RetrogeneDB ID: retro_meug_152

Retrocopy location

• Organism: Wallaby (Macropus eugenii)
• Coordinates: GeneScaffold_4459:38746..39225(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MTHFD2
• Ensembl ID: ENSMEUG00000013987
• Aliases: None
• Description: methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 2, methenyltetrahydrofolate cyclohydrolase [Source:HGNC Symbol;Acc:7434]

Sequence

>retro_meug_152
AATGAAGCCATTGGGATTTCTGGAAAGAAGCTGGCCCAGCAGATCGGCAGGAGGCCCGGCAGGAGGTGGAACGGTGGGTT
GCCTTAGGTAACCAAAGGCCCCACTTGAGTGTGGTCCTGGTAGGAGAAAACCCTGCAAGTCACTCCTATGTCTTGAACAA
GACCAAGGCTGCTGCAGATGTGGGAATCAGCAGTGGAACAATTTTGAAACCTGCCTCCATTTCAGAGGAAGAGCTTCTGG
ATTGAATCAGTAAACTCAAGGATGATGACCATGTCGACGGCCTTCTGGTTCAGCTCCCTCTTCCTGAACCCATCGATGAG
AGAAAGGTCTGCAATGCTGTGGCTCCAGATAAGGATGTGGATGGCTTTCATGGGATCAACGTGGGGTGCATGTGCCTGGA
CCAGTACTCCATGCTCCCCGTGAAGCCCTGGGGGGAGTGGGAGATCATTAAGCGGACAGGCATTCCCACATTGCGGAAA

Alignment

ORF - retro_meug_152 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.68 %
• Parental protein coverage: 50.79 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  NEAIVISGKKLAQQI-RQEARQEVEQWVALGNKRPHLSVVLVGENPASHSYVLNKTKAAADVGISSETIL
          NEAI.ISGKKLAQQI.RQEARQEVE.WVALGN.RPHLSVVLVGENPASHSYVLNKTKAAADVGISS.TIL
Retrocopy NEAIGISGKKLAQQI<RQEARQEVERWVALGNQRPHLSVVLVGENPASHSYVLNKTKAAADVGISSGTIL

Parental  KPASISEEDLLDLISKLNDDDHVDGLLVQLPLPEHIDERKVCNAVAPDKDVDGFHVINVGRMCLDQYSML
          KPASISEE.LLD.ISKL.DDDHVDGLLVQLPLPE.IDERKVCNAVAPDKDVDGFH.INVG.MCLDQYSML
Retrocopy KPASISEEELLD*ISKLKDDDHVDGLLVQLPLPEPIDERKVCNAVAPDKDVDGFHGINVGCMCLDQYSML

Parental  PATPWGVWEIIKRTGIPTLGK
          P..PWG.WEIIKRTGIPTL.K
Retrocopy PVKPWGEWEIIKRTGIPTLRK

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_152 retrocopy.

TSS

Macropus eugenii was not studied using FANTOM5 data.

Lab

retro_meug_152 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 12 parental genes, and 34 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017345	2 retrocopies	retro_amel_1098, retro_amel_1584,
Canis familiaris	ENSCAFG00000008716	1 retrocopy	retro_cfam_580,
Callithrix jacchus	ENSCJAG00000017810	3 retrocopies	retro_cjac_2225, retro_cjac_2568, retro_cjac_3078,
Homo sapiens	ENSG00000065911	5 retrocopies	retro_hsap_2732, retro_hsap_2817, retro_hsap_3002, retro_hsap_3309, retro_hsap_3874,
Macropus eugenii	ENSMEUG00000013987	4 retrocopies	retro_meug_1468, retro_meug_152 , retro_meug_1577, retro_meug_2074,
Mustela putorius furo	ENSMPUG00000007829	3 retrocopies	retro_mputfur_1087, retro_mputfur_1397, retro_mputfur_1551,
Nomascus leucogenys	ENSNLEG00000000326	5 retrocopies	retro_nleu_1196, retro_nleu_207, retro_nleu_2501, retro_nleu_595, retro_nleu_749,
Otolemur garnettii	ENSOGAG00000009089	1 retrocopy	retro_ogar_3390,
Pongo abelii	ENSPPYG00000012283	3 retrocopies	retro_pabe_2271, retro_pabe_2729, retro_pabe_3077,
Pan troglodytes	ENSPTRG00000012081	4 retrocopies	retro_ptro_1846, retro_ptro_1910, retro_ptro_2162, retro_ptro_2641,
Pteropus vampyrus	ENSPVAG00000013948	2 retrocopies	retro_pvam_1357, retro_pvam_1414,
Rattus norvegicus	ENSRNOG00000010833	1 retrocopy	retro_rnor_2170,