RetrogeneDB ID: retro_pvam_1357

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: scaffold_68131:654..1229(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MTHFD2
• Ensembl ID: ENSPVAG00000013948
• Aliases: None
• Description: methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 2, methenyltetrahydrofolate cyclohydrolase [Source:HGNC Symbol;Acc:7434]

Sequence

>retro_pvam_1357
CATTGTCCCTTCTACTTCTTGCTTGTTCAAAATGAAGCTGTTGTCATTTCTGGAAAGAAACTTGCCCAGCAGATCAAGCA
GAAAGTGCAGCAAGAGGTGAAAGTGTGGGTGGAATCTAGCAACAAACAACCACACCAGAGCATGGTTCTGGTTGATGAGA
ATCCTGCAAGTCATTTGTATGTCCTCAACAAAACCAGGGCCACTGCAGATGTGGGGATCAACAATGAGGCGATTATGAAA
CCAGCTTCAATTTCAGAGGAAGAACTGTTAAATTTAAATTTAATCAATAAATTAAATAACGATGATAATGTAAATGGCCT
CCTTGTTTAGCTGCCTCTTCCAGAGCACATCGATGAGAGAAAGATCTGCAAAGTTGTTTCTCCAGACAAGGATGTTGATG
GCTTTCATATAATTCATGTAAGGCGAATGTGTTCGGACTAGTATTCCATGTTACTGGCTACACCATGGGGTGTGTGGGAA
ATAATTAAGCTACCTGGCATTCTAACGTAGGGAAGAATGTGGTTGTAGCTGGAAGGTCAAAAAATGTTGGAATGCGCATT
GCAATGTTACTACAC

Alignment

ORF - retro_pvam_1357 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.72 %
• Parental protein coverage: 54.15 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  HRPFHLSAVRNEAVVISGRKLAQQIKQEVRQEVEEWVASGNKRPHLSVVLVGENPASHSYVLNKTRAAAD
          H.PF....V.NEAVVISG.KLAQQIKQ.V.QEV..WV.S.NK.PH.S.VLV.ENPASH.YVLNKTRA.AD
Retrocopy HCPFYFLLVQNEAVVISGKKLAQQIKQKVQQEVKVWVESSNKQPHQSMVLVDENPASHLYVLNKTRATAD

Parental  VGINSETIVKPASISEEELLNL--ISKLNNDDNVDGLLVQLPLPEHIDERKICNAVSPDKDVDGFHVINV
          VGIN.E.I.KPASISEEELLNL..I.KLNNDDNV.GLLV.LPLPEHIDERKIC..VSPDKDVDGFH.I.V
Retrocopy VGINNEAIMKPASISEEELLNLNLINKLNNDDNVNGLLV*LPLPEHIDERKICKVVSPDKDVDGFHIIHV

Parental  -RMCVVHHSMLPATPWGVWEIIKRTGIPT-LGKNVVVAGRSKNVGMPIAMLLH
          .RMC....SML.ATPWGVWEIIK..GI.T..GKNVVVAGRSKNVGM.IAMLLH
Retrocopy RRMCSD*YSMLLATPWGVWEIIKLPGILT<VGKNVVVAGRSKNVGMRIAMLLH

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Pteropus vampyrus was not studied using RNA-Seq expression data.

ChIP-Seq

Pteropus vampyrus was not studied using ChIP-Seq data.

EST

Pteropus vampyrus was not studied using EST data.

TSS

Pteropus vampyrus was not studied using FANTOM5 data.

Lab

retro_pvam_1357 was not experimentally validated.

Homology

Retrocopy orthology:

Pteropus vampyrus 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 11 parental genes, and 33 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,