RetrogeneDB ID: retro_meug_1840

Retrocopy location

• Organism: Wallaby (Macropus eugenii)
• Coordinates: Scaffold6441:19087..19433(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GABARAPL3
• Ensembl ID: ENSMEUG00000002873
• Aliases: None
• Description: GABA(A) receptors associated protein like 3, pseudogene [Source:HGNC Symbol;Acc:4069]

Sequence

>retro_meug_1840
GAAATCCAATACAAGGAGGATCATCCTTTAGTGTACCGGAAAAAAGAAGATAAGATTCGGAAGAAATACCCTGACAGAGT
CCCTGTAGTTGTGGAGAAGACACCTAAAGCCAGAGTCCCTGACCTGGACAAAAGGAATTACCTGGTGCCCGCTGACCTTA
CAGTTGGTCAATTTTACTTCTTAATTTGGAAGTGGATCCACCTTCGGCTAAAAGATGCATTTTTTCTTCTTTGTCAACAA
CACTATCCCTCCTACTAGCTCTACCATGGGCCAACTTTATGAGGACAACCATGAGGAAGACTATTTTCTCTACGTGGCCT
ACAGTGATGAAAGCGTCTATGGGAAG

Alignment

ORF - retro_meug_1840 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.47 %
• Parental protein coverage: 99.15 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KFQYKEDHPFEYRKKEGEKIRKKYPDRVPVIVEKAPKARVPDLDKRKYLVPSDLTVGQFYFLIRKRIHLR
          ..QYKEDHP..YRKKE..KIRKKYPDRVPV.VEK.PKARVPDLDKR.YLVP.DLTVGQFYFLI.K.IHLR
Retrocopy EIQYKEDHPLVYRKKE-DKIRKKYPDRVPVVVEKTPKARVPDLDKRNYLVPADLTVGQFYFLIWKWIHLR

Parental  PEDA-LFFFVNNTIPPTSATMGQLYEDNHEEDYFLYVAYSDESVYGK
          ..DA..FFFVNNTIPPTS.TMGQLYEDNHEEDYFLYVAYSDESVYGK
Retrocopy LKDA>FFFFVNNTIPPTSSTMGQLYEDNHEEDYFLYVAYSDESVYGK

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_1840 retrocopy.

TSS

Macropus eugenii was not studied using FANTOM5 data.

Lab

retro_meug_1840 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 6 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000014832	1 retrocopy	retro_ecab_673,
Homo sapiens	ENSG00000139112	1 retrocopy	retro_hsap_60,
Gorilla gorilla	ENSGGOG00000022360	1 retrocopy	retro_ggor_1219,
Macropus eugenii	ENSMEUG00000002873	3 retrocopies	retro_meug_1584, retro_meug_1840 , retro_meug_905,
Sarcophilus harrisii	ENSSHAG00000007434	1 retrocopy	retro_shar_82,
Ictidomys tridecemlineatus	ENSSTOG00000002246	1 retrocopy	retro_itri_391,