RetrogeneDB ID: retro_etel_1251

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_235406:3048..4187(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSETEG00000019580
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SENP3
• Ensembl ID: ENSETEG00000006699
• Aliases: None
• Description: SUMO1/sentrin/SMT3 specific peptidase 3 [Source:HGNC Symbol;Acc:17862]

Sequence

>retro_etel_1251
CCACCTCCCCGGCTGGGTCTGCTAGGTGCTCTCATGGCTGAGGATGGTGTGAGAGAGTCTCCACCTGTGCCCTCTGGGCC
CCACATGGAAGAAGATGGGCTCAGATGGACTCCAAAGTCTCCTCTGGAGCCTGACTCAGGCCTCCTCTCGTATACTCTGC
CCAATGGCTTTGGTGGCCCACCTGGTCCAGAAGGGGAGCACAGTTTGGCACCCCCTGATGCCAGCATCCTCATCAGCAAT
GTGGCCCAGGACCATGTGGCCGAGGAGCTTTTTCAGGGCTCAGATTTGGGCACTGTGGAAGAGGCAGAGTGCCCTGGAGA
GAAACCTGGCCAGCACAGCCCACTGAGGGAGGAGCACGTGACCTGTGTGCAGAGCATCCTAGATGAATTCCTCCAAACTT
ACGGCAGCCTCATCCCCCTCAGCACTGATGAGGTAGTGGAGAAGTTAGAGGACATTTTCCAGCAAGAGTTTTCTACACCT
TCCAGGAAGGGCCTAGTGCTGCAGCTGATCCAATCCTACCAGAGGATGCCAGGCAATGCCATGGTGAGGGGCTTCCGAGT
GACCTATAAGCGACATGTGCTGACCATGGACGACTTAGGGACCTTGTATGGGCAGAACTGGCTCAATGACCAGGTGATGA
ACATGTATGGAGACCTGGTCATGGACACGGTCCCAGAAAGGGTGCATTTCTTCAACAGTTTCTTCCATGATCAGCTCCAT
ACCAAGGGTTATGATGGGGTGAAAAGGTGGACCAGAAATGTTGACATCTTCAATAAGGAGCTGTTGCTAACACCCACCCA
CCTGGAGGCGCATTGGTCTCTCATTTCTGTTGACCTGGGGCGATGCTCCATTGCCTATTTTGACTCGCAGCGCAATCTAA
ACCGCCGCTGCCCTAAGCATATTGCCAAGTATCTACGGGCAGAGGCTTTGAAGAAAGACCGACTGGATTTCACCAGGGCA
GGTAAGGTTACTTCAAAATGAATGTGGGCAGGTAGACTCATGACAGGGACTGTGGCGCCTTCGTGCTGCAGTACTGCAAG
CACCTGGCCCTGTCTCAGCCATTCAGCTTCACCCCACAGGACATGCCCAAACTCCGTCGGCAGATCTACAAGGAGCTGTG
TCACTGCAAACTCACTGTG

Alignment

ORF - retro_etel_1251 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.86 %
• Parental protein coverage: 66.67 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PPPRLGLLGALMAEDGVRGSPPVPSGPHMEEDGLRWTPKSPLDPDSGLLSCTLPNGFGGPPGPEGEHSLA
          PPPRLGLLGALMAEDGVR.SPPVPSGPHMEEDGLRWTPKSPL.PDSGLLS.TLPNGFGGPPGPEGEHSLA
Retrocopy PPPRLGLLGALMAEDGVRESPPVPSGPHMEEDGLRWTPKSPLEPDSGLLSYTLPNGFGGPPGPEGEHSLA

Parental  PPDASILISNVCSIGDHVAQELFQGSDLSTVEEAERLGEKPGQHSPLREEHVTCVQSILDEFLQTYGSLI
          PPDASILISNV....DHVA.ELFQGSDL.TVEEAE..GEKPGQHSPLREEHVTCVQSILDEFLQTYGSLI
Retrocopy PPDASILISNVAQ--DHVAEELFQGSDLGTVEEAECPGEKPGQHSPLREEHVTCVQSILDEFLQTYGSLI

Parental  PLSTDEVVEKLEDIFQQEFSTPSRKGLVLQLIQSYQRMPGNAMVRGFRVTYKRHVLTMDDLGTLYGQNWL
          PLSTDEVVEKLEDIFQQEFSTPSRKGLVLQLIQSYQRMPGNAMVRGFRVTYKRHVLTMDDLGTLYGQNWL
Retrocopy PLSTDEVVEKLEDIFQQEFSTPSRKGLVLQLIQSYQRMPGNAMVRGFRVTYKRHVLTMDDLGTLYGQNWL

Parental  NDQVMNMYGDLVMDTVPEKVHFFNSFFYDKLRTKGYDGVKRWTKNVDIFNKELLLIPIHLEVHWSLISVD
          NDQVMNMYGDLVMDTVPE.VHFFNSFF.D.L.TKGYDGVKRWT.NVDIFNKELLL.P.HLE.HWSLISVD
Retrocopy NDQVMNMYGDLVMDTVPERVHFFNSFFHDQLHTKGYDGVKRWTRNVDIFNKELLLTPTHLEAHWSLISVD

Parental  VRRRTITYFDSQRTLNRRCPKHIAKYLQAEALKKDRLD-FHQGWKGYFKMNVARQNNDSDCGAFVLQYCK
          ..R..I.YFDSQR.LNRRCPKHIAKYL.AEALKKDRLD.FHQG..GYFKMNV.R...D.DCGAFVLQYCK
Retrocopy LGRCSIAYFDSQRNLNRRCPKHIAKYLRAEALKKDRLD<FHQGR*GYFKMNVGR*THDRDCGAFVLQYCK

Parental  HLALSQPFSFTQQDMPKLRRQIYKELCHCKLTV
          HLALSQPFSFT.QDMPKLRRQIYKELCHCKLTV
Retrocopy HLALSQPFSFTPQDMPKLRRQIYKELCHCKLTV

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_1251 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 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000000131	1 retrocopy	retro_btau_710,
Echinops telfairi	ENSETEG00000006699	2 retrocopies	retro_etel_1251 , retro_etel_545,
Mus musculus	ENSMUSG00000005204	1 retrocopy	retro_mmus_1196,