RetrogeneDB ID: retro_meug_1308

Retrocopy location

• Organism: Wallaby (Macropus eugenii)
• Coordinates: Scaffold363399:171..770(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CHMP2A
• Ensembl ID: ENSMEUG00000013531
• Aliases: None
• Description: charged multivesicular body protein 2A [Source:HGNC Symbol;Acc:30216]

Sequence

>retro_meug_1308
ATGAATCTACTGTTTGGGCTACAGTAAATTCCCAAGGAGATGCTGTGGAAGAACCAGCAGGCCCTGAATGGGGCCATGTG
CATGGGGCTGGACAGGGAACTTCAGAAGCTGGAGGCCCAGGAGAAACAAATCATTGCTGACATCAAGAAGATGACCAAGC
AGGGCCAGATAGATGCTGTGAAAATCATGACCCATAATCTGGTGACATGCCGCTATGTCAGCAAATTTGTGAGGATGTGA
GTCAACATCCAGGTCATGTCCCTGAAGATACAGATGCTTAAATCCAACCACTCCTTGGCTCAGGCCATGAAGGGTTTCAC
AAAGGTTATAGGGATCATGAACAGGCAGCTGAAGCTGCCCCAGATCCAGAAGATCATGTTGGAATTTGAGCACCAAACAG
GGATCATGGACATGAAGGAAGAGATGATGAATGATGCCATCGATAAGGCCATGGGGGATGAGGAAGATGAGAAGGAGAGT
GATGTTATGGTGTCCCAAGTGTTGGATGACCTCAGCCTGAGTTGACAGATGAACTCTCCAATCTCCCTTTCATAAGTGGC
TCCTTCTTCATGACTGTTGGGGGCAAGAAGACTGAACCT

Alignment

ORF - retro_meug_1308 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.28 %
• Parental protein coverage: 90.5 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MDLLFGRRKTPEELLRQNQRALNRAM-RELDRERQKLETQEKKIIADIKKMAKQGQMDAVKIMARDLVRT
          M.LLFG....P.E.L..NQ.ALN.AM...LDRE.QKLE.QEK.IIADIKKM.KQGQ.DAVKIM...LV.T
Retrocopy MNLLFGLQ*IPKEMLWKNQQALNGAMCMGLDRELQKLEAQEKQIIADIKKMTKQGQIDAVKIMTHNLV-T

Parental  RRYVSKFVMMRANIQAVSLKIQTLKSNNSMAQAMKGVTKAMGTMNRQLKLPQIQKIMMEFERQAEIMDMK
          .RYVSKFV.M..NIQ..SLKIQ.LKSN.S.AQAMKG.TK..G.MNRQLKLPQIQKIM.EFE.Q..IMDMK
Retrocopy CRYVSKFVRM*VNIQVMSLKIQMLKSNHSLAQAMKGFTKVIGIMNRQLKLPQIQKIMLEFEHQTGIMDMK

Parental  EEMMNDAIDDAMGDEEDEEESDAVVSQVLDELGLS-LTDELSNLPSTGGSLSVAAGGKKAEP
          EEMMNDAID.AMGDEEDE.ESD..VSQVLD.L.LS.LTDELSNLP...GS.....GGKK.EP
Retrocopy EEMMNDAIDKAMGDEEDEKESDVMVSQVLDDLSLS<LTDELSNLPFISGSFFMTVGGKKTEP

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_1308 retrocopy.

TSS

Macropus eugenii was not studied using FANTOM5 data.

Lab

retro_meug_1308 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 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Macropus eugenii	ENSMEUG00000012195	1 retrocopy	retro_meug_106,
Macropus eugenii	ENSMEUG00000013531	1 retrocopy	retro_meug_1308 ,
Mus musculus	ENSMUSG00000033916	1 retrocopy	retro_mmus_1039,
Otolemur garnettii	ENSOGAG00000005628	2 retrocopies	retro_ogar_1870, retro_ogar_2753,
Pongo abelii	ENSPPYG00000010511	1 retrocopy	retro_pabe_196,