RetrogeneDB ID: retro_meug_2079

Retrocopy location

• Organism: Wallaby (Macropus eugenii)
• Coordinates: Scaffold8786:18042..18334(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SUPT4H1
• Ensembl ID: ENSMEUG00000010164
• Aliases: None
• Description: suppressor of Ty 4 homolog 1 (S. cerevisiae) [Source:HGNC Symbol;Acc:11467]

Sequence

>retro_meug_2079
TTGGTCAAGACCATAGACCAATTTGAGGTATGATGGCTGTGATAATTACTACTCATACCTACAGATGAAAGGTAACTGAG
AGATGGTACATGACTGTACAAGCTCTTCTTTTGATGGAATCATTGCAATGATGAGTCTGGAGGACAGCTGGGTCTCTAAA
TGGCAGTGAGTCAGTACCTTCAAGCCTGGAGTTTATGCCATGTCTGTCACTGGCCGCCTGCCTCAAGGAATTGTTTGGGA
ACTGAAGAGCCAAGGCGTGATCTACAAATCCAGAGACACAGCAATAAAGACT

Alignment

ORF - retro_meug_2079 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.78 %
• Parental protein coverage: 82.91 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LVKTIDQFE-YDGCDNCDSYLQMKGNREMVYDCTSSSFDGIIAMMSPEDSWVSKWQRVSTFKPGVYAVSV
          LVKTIDQFE.YDGCDN..SYLQMKGN.EMV.DCTSSSFDGIIAMMS.EDSWVSKWQ.VSTFKPGVYA.SV
Retrocopy LVKTIDQFE>YDGCDNYYSYLQMKGN*EMVHDCTSSSFDGIIAMMSLEDSWVSKWQ*VSTFKPGVYAMSV

Parental  TGRLPQGIVRELKSRGVVYKSRDTAIKT
          TGRLPQGIV.ELKS.GV.YKSRDTAIKT
Retrocopy TGRLPQGIVWELKSQGVIYKSRDTAIKT

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_2079 retrocopy.

TSS

Macropus eugenii was not studied using FANTOM5 data.

Lab

retro_meug_2079 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 16 parental genes, and 30 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000017524	2 retrocopies	retro_cfam_1399, retro_cfam_553,
Callithrix jacchus	ENSCJAG00000017369	3 retrocopies	retro_cjac_1196, retro_cjac_1990, retro_cjac_4216,
Dipodomys ordii	ENSDORG00000002826	2 retrocopies	retro_dord_177, retro_dord_220,
Homo sapiens	ENSG00000213246	2 retrocopies	retro_hsap_1081, retro_hsap_2280,
Gorilla gorilla	ENSGGOG00000007232	2 retrocopies	retro_ggor_1693, retro_ggor_854,
Macropus eugenii	ENSMEUG00000010164	1 retrocopy	retro_meug_2079 ,
Myotis lucifugus	ENSMLUG00000025583	1 retrocopy	retro_mluc_761,
Macaca mulatta	ENSMMUG00000007579	2 retrocopies	retro_mmul_1005, retro_mmul_842,
Mus musculus	ENSMUSG00000020485	2 retrocopies	retro_mmus_2857, retro_mmus_633,
Nomascus leucogenys	ENSNLEG00000008159	3 retrocopies	retro_nleu_1619, retro_nleu_1962, retro_nleu_2714,
Oryctolagus cuniculus	ENSOCUG00000025823	2 retrocopies	retro_ocun_1613, retro_ocun_1636,
Otolemur garnettii	ENSOGAG00000031972	1 retrocopy	retro_ogar_2702,
Pongo abelii	ENSPPYG00000008233	1 retrocopy	retro_pabe_1940,
Pan troglodytes	ENSPTRG00000009451	2 retrocopies	retro_ptro_1614, retro_ptro_735,
Pteropus vampyrus	ENSPVAG00000002320	1 retrocopy	retro_pvam_477,
Rattus norvegicus	ENSRNOG00000007845	3 retrocopies	retro_rnor_1255, retro_rnor_1973, retro_rnor_556,