RetrogeneDB ID: retro_etel_88

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: GeneScaffold_1515:432598..433358(-)
• Located in intron of: ENSETEG00000008278

Retrocopy information

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

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_88
ATGGAGGACGAGTTCATGTGCGGCGATGAGGAGGACGTGACCTGGAATACTCTGAAGAGAGTTGCTCTGAACCAAATGTG
GGTTTGGAAAAGCAGGACGACCCTTCCAAAACATTCAAAGATGACCCCAAAGCAGCGTTAGGCAGTCTCCAAGAGTTTGG
AACTTGCAGGTGAAAAAGGAAAATGGGGATTTAAAGCACTGAAACAAACGATCGAGATTAACCTCACATTGACAATTTTT
CCAGAAATGATGAACAGATATAAACAACTATGGACCTATATTCAGAGTGCAGTCAAAAAAAAGTCGATTAATTCTATCCT
TGATTCTATCTCCACTTCTAAACAGGATTCTGATTTTTTATGTCAGATGGAGCTGCAGGAATTCTATGAAACAGCACTGG
AAACTTCGGAAGATGCTAAGAACGATAGACTATGCTTTAAGACAAGCACAAAGCTTGGAAAATTATATTTAGAGCAAGAA
GAATATGGAAAGCTTCAAAAACATGTACGCCAACTACACCCATCCTGCCAAACTGACGCTGGTGAAAATGACCTGAGAAA
AAGGTACACCGTTATTAGGAAGATACACTTTGGAAATTCAAAGGTACACAGCGCAGAAGAGTAACAGAAACCTTAAAGCA
CTCTATGAATACTCACTTCACATCAAGTCTGCCATCCCTCATCCACCATTCATGGGAGTCATCAGAGGATGTGGAGGTAA
AAGGCACTTGCGAGAAGGTGAATTTGAAAAGGCACACACT

Alignment

ORF - retro_etel_88 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.66 %
• Parental protein coverage: 58.06 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MEDDFMCDDEEDY-DLEYSEDSNSEPNVDLENQYYNSKALKEDD-PKAALSSFQKV-LELEGEKGEWGFK
          MED.FMC.DEED..DLEYSE.S.SEPNV.LE.Q...SK....DD.P.........V.LEL.GEKG.WGFK
Retrocopy MEDEFMCGDEEDV<DLEYSEESCSEPNVGLEKQDDPSKTF-KDD<PQSSVRQSPRV<LELAGEKGKWGFK

Parental  ALKQMIKINFKLTNFPEMMNRYKQLLTYIRSAVTRNYSEKSINSILDYISTSKQNSDFLCQMDLLQEFYE
          ALKQ.I.IN..LT.FPEMMNRYKQL.TYI.SAV..........SI....STSKQ.SDFLCQM..LQEFYE
Retrocopy ALKQTIEINLTLTIFPEMMNRYKQLWTYIQSAVXXXSINSILDSI----STSKQDSDFLCQME-LQEFYE

Parental  TTLEALKDAKNDRLWFKTNTKLGKLYLEREEYGKLQKILRQLHQSCQTDDGEDDLK-KGTQLLEIYALEI
          T.LE...DAKNDRL.FKT.TKLGKLYLE.EEYGKLQK..RQLH.SCQTD.GE.DL..KGT.LL..Y.LEI
Retrocopy TALETSEDAKNDRLCFKTSTKLGKLYLEQEEYGKLQKHVRQLHPSCQTDAGENDLR>KGTPLLGRYTLEI

Parental  QMYTAQKNNKKLKALYEQSLHIKSAIPHPLIMGVIRGKFECGGKMHLREGEFEKAHT
          Q.YTAQK.N..LKALYE.SLHIKSAIPHP..MGVIRG...CGGK.HLREGEFEKAHT
Retrocopy QRYTAQKSNRNLKALYEYSLHIKSAIPHPPFMGVIRG---CGGKRHLREGEFEKAHT

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_88 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,