RetrogeneDB ID: retro_meug_2018

Retrocopy location

• Organism: Wallaby (Macropus eugenii)
• Coordinates: Scaffold80097:5685..6372(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMEUG00000001969
• Aliases: None
• Description: None

Sequence

>retro_meug_2018
GCCAGCACCAAGAGGAATGAGGAAAATATCACTGGTGGTCAAACATGCATTCCCCACCCCCAGTCCTGGTAGTCTCCACC
GTTCATTTCTCAAAGTTTCCACTGTGGGGGTATCCTGCTGTCTGATCAGTGAGTCCTCACAGAAGCTCACTGGAACCTCA
ACTGATCTCAAGAAAACACAATCTCCAGCTCCTGGAGCCCTTGCAACAACTGGTCAGGGTGGAGAACCAGGTACTGAACC
CCAAATATAACTTCAGAATAGCAACCACAACCTTATGCTACTCTTTCTGAAGAAGGCAATAAATCTGACCCCCAAGTTCC
CCCATCTGGCTGGCCAAAAGATGGTGCCAATCCTGAATCAATTTGCTGAGTGTCTGGCAGGGGGACCATTTCCAGTCCTT
TTGTCAAATATCCCAGCATCCTCCAGTGCATGAACATCAGTATCTCATCTGAGGAAGAATGCAAAAGTGCATATGAAAGA
GCCAGAACTCCAGGCATGATCTGTGCTAGAGATGGGAAAGGTGGGAAGGATTCTTGGCAGGATAACTCCAGAGGCCCCTT
GGCATTCATTGGAGCCCTGAAAGGCCTTGTGTCTTGGGCCATGGAAGACTGCACCCTGGCCAGGTTTTCTCCCATTTATA
CCAACATGCCCCATTACCAGACCTGGATCCTAAACGAAATGCAGAAG

Alignment

ORF - retro_meug_2018 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.43 %
• Parental protein coverage: 99.15 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  ANGREDEEKIIGGYTCIPNSQPWQAALLANRQFRCGGVLLSNRWVLTAAHCNHWNL-RVVLGKHNIRLLE
          A.....EE.I.GG.TCIP..Q.W.........F.CGG.LLS...VLT.A...HWNL......KHN..LLE
Retrocopy ASTKRNEENITGGQTCIPHPQSW*SPPFISQSFHCGGILLSDQ*VLTEA---HWNL<QLISRKHNLQLLE

Parental  PSQQSVGVERRVPHPSYSPR-TSNNDLMLLYLEKPVKLTN-QVKPIQLAKNCANPGTDCLVSGWGTVSSP
          P.QQ.V.VE..V..P.Y..R..SN..LMLL.L.K...LT..QV.P....K..ANP...C.VSG.GT.SSP
Retrocopy PLQQLVRVENQVLNPKYNFR<NSNHNLMLLFLKKAINLTP<QVPPSGWPKDGANPESIC*VSGRGTISSP

Parental  FARYPSTLQCLKISIFSEESCKNAYYGKAITPGMVCAGDKKGGKDSCQGDSGGPLVCNGVLQGLVSWGME
          F..YPS.LQC..ISI.SEE.CK.AY...A.TPGM.CA.D.KGGKDS.Q..S.GPL...G.L.GLVSW.ME
Retrocopy FVKYPSILQCMNISISSEEECKSAYE-RARTPGMICARDGKGGKDSWQDNSRGPLAFIGALKGLVSWAME

Parental  HCALPGYPGVYTNLCRYRTWILNEMQK
          .C.L......YTN...Y.TWILNEMQK
Retrocopy DCTLARFSPIYTNMPHYQTWILNEMQK

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_2018 retrocopy.

TSS

Macropus eugenii was not studied using FANTOM5 data.

Lab

retro_meug_2018 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 3 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Macropus eugenii	ENSMEUG00000001969	7 retrocopies	retro_meug_1025, retro_meug_1028, retro_meug_1038, retro_meug_1108, retro_meug_1959, retro_meug_2018 , retro_meug_707,
Macropus eugenii	ENSMEUG00000014123	1 retrocopy	retro_meug_1950,
Monodelphis domestica	ENSMODG00000020815	1 retrocopy	retro_mdom_1516,