.43 %
• Parental protein coverage: 91.17 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  EYSEDSNSEPNVDLENQYYNSKALKEDDPKAALSSFQKVLELEGEKGEWGFKALKQMIKINFKLTNFPEM
          E.SEDSNSEPNVDLENQY.NSKALKE.DPKAALS.FQKVLELEGE.GEWGFKALKQMIKINFKLTNFPEM
Retrocopy EDSEDSNSEPNVDLENQYCNSKALKEYDPKAALSTFQKVLELEGEQGEWGFKALKQMIKINFKLTNFPEM

Parental  MNRYKQLLTYIRSAVTRNYSEKSINSILDYISTSKQNSDFLCQMDLLQEFYETTLEALKDAKNDRLWFKT
          MNRYKQLLTYI.SAVTRNYSEKSINSILDYIS.S.QNS.FLCQMDLLQEFY.T.LEALKDAKND.LWFKT
Retrocopy MNRYKQLLTYIQSAVTRNYSEKSINSILDYISSSNQNSHFLCQMDLLQEFYYTPLEALKDAKNDGLWFKT

Parental  NTKLGKLYLEREEYGK-LQKILRQLHQSCQTDDGEDDLKKGTQLLEIYALEIQMYTAQKNNKKLKALYEQ
          NTKLGKLYLEREEYGK.L..ILRQLHQSCQ.DDGE.DL.KGT.LLEI.ALEIQMYTAQK.N.K.KALYEQ
Retrocopy NTKLGKLYLEREEYGK>LKTILRQLHQSCQADDGENDLEKGTRLLEIHALEIQMYTAQKDNRKRKALYEQ

Parental  SLHIKSAIPHPLIMGVIRGKFECGGKMHLREGEFEKAHTDFFEAFKNYDESGSPRRTTCLKYLVLANMLM
          SLHIK.AIPHPLIMGVIR...ECGGKMHL.EGEFEK.HTDFFEAFKNYDESG.PR.TTCLKYLVL.NMLM
Retrocopy SLHIKAAIPHPLIMGVIR---ECGGKMHLGEGEFEKEHTDFFEAFKNYDESGNPR*TTCLKYLVLENMLM

Parental  -KSGINPFDSQEAKPYKNDPEILAMTNLVSAYQNNDITEFEKILKTNHSNIMDDPFIREHIEELLRNIRT
          ...GINPFDSQEAK.YKNDPEIL.MTNLVSAYQNN.ITEFEKIL.TN.SNIMDDPFIR.HIEE.LRNIRT
Retrocopy <ELGINPFDSQEAKLYKNDPEILSMTNLVSAYQNNNITEFEKILNTNRSNIMDDPFIRKHIEEILRNIRT

Parental  QVLIKLIKPYTRIHIPFISKELNIDVADVESLLVQCILDNTIHGRIDQVNQLLELDHQKRGGARY
          QVLIKLI.PYTRIH.PFISKELNIDVADVESLLVQCIL.NTIHGRIDQV.Q.LELDHQKR.GARY
Retrocopy QVLIKLITPYTRIHVPFISKELNIDVADVESLLVQCILVNTIHGRIDQVDQPLELDHQKRSGARY

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_2160 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 10 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000013425	1 retrocopy	retro_btau_452,
Choloepus hoffmanni	ENSCHOG00000013375	7 retrocopies	retro_chof_1083, retro_chof_1288, retro_chof_2209, retro_chof_2371, retro_chof_2520, retro_chof_2550, retro_chof_678,
Callithrix jacchus	ENSCJAG00000001585	2 retrocopies	retro_cjac_3105, retro_cjac_3117,
Echinops telfairi	ENSETEG00000019523	2 retrocopies	retro_etel_2160 , retro_etel_88,
Macaca mulatta	ENSMMUG00000009838	1 retrocopy	retro_mmul_62,
Monodelphis domestica	ENSMODG00000002466	1 retrocopy	retro_mdom_891,
Oryctolagus cuniculus	ENSOCUG00000006455	1 retrocopy	retro_ocun_1296,
Otolemur garnettii	ENSOGAG00000013284	1 retrocopy	retro_ogar_1513,
Tupaia belangeri	ENSTBEG00000008306	1 retrocopy	retro_tbel_4497,
Tursiops truncatus	ENSTTRG00000000462	1 retrocopy	retro_ttru_328,