RetrogeneDB ID: retro_meug_1745

Retrocopy location

• Organism: Wallaby (Macropus eugenii)
• Coordinates: Scaffold56228:2690..3257(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RFFL
• Ensembl ID: ENSMEUG00000012628
• Aliases: None
• Description: ring finger and FYVE-like domain containing E3 ubiquitin protein ligase [Source:HGNC Symbol;Acc:24821]

Sequence

>retro_meug_1745
ACAGTGCCTTCCTTTGCTGTCTCTGCTTTGTTTCCTCACCACAGCCTTTCATCAAGAAAAGCTGATGAAAATGAAGACTG
ATGGCCATGTGCCCCAGGACCAAGAAGAAGTGATATGCCTGGAGAATGTAGCAAGCACTTCAACCGAGGATGAAACACAG
TCTACTGACTCTGAGGACAATTTGATGCCAGGGCAATGGAGTCTGATCTGTGTGAATATGGAGGACATTGAGATCCTCAC
TGTATGGCAGCTCAAAGAGATCCTGGCTCAGAACTTTGTCAATTACAAAGGCTGCTGTGAGAAATGGGAGCTGATGGAGA
GGGTGGCTTGGCTATACAAGGAACAGAAGGTCTTCCAGCTTTTGGTATCTGGCACTGCAGATCACAATAAGGAGCCAGCA
CTATCTAGTGCAGAGGAAAATATATGTAGATCTGCATGGACTCAACTGTCAACTGTGTCCTATTGGAGTGTGGCCAAATG
ACCACTTGTACCAAGTGTGGGAAATAAATGAACAAGAGCCCCATCAGCCACCATTATGGGATCTGAGCTGTGTATGTCTC
CAGATCC

Alignment

ORF - retro_meug_1745 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.07 %
• Parental protein coverage: 52.62 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  TSPNLPPSPAQPTSTPSTQAQENQQ-ANGHVPHDQEEVICVENVVSAPTEDETQSIDSEDNLVPGRRASL
          T.P....S...P....S...........GHVP.DQEEVIC.ENV.S..TEDETQS.DSEDNL.PG.....
Retrocopy TVPSFAVSALFPHHSLSSRKADENE>TDGHVPQDQEEVICLENVASTSTEDETQSTDSEDNLMPGQWSLI

Parental  SDLANVEDIEALTVRQLKEILARNFVNYKGCCEKWELMERVTRLFREQRDLQHLXXXXXXXXXDPAPSSA
          ....N.EDIE.LTV.QLKEILA.NFVNYKGCCEKWELMERV..L..EQ...Q.L..........PA.SSA
Retrocopy C--VNMEDIEILTVWQLKEILAQNFVNYKGCCEKWELMERVAWLYKEQKVFQLLVSGTADHNKEPALSSA

Parental  EENICK-ICMDSPIDCVLLECGHMVTCTKCGKRMNECPICRQYVIRAVHVFRS
          EENIC..ICMDS...CVLLECG.M.TCTKCGK.MN..PI...Y.I.AV.V.RS
Retrocopy EENICR<ICMDSTVNCVLLECGQMTTCTKCGK*MNKSPISHHYGI*AVYVSRS

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_1745 retrocopy.

TSS

Macropus eugenii was not studied using FANTOM5 data.

Lab

retro_meug_1745 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 5 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000001950	2 retrocopies	retro_chof_1069, retro_chof_285,
Macropus eugenii	ENSMEUG00000012628	1 retrocopy	retro_meug_1745 ,
Otolemur garnettii	ENSOGAG00000024777	1 retrocopy	retro_ogar_621,
Ochotona princeps	ENSOPRG00000011769	1 retrocopy	retro_opri_385,
Tarsius syrichta	ENSTSYG00000008923	2 retrocopies	retro_tsyr_1749, retro_tsyr_2060,