RetrogeneDB ID: retro_meug_117

Retrocopy location

• Organism: Wallaby (Macropus eugenii)
• Coordinates: GeneScaffold_3063:63064..63589(+)
• Located in intron of: ENSMEUG00000000236

Retrocopy information

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

Parental gene information

• Parental gene symbol: TSR3
• Ensembl ID: ENSMEUG00000007498
• Aliases: None
• Description: TSR3, 20S rRNA accumulation, homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:14175]

Sequence

>retro_meug_117
GCTCTGAGCCTCAGTAGAAAAGATGCTGAAGGTGCTTCATCCGAGTTGGAACTGCTTAGCCCTCTCCCCATGTGGGAGCT
TGCTACTATAACCCCTGGAAGCACACTGGCAGGAAGCTGGCCCGTCAAAGTCTGATTCAAACTGACCTACTGAACCAAAA
TTTCAACAGTCCAATTCTTAGCCCTATGAGCACTCACTCTGTATCCCTGGAAGATAAGCTAAGTGGTGGCTCAGAGTTGA
GTTGCAGTTATTGACTGCTACTAGGCCAATCTGTAAGAAACTCTGGGAAAGATGTAGGGGAACCACCTTCAGTAGCTACC
CCACCTAGGGCTGCCAACCCTGGCAACTATGGAAGACCTCTCCAAGTGGTCCTTTGTGGAGGCTTTTGCCGCCACTTTTG
CATTCTGACTTTTCTGATCTTTCCATCATCTTGCTGCAAAAATTCAAGTAGGAGAAGGGATTTTTGGACCTGAATAGTCA
GCTTCTAGATAAGTATGCAGCCAAAGCAGCTCTGAGGATGTACTA

Alignment

ORF - retro_meug_117 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.5 %
• Parental protein coverage: 71.08 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  ARSLDSFTEEVEAALLELPCPLAMWDLG-HCDPRKCTGRKLARQGLVRTLRLNQRFNGLILSPMGTHYVS
          A.SL.....E.....LEL..PL.MW.L.....P.K.TGRKLARQ.L..T..LNQ.FN..ILSPM.TH.VS
Retrocopy ALSLSRKDAEGASSELELLSPLPMWELA<YYNPWKHTGRKLARQSLIQTDLLNQNFNSPILSPMSTHSVS

Parental  PADKQ-LVAQWGVAVIDCSWAKLEETPFGKMRGTHLRLLPYL-VAANPVNYGRP-CKLSCVEAFAAT-FC
          ..DK...VAQ..VAVIDC..A.L.ET..GKM.G.HL..LP.L..AANP.NYGRP..K.S.VEAFAAT.FC
Retrocopy LEDKL>VVAQS*VAVIDCY*ANL*ET-LGKM*GNHLQ*LPHL<RAANPGNYGRP>SKWSFVEAFAAT<FC

Parental  IL-GFSELAIILLRKFKWGKGFLDLNGQLLDKYAA-CSSPEDVL
          IL..FS.L.IILL.KFK..KGFLDLN.QLLDKYAA..SS.EDVL
Retrocopy IL<DFSDLSIILLQKFK*EKGFLDLNSQLLDKYAA<QSSSEDVL

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Macropus eugenii was not studied using RNA-Seq expression data.

ChIP-Seq

Macropus eugenii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_meug_117 retrocopy.

TSS

Macropus eugenii was not studied using FANTOM5 data.

Lab

retro_meug_117 was not experimentally validated.

Homology

Retrocopy orthology:

Macropus eugenii 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000013501	1 retrocopy	retro_ecab_893,
Macropus eugenii	ENSMEUG00000007498	1 retrocopy	retro_meug_117 ,
Myotis lucifugus	ENSMLUG00000008158	1 retrocopy	retro_mluc_744,
Tursiops truncatus	ENSTTRG00000011979	1 retrocopy	retro_ttru_630,