RetrogeneDB ID: retro_etel_1975

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_321367:1329..2222(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TRUB2
• Ensembl ID: ENSETEG00000009114
• Aliases: None
• Description: TruB pseudouridine (psi) synthase homolog 2 (E. coli) [Source:HGNC Symbol;Acc:17170]

Sequence

>retro_etel_1975
ATGAGGTCTGCTGGCCTGGCTCGACTGCATGGGCTCATTTGAGACGTACAAGCCCTCTGGGCTAAACTGGAAGCTCCTGT
GAGACACCGTGGAGACGCAGCTTTTGAAAGGTCTCAATGCTGGGACGCCGCCTGCCCCAGAACAGCTTGTTCGCTTCCTC
CTGGGCCCCATGGAAGGCAGTGAGGAGAAGGAACTGACCCTCACAGCCAGTAGTGTGCCCAGCCTTATCAACCGTCCTCT
GGTGTGCGGACCACAGTTCACCAGTCTGAAGGTTGGTGTTGGACACCAGCTGGATGCGGAGGCTTCTGGGGTTCTGTGCT
CGGTGTGGGACAGGGATGCAGGCTCCTCACCGACATGTACAACGCTTATCTCACCAAGGGTTACACAGTGCGGGGCCTCC
TGGGCAGAGCCACAGAGGACTTTGGTGCAGATGGTCAGCTGGTGGAGAAGATGACGTTTGACCACGTGACCAGAGAGAAG
CTGGACCGAATCCTGGCAATGATCCAAGGCTCCCATCAGAAGGCCCTGGTGATGTACTCTAACCTCGACCTGAAGACCCA
GGAGGTTACGAGATGGCTGTGAGCAGCTTCATCCAGCCCATGGACAAGTCCCCCATGCAGATCACCAGCATCCAGTGCCT
CCACTTTGCACCCCTCAAATTCCTCTTAGAGGTTCGGTACATGCATGAGACTCAGAAGCAGCTCTGGAAGCTGGTGCATG
AGATCGGCCGGGAGCTGAAGACCGCCGCAGTCTGTTCCCAAGTGGGGCGCACGAGAGACAGCCTCTTCACGCTGGACGAT
GCTCTGCTGAGGACCCAGTGGGGCCTACACAGCATCCAGGATGCCATCCGGGCTGCAATCCCCCGGGGGGCAATGGAGCT
GGAGGAGAGTTTG

Alignment

ORF - retro_etel_1975 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.39 %
• Parental protein coverage: 92.26 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MASAGLARLHGL-FATYKPPGLKWKFLRDTVETQLLKGLNAGTPPAQEQRVRFLLGPMEGSEEKELTLTA
          M.SAGLARLHGL.F.TYKP.GL.WK.L.DTVETQLLKGLNAGTPPA.EQ.VRFLLGPMEGSEEKELTLTA
Retrocopy MRSAGLARLHGL>FETYKPSGLNWKLL*DTVETQLLKGLNAGTPPAPEQLVRFLLGPMEGSEEKELTLTA

Parental  RSVPSLINHPLVRGPQFTSLKVGVGHRLDAEASGVL-VLGVGQGCRLLTDMYDAHLTKDYTVRGLLGRAT
          .SVPSLIN.PLV.GPQFTSLKVGVGH.LDAEASGVL.VLGVGQGCRLLTDMY.A.LTK.YTVRGLLGRAT
Retrocopy SSVPSLINRPLVCGPQFTSLKVGVGHQLDAEASGVL<VLGVGQGCRLLTDMYNAYLTKGYTVRGLLGRAT

Parental  DDFGAHGQLVEKTTFDHVIREKLDRILAMIQGSHQKALVTYSNLDLKTQEA-YEMAVSGFIRPMNKSPML
          .DFGA.GQLVEK.TFDHV.REKLDRILAMIQGSHQKALV.YSNLDLKTQE..YEMAVS.FI.PM.KSPM.
Retrocopy EDFGADGQLVEKMTFDHVTREKLDRILAMIQGSHQKALVMYSNLDLKTQEV<YEMAVSSFIQPMDKSPMQ

Parental  ITSIRCLHFAPPEFLLEVQCMHETQQQLRKLVHEIGLELKTTAACSQVRRTRDGFFTLDDALLRTQWDLH
          ITSI.CLHFAP..FLLEV..MHETQ.QL.KLVHEIG.ELKT.A.CSQV.RTRD..FTLDDALLRTQW.LH
Retrocopy ITSIQCLHFAPLKFLLEVRYMHETQKQLWKLVHEIGRELKTAAVCSQVGRTRDSLFTLDDALLRTQWGLH

Parental  SIQGAIRAAAPRVATELEKSL
          SIQ.AIRAA.PR.A.ELE.SL
Retrocopy SIQDAIRAAIPRGAMELEESL

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_1975 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
Echinops telfairi	ENSETEG00000009114	1 retrocopy	retro_etel_1975 ,
Otolemur garnettii	ENSOGAG00000003511	2 retrocopies	retro_ogar_440, retro_ogar_441,
Tupaia belangeri	ENSTBEG00000000586	1 retrocopy	retro_tbel_4734,