RetrogeneDB ID: retro_etel_2093

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_54182:32..635(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PSMB7
• Ensembl ID: ENSETEG00000005432
• Aliases: None
• Description: proteasome (prosome, macropain) subunit, beta type, 7 [Source:HGNC Symbol;Acc:9544]

Sequence

>retro_etel_2093
AGAATACATTGCCCCGGGCGGACCATTTATTGTTGTGGTTCAGGTCAACCCCAGCCATAGATGTAACAACCAGCTCATTT
CCTCCATCTTGGGACTCCATTCCAGCTCCACTGGCTGCCTTCCCAGAGTTGTGATGGCCGATCACAGGCAAAAGCAAATG
CTTCTTAGGTACCAAGCTTGCAGTGGGGCAGCACTACATTTGGGAGGGGTAGCTATTACTGGATCTCACTTCCACAGCAT
CCATCTCCATGGACCAACTGATAATCGTCTTATGTCACCGTGGGTTCAGATTCCTTGGCAGCAATGGTTGTATGTGGAAA
TAAATTTCAGCCAGACATGGAGGAGGAGGAAGCCAAGGAGGGGGTGAATAGGGCTGTTGCAGCCAGCATCTTCAATGGCT
TCGGATCTGGAAGCAACCTGGTTCTCTGCGTCATCAGCAAGAGCAAGCTGGGCTTTCTCTGCCTCCTCTCAGGGCCCAGT
GAAAAGGGCACCAGTTTTGGCCAGAACAGGCATGAGGAAGGGACAACTGCCGCACTCACTGAGAAGCTCCCCACCCTGGA
AATTGAAGTCCTGGAAGAAATGGTCCAAGCGATGGACACTTCT

Alignment

ORF - retro_etel_2093 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.46 %
• Parental protein coverage: 72.92 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  KIHFISPNIYCCGAG-TAADTDMTT-QLISSNLELHSLSTGRLPRVVTANRMLKQMLFRYQGYIGAALVL
          .IH.....IYCCG.G......D.TT.QLISS.L.LHS.STG.LPRVV.A....KQML.RYQ...GAAL.L
Retrocopy RIHCPGRTIYCCGSG<STPAIDVTT<QLISSILGLHSSSTGCLPRVVMADHRQKQMLLRYQACSGAALHL

Parental  GGVDVTGPHLYSIYPHGSTDKL-PYVTMGSGSLAAMAVFEDKFRPDMEEEEAKKLVSEAIGAGVFNDLGS
          GGV..TG.H..SI..HG.TD....YVT.GS.SLAAM.V...KF.PDMEEEEAK..V..A..A..FN..GS
Retrocopy GGVAITGSHFHSIHLHGPTDNR<SYVTVGSDSLAAMVVCGNKFQPDMEEEEAKEGVNRAVAASIFNGFGS

Parental  GSNIDLCVISKSKLDFLRPFSVPNKKGTRLGRYRCEKGTTAVLTEKVTTLDIEVLEETVQTMDTS
          GSN..LCVISKSKL.FL...S.P..KGT..G..R.E.GTTA.LTEK..TL.IEVLEE.VQ.MDTS
Retrocopy GSNLVLCVISKSKLGFLCLLSGPSEKGTSFGQNRHEEGTTAALTEKLPTLEIEVLEEMVQAMDTS

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_2093 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 12 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000003067	2 retrocopies	retro_btau_1722, retro_btau_983,
Echinops telfairi	ENSETEG00000005432	2 retrocopies	retro_etel_2093 , retro_etel_231,
Homo sapiens	ENSG00000136930	1 retrocopy	retro_hsap_1303,
Gorilla gorilla	ENSGGOG00000012164	1 retrocopy	retro_ggor_1019,
Nomascus leucogenys	ENSNLEG00000017268	1 retrocopy	retro_nleu_2947,
Otolemur garnettii	ENSOGAG00000003513	1 retrocopy	retro_ogar_2828,
Pongo abelii	ENSPPYG00000019596	1 retrocopy	retro_pabe_1092,
Pan troglodytes	ENSPTRG00000021354	1 retrocopy	retro_ptro_893,
Pteropus vampyrus	ENSPVAG00000000204	2 retrocopies	retro_pvam_1271, retro_pvam_866,
Rattus norvegicus	ENSRNOG00000011732	3 retrocopies	retro_rnor_1581, retro_rnor_1582, retro_rnor_2469,
Sorex araneus	ENSSARG00000009395	1 retrocopy	retro_sara_532,
Tupaia belangeri	ENSTBEG00000009196	2 retrocopies	retro_tbel_2889, retro_tbel_751,