RetrogeneDB ID: retro_meug_1370

Retrocopy location

• Organism: Wallaby (Macropus eugenii)
• Coordinates: Scaffold383571:1510..2049(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CHMP6
• Ensembl ID: ENSMEUG00000003320
• Aliases: None
• Description: charged multivesicular body protein 6 [Source:HGNC Symbol;Acc:25675]

Sequence

>retro_meug_1370
CAATTGAAATAACAATGGAATAAGTTGAAACAGTATCAGAAGAGGATCACCCAGTAACTGGAGAAGGAAAGGGAATTTGC
CAGGCAACATCTTCATGATGGAAAGAAAGAAAGAGCAAAGTTATGCTTAAGAAGAAGCGCTACTAGGAACAGCTCTTGCA
TAAGACAGAAAACCAGATCACAAATCTGGAAAGTATGGTTCAGAATGTTGAGTTTACCCAGACTGAAATGAAAGTGATCG
AAGGCCTGAAGTTTGGAAATGAATGTCTGAATAGAATGCATCAGATTATGTCCATAGAAAAAGTGGAAAGGATAATGCAT
GAAACCTGGGATGCTATGGAATACCAGAAGCAAATAGGTGATTTCTTGGCTGGCAGTTTTACTCAAGAAGATGAAGATGC
TACCTTAGAGGAACTGGAAGTGATCACTCAGGAACAAGTAGAACTTCCAGAAGTTCCTTCAGAACCCGAATCTAAGAAGA
TTGCAGGGAAAGAATCCATCAAGATAAGGGCAAAACATCCAGAACTGGTGGCAGCATCT

Alignment

ORF - retro_meug_1370 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.87 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  QLKQQRDKLKQYQKRITQQLEREREFARQLLRDGKKERAKL-LLKKKRYQEQLLDKTENQITNLETMVQN
          QLK.Q..KLKQYQKRITQ.LE.EREFARQ.L.DGKKERAKL..LKKKRY.EQLL.KTENQITNLE.MVQN
Retrocopy QLK*QWNKLKQYQKRITQ*LEKEREFARQHLHDGKKERAKL<MLKKKRY*EQLLHKTENQITNLESMVQN

Parental  IEFTQIEMKVIEGLKFGNECLNKMHQVMSIEEVERIMDETRDAVEYQKQIDDLLAGSFTQEDEDAILEEL
          .EFTQ.EMKVIEGLKFGNECLN.MHQ.MSIE.VERIM.ET.DA.EYQKQI.D.LAGSFTQEDEDA.LEEL
Retrocopy VEFTQTEMKVIEGLKFGNECLNRMHQIMSIEKVERIMHETWDAMEYQKQIGDFLAGSFTQEDEDATLEEL

Parental  EAITQEQVELPEVPSEPPSEKIPEKEPIKTRAKQPELVAAS
          E.ITQEQVELPEVPSEP.S.KI..KE.IK.RAK.PELVAAS
Retrocopy EVITQEQVELPEVPSEPESKKIAGKESIKIRAKHPELVAAS

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_1370 retrocopy.

TSS

Macropus eugenii was not studied using FANTOM5 data.

Lab

retro_meug_1370 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 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Macropus eugenii	ENSMEUG00000003320	2 retrocopies	retro_meug_1370 , retro_meug_762,
Mus musculus	ENSMUSG00000025371	1 retrocopy	retro_mmus_2033,
Rattus norvegicus	ENSRNOG00000004014	1 retrocopy	retro_rnor_782,