RetrogeneDB ID: retro_meug_2118

Retrocopy location

• Organism: Wallaby (Macropus eugenii)
• Coordinates: Scaffold92088:564..906(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RAB5C
• Ensembl ID: ENSMEUG00000005614
• Aliases: None
• Description: RAB5C, member RAS oncogene family [Source:HGNC Symbol;Acc:9785]

Sequence

>retro_meug_2118
TTGGACAACACAACGGTCAAATTTCACATCTGGGACACAGCAGGACAAGAGAGGTATCACAGTCTGGCCCCAGTGTACCA
TTGGGGCTCTCAGGCAGACGTTGCAGTCTACAATATCACAAATACAGATACATCTGCACAGGCCAAGAACGGGGTGAAAG
AGCTGCACCGGCAGGCTAGTCCCAACATAATCATTGCACTTGCCAGCAACAAGGCTGACCTGGCCAGCAAGAGAGCTGTG
GACTTCCAAGAAGCACAGGCCTACCCAGATGACAACAGTTTGACGTTCATGGAAACATCAGCAAAGCCAGCAATAAATGA
GAATGAAATTTTCATGGCAGTA

Alignment

ORF - retro_meug_2118 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.7 %
• Parental protein coverage: 52.78 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LDDTTVKFEIWDTAGQERYHSLAPMYYRGAQAAIVVYDITNTDTFARAKNWVKELQRQASPNIVIALAGN
          LD.TTVKF.IWDTAGQERYHSLAP.Y..G.QA...VY.ITNTDT.A.AKN.VKEL.RQASPNI.IALA.N
Retrocopy LDNTTVKFHIWDTAGQERYHSLAPVYHWGSQADVAVYNITNTDTSAQAKNGVKELHRQASPNIIIALASN

Parental  KADLASKRAVDFQEAQAYADDNSLLFMETSAKTAMNVNEIFMAI
          KADLASKRAVDFQEAQAY.DDNSL.FMETSAK.A.N.NEIFMA.
Retrocopy KADLASKRAVDFQEAQAYPDDNSLTFMETSAKPAINENEIFMAV

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_2118 retrocopy.

TSS

Macropus eugenii was not studied using FANTOM5 data.

Lab

retro_meug_2118 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 14 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006003	1 retrocopy	retro_amel_543,
Callithrix jacchus	ENSCJAG00000000472	2 retrocopies	retro_cjac_189, retro_cjac_1948,
Cavia porcellus	ENSCPOG00000011190	2 retrocopies	retro_cpor_333, retro_cpor_473,
Dipodomys ordii	ENSDORG00000006819	1 retrocopy	retro_dord_428,
Gorilla gorilla	ENSGGOG00000005472	1 retrocopy	retro_ggor_2182,
Macropus eugenii	ENSMEUG00000001728	1 retrocopy	retro_meug_1131,
Macropus eugenii	ENSMEUG00000005614	1 retrocopy	retro_meug_2118 ,
Macaca mulatta	ENSMMUG00000014761	1 retrocopy	retro_mmul_2022,
Monodelphis domestica	ENSMODG00000014792	1 retrocopy	retro_mdom_1399,
Otolemur garnettii	ENSOGAG00000009456	2 retrocopies	retro_ogar_2175, retro_ogar_985,
Pongo abelii	ENSPPYG00000008398	1 retrocopy	retro_pabe_2664,
Pan troglodytes	ENSPTRG00000009194	1 retrocopy	retro_ptro_2237,
Rattus norvegicus	ENSRNOG00000018568	2 retrocopies	retro_rnor_393, retro_rnor_73,
Tupaia belangeri	ENSTBEG00000007092	1 retrocopy	retro_tbel_4668,