RetrogeneDB ID: retro_meug_256

Retrocopy location

• Organism: Wallaby (Macropus eugenii)
• Coordinates: GeneScaffold_8098:22152..22506(-)
• Located in intron of: ENSMEUG00000004324

Retrocopy information

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

Parental gene information

• Parental gene symbol: EIF3J
• Ensembl ID: ENSMEUG00000010372
• Aliases: None
• Description: eukaryotic translation initiation factor 3, subunit J [Source:HGNC Symbol;Acc:3270]

Sequence

>retro_meug_256
AAAAGGTTGGAAGAGCCTGAAGAATCTAAAGAGCTTACACCAGAAGAACAATTAGCAGATAAACTATGGCTAAAGAAATT
ACAGGAAGAGGCAGACCTTGAATTAGCAAAAGAAACCTTTGGTGTTAATAACACAATCTGTGATATAGATGCCATGAACC
CCTCTTCAAGAGATGACTTCATAGAGTTTGGCAAGTTACTAGAAGATAAAATTACACAGTATGAAAAATCTCTATATTTT
GCCAGTTTCTTGGAAGCATTAGTTTGAGATGTGTGTATTTCATTGGAAATCGATGACTTGAAAAAAATGACCCGTTCATT
GACAGTGCTATGCAGTGAAAAGCAGAAACAAGAA

Alignment

ORF - retro_meug_256 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.22 %
• Parental protein coverage: 71.08 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KRLEEPEESKELTPEEQLADKLRLKKLQEEADLELAKETFGVNNTICGIDAMNPSSRDDFTEFGKLLKDK
          KRLEEPEESKELTPEEQLADKL.LKKLQEEADLELAKETFGVNNTIC.IDAMNPSSRDDF.EFGKLL.DK
Retrocopy KRLEEPEESKELTPEEQLADKLWLKKLQEEADLELAKETFGVNNTICDIDAMNPSSRDDFIEFGKLLEDK

Parental  ITQYEKSLYYASFLEALVRDVCISLEIDDLKKITNSLTVLCSEKQKQE
          ITQYEKSLY.ASFLEALV.DVCISLEIDDLKK.T.SLTVLCSEKQKQE
Retrocopy ITQYEKSLYFASFLEALV*DVCISLEIDDLKKMTRSLTVLCSEKQKQE

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_256 retrocopy.

TSS

Macropus eugenii was not studied using FANTOM5 data.

Lab

retro_meug_256 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 15 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000002412	1 retrocopy	retro_cjac_589,
Cavia porcellus	ENSCPOG00000012396	3 retrocopies	retro_cpor_1357, retro_cpor_1358, retro_cpor_500,
Dipodomys ordii	ENSDORG00000008339	7 retrocopies	retro_dord_208, retro_dord_364, retro_dord_451, retro_dord_470, retro_dord_633, retro_dord_738, retro_dord_746,
Equus caballus	ENSECAG00000008716	1 retrocopy	retro_ecab_635,
Echinops telfairi	ENSETEG00000005052	1 retrocopy	retro_etel_1376,
Homo sapiens	ENSG00000104131	1 retrocopy	retro_hsap_4189,
Gorilla gorilla	ENSGGOG00000000548	2 retrocopies	retro_ggor_1687, retro_ggor_41,
Macropus eugenii	ENSMEUG00000010372	1 retrocopy	retro_meug_256 ,
Microcebus murinus	ENSMICG00000005006	1 retrocopy	retro_mmur_100,
Monodelphis domestica	ENSMODG00000017696	1 retrocopy	retro_mdom_141,
Mus musculus	ENSMUSG00000027236	1 retrocopy	retro_mmus_18,
Nomascus leucogenys	ENSNLEG00000005568	1 retrocopy	retro_nleu_2848,
Oryctolagus cuniculus	ENSOCUG00000005376	1 retrocopy	retro_ocun_1350,
Otolemur garnettii	ENSOGAG00000004694	1 retrocopy	retro_ogar_1227,
Pongo abelii	ENSPPYG00000006431	1 retrocopy	retro_pabe_3429,