RetrogeneDB ID: retro_etel_545

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: GeneScaffold_8962:130007..131083(+)
• Located in intron of: ENSETEG00000008969

Retrocopy information

• Ensembl ID: ENSETEG00000008971
• 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_545
GTGCCCTCTGGGCCCCACATGGAAGAAGATGGGCTCAGGTGGACTTCAAAGTCTCCTCTGGACCCTGACTCAGACCTCCT
CTCGTGTACTCTGCCCAATGGCTTTGGGGGCCCACCTGGTCCAGAAAGGGAGCATAGTTTGGCATCCCCTGATGCCAGCA
TCCTCATCAGCATTGTGTATAGCCTCGGGGACCATGTGGCCCAGGAGCTTTTTCAGGGCTCAGATTTGGGCACTGTGGAA
GAGGCAGAGCGTCTTGGAGAGAAATCTGGCCAGCACAGCCCACTGAGAGAGGAGCACGTGACCTGTGTGCAGAGTATCTT
AGATGAATTCCTCCAAACTTATGGCAGCCTCATTCCCCTCAGCACTGATGAGGTAGTAGAGAAGTTAGAGGACATTTTCC
AGCAAGAGTTTTCTACACCTTCCAGGAAGGACCTAGTGCTGCAGCTGATCCAATCCTATCAGAGGATGCCAGGCAATGCC
ATAGTGAGGGGCTTCCGAGTGACCTATAAGTGGCATGTGCTGACCATGGATGACTTAGGGACCTTGTATGGACAGAATTG
GCTCAATGACCAGGTGATGAACATATATGGAGATCTGGTCATGGACACAGTCCCAGAAAAGGTGCATTTCTTCAACAATT
TCTTCTATGATAAACTCCGTACCAAGGGTTACGATGGGGTGAAAAGGTAGACCAAAAATGTAGACATCTTCAATAAAGAG
CTTCTGCTAACCCCCATCCACCTGGAGGTGCATTGGTCTCTCATCTCTGTTGACATGAGGGGATGCACCATCACCGATTT
TGACTCGCAGTGCACTCTAAACCATCGTTGTCCTAAGCATAGTGCCAAGTATCTACAAGCAGAGGCTTTGAAGAAAGACC
AACTGGATTTCCACCAGGGCTGGAAAGGTTACTTCAAAATGAATGTGGCCAGGCAGAACAATGGTAGTAACTGTGGCGCC
TTCATGTTGCAGTACTGCAAGCACCTGCCCTATCTCAGCCATTCAGCTTCACCCAGCAGGACATGCCCAAACTCCATTGG
CAGATCTACAAGGAGCTGTGTCACTGCAGACTCACT

Alignment

ORF - retro_etel_545 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.39 %
• Parental protein coverage: 62.65 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VPSGPHMEEDGLRWTPKSPLDPDSGLLSCTLPNGFGGPPGPEGEHSLAPPDASILISNVCSIGDHVAQEL
          VPSGPHMEEDGLRWT.KSPLDPDS.LLSCTLPNGFGGPPGPE.EHSLA.PDASILIS.V.S.GDHVAQEL
Retrocopy VPSGPHMEEDGLRWTSKSPLDPDSDLLSCTLPNGFGGPPGPEREHSLASPDASILISIVYSLGDHVAQEL

Parental  FQGSDLSTVEEAERLGEKPGQHSPLREEHVTCVQSILDEFLQTYGSLIPLSTDEVVEKLEDIFQQEFSTP
          FQGSDL.TVEEAERLGEK.GQHSPLREEHVTCVQSILDEFLQTYGSLIPLSTDEVVEKLEDIFQQEFSTP
Retrocopy FQGSDLGTVEEAERLGEKSGQHSPLREEHVTCVQSILDEFLQTYGSLIPLSTDEVVEKLEDIFQQEFSTP

Parental  SRKGLVLQLIQSYQRMPGNAMVRGFRVTYKRHVLTMDDLGTLYGQNWLNDQVMNMYGDLVMDTVPEKVHF
          SRK.LVLQLIQSYQRMPGNA.VRGFRVTYK.HVLTMDDLGTLYGQNWLNDQVMN.YGDLVMDTVPEKVHF
Retrocopy SRKDLVLQLIQSYQRMPGNAIVRGFRVTYKWHVLTMDDLGTLYGQNWLNDQVMNIYGDLVMDTVPEKVHF

Parental  FNSFFYDKLRTKGYDGVKRWTKNVDIFNKELLLIPIHLEVHWSLISVDVRRRTITYFDSQRTLNRRCPKH
          FN.FFYDKLRTKGYDGVKR.TKNVDIFNKELLL.PIHLEVHWSLISVD.R..TIT.FDSQ.TLN.RCPKH
Retrocopy FNNFFYDKLRTKGYDGVKR*TKNVDIFNKELLLTPIHLEVHWSLISVDMRGCTITDFDSQCTLNHRCPKH

Parental  IAKYLQAEALKKDRLDFHQGWKGYFKMNVARQNNDSDCGAFVLQYCKHL-ALSQPFSFTQQDMPKLRRQI
          .AKYLQAEALKKD.LDFHQGWKGYFKMNVARQNN.S.CGAF.LQYCKHL.ALSQPFSFTQQDMPKL..QI
Retrocopy SAKYLQAEALKKDQLDFHQGWKGYFKMNVARQNNGSNCGAFMLQYCKHL<ALSQPFSFTQQDMPKLHWQI

Parental  YKELCHCKLT
          YKELCHC.LT
Retrocopy YKELCHCRLT

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_545 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.

---

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,