RetrogeneDB ID: retro_etel_1053

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_204469:4878..5492(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSETEG00000018801
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PSMA5
• Ensembl ID: ENSETEG00000012916
• Aliases: None
• Description: proteasome (prosome, macropain) subunit, alpha type, 5 [Source:HGNC Symbol;Acc:9534]

Sequence

>retro_etel_1053
GGCCACCAAGCCATTGGGATCCAGACAGCTGAGGGTGTGTGCCTGGCTGCGGAGAAGGGGATGACCTCCCCCTCTAGGAG
CCCAGCAACATCGAGGAAATTGTAGAGATTGATGCTCACATCGGCTGTGCCTGAGTGGCTAACTGCTGATGCCAAGACTT
TGATGGGTAAAGCCAGAGTGGAGACACAGAACCCCCGGTTCACCTCCACTGAGACCATGGCCATGGGGAGTGTGATCCAG
GCTGTGTCCGATCTGGCTTCACCGTTTGGAGAAGAAGATGCCGATCCAGGTGCCACGTCTCGGCCCTTTGGAGCAGCAGC
GTTATTTGGAGCGTTGATGAGAAAGGACCACAGCTGTTTCACCTGGACCCATCTGGAACCTTCGTCCAGTGTGATGCTCG
AGCGATGGACTCTGCTTCAGAGGGCGCCCAGAGCTTCTTGCGAGAAGCTCATCACAAGTCGATGACACTGAAAGAAGCCA
CCAAGTCTTCCCGCATCGTTCTCCAACAAGTAACGGAAGAGCGGCTAACTGCAACGCACACGGAGCCAGCTGTGGGGCCG
CCTGGCCGGAATAGCCACATGTCCACCAAGGAAGCCCTGGAAGAGGCGCTCAAG

Alignment

ORF - retro_etel_1053 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.43 %
• Parental protein coverage: 85.48 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  GSTAIGIQTAEGVCLAVEKRITSP-LMEPSSIEKIVEIDAHIGCA-MSG-LIADAKTLIDKARVETQNHW
          G..AIGIQTAEGVCLA.EK..TSP.L.EPS.IE.IVEIDAHIGCA..SG.L.ADAKTL..KARVETQN..
Retrocopy GHQAIGIQTAEGVCLAAEKGMTSP<L*EPSNIEEIVEIDAHIGCA<LSG<LTADAKTLMGKARVETQNPR

Parental  FTYNETMTVESVTQAVSNLALQFGEEDADPGAMSRPFGVALLFGG-VDEKGPQLFHMDPSGTFVQCDARA
          FT..ETM...SV.QAVS.LA..FGEEDADPGA.SRPFG.A.LFG..VDEKGPQLFH.DPSGTFVQCDARA
Retrocopy FTSTETMAMGSVIQAVSDLASPFGEEDADPGATSRPFGAAALFGA<VDEKGPQLFHLDPSGTFVQCDARA

Parental  IGSASEGAQSSLQEVYHKSMTLKEAIKSSLIILKQVMEEKLNATNIELATVQPVQTFHMFAKEELEEVIK
          ..SASEGAQS.L.E..HKSMTLKEA.KSS.I.L.QV.EE.L.AT..E.A...P....HM..KE.LEE..K
Retrocopy MDSASEGAQSFLREAHHKSMTLKEATKSSRIVLQQVTEERLTATHTEPAVGPPGRNSHMSTKEALEEALK

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_1053 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 7 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000013670	1 retrocopy	retro_cpor_1063,
Equus caballus	ENSECAG00000011835	1 retrocopy	retro_ecab_1106,
Echinops telfairi	ENSETEG00000012916	1 retrocopy	retro_etel_1053 ,
Mus musculus	ENSMUSG00000068749	1 retrocopy	retro_mmus_52,
Ochotona princeps	ENSOPRG00000008863	1 retrocopy	retro_opri_449,
Rattus norvegicus	ENSRNOG00000019868	2 retrocopies	retro_rnor_1230, retro_rnor_658,
Sus scrofa	ENSSSCG00000006830	2 retrocopies	retro_sscr_1156, retro_sscr_1194,