RetrogeneDB ID: retro_mmur_1462

Retrocopy location

• Organism: Mouse Lemur (Microcebus murinus)
• Coordinates: scaffold_6461:18339..20216(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MTHFD1
• Ensembl ID: ENSMICG00000013011
• Aliases: None
• Description: methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 1, methenyltetrahydrofolate cyclohydrolase, formyltetrahydrofolate synthetase [Source:HGNC Symbol;Acc:7432]

Sequence

>retro_mmur_1462
GTTGGCGACAGAGATGATTCCAATCTTTATATAAATGTGAAGCTGAAGGCTGCTGAAGAGGTTGGGATCAAAGCCACTCA
CGTTAAATTACCAAGAACAGCCACAGAATCTGAGGTGTTAAAGTACATTAGATCTTTGAATGAAGACTCTACCATACATG
GATTCATACTGCAGCTACCTTTAGATTCAGAAAATGCTATCAACACTGAAGCAGTGATCAATGCTATCGCACCCGAAAAG
GATGTGGATGGATTGACTAGTATCAGTGCTGGGAAACTCTCTAGAGGTGATCTAAATGACTATTTCATCCCTTGTACGCC
TAAAGGATGCTTGGAACTCATCAAAGAGACAGGGGTGCCGATCGCCGGAAAGCATGCCGTGGTGGCTGGGCGCAGTAAAA
TAGTAGGAGCCCCAGTGCATGACTTGCTTCTGTGGAACAATGCCACAGTGACCACCTGCCACTCCAAGACTGCCAACCTG
GGCGAGGAGGTAAATAAAGGTGACATCCTGGTGGTTGCAACTGGTCAGCCTGAATGGTGAAAGGAGAGTGGATCAAACCT
GGGGCAATAGTCATCGACTGTGGGATCAATTATATCCCAGATGATACAAAATCAAACGGGAGAAGGATTGTGGGTGATGT
GGCATACAAGGAGGCCAAAGAGCGGGCGGGCTTCATCACTCCTGTTCCTGGCGGCGTCGGGCCCATGACGGTGGCCATGC
TGATGCAGAGCACGGTAGAGAGTGCAAGGGGTTTCCTGGAGAAATACAAGCCAGGAAAGTGGAGTATTCAGTATAACAAC
CTTAACCTGAAGACACCTGTTCCAAGTGACATTGCTATATCACGATCTTGCAAACCAAAGCGCATTAGCACGCTGGCTCG
AGAAATTGGCCTGTTCTCTGAAGAGGTGGAATAGTATGGTGAGACAAAGGCCAAAGTCCTGCTGTCAGCACTGGAACGCC
TGAAACACCAGCCTGACGGGAAATACGTGGTGGTGACTGGAATAACTCCAGTGCCCCTGGGAGAAGGGAAAAGTACAACC
ACAATCGGGCTGGTGCAACCCTGGGTGCCCATCTTTTCCAGAATGTCTTTGCGTGTGTGCGACAGCCTTCCCAGGGCCCC
CACCTTTGGAATAAAAGGTGGTGCTGCAGGAGGCGGCTACTCCCAGGTCATTCCTAGGGAAGAGTTTAATCTCCACCTCA
CTGGTGACATCCATGCCATCACTGCAGCTAATAACCTGCTTGCTGCGGCCATTGATGCCCGGATATTCCATGAACTGACC
CAGACAGACAAGGCTCTCTTTAATCGTTTGGTGCCCTCAGTAAATGGAGTGAGAAAGTTCTCTGATATCCAAACCCGAAG
GTTAAGGAGACTAGGCATTGAAAAGACTGACCCTACCACACTGACAGACGAAGAGATAAACAGATTTGCAAGATTGGATA
TTGATCCAGAAACCATAACTTGGCAAAGAGTGTTGGATACCAATGATAGATTCCTGCGGAAGATCACAATTGGACAGGCT
CCAACGGAGAAAGGGCACACACGGACGACCCAGTTTGATATCTCAGTTGCCAGTGAGATCATGGCTGTCCTGGCCCTCAC
CAGTTCTCTGGAAGACATGAGAGAGAGACTGGGCAAAATGGTGGTGGCCTCCAGCAAGAAAGGGGAGCCCATCAGTGCCA
AAGACCTGGGGGTGAGTGGCGCGTTGACAGTGCTTATGAAGGACGCGATCAAGCCTAACCTCATGCAGATGTTAGAGGGC
ACTCCAGTGTTTGTCCACGCCGGCCCCTTCGCCAACATCGCACATGGCAATTCGTCTATCATCGCAGACCGGGTCGCACT
CAAGCTTGTCAGCCCAGAAGGGTTTGTAGTGACCGAA

Alignment

ORF - retro_mmur_1462 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.18 %
• Parental protein coverage: 69.03 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  VGDRDDSNLYINVKLKAAEEVGIKATHVKLPRTATESEV-KYIRSL-EDSTIHGFILQLPLDSENAINTE
          VGDRDDSNLYINVKLKAAEEVGIKATHVKLPRTATESEV.KYIRSL.EDSTIHGFILQLPLDSENAINTE
Retrocopy VGDRDDSNLYINVKLKAAEEVGIKATHVKLPRTATESEVLKYIRSLNEDSTIHGFILQLPLDSENAINTE

Parental  AVINAIAPEKDVDGLTSISAGKLSRGDLNDCFIPCTPKGCLELIKETGVQIAGKHAVVVGRSKIVGAPMH
          AVINAIAPEKDVDGLTSISAGKLSRGDLND.FIPCTPKGCLELIKETGV.IAGKHAVV.GRSKIVGAP.H
Retrocopy AVINAIAPEKDVDGLTSISAGKLSRGDLNDYFIPCTPKGCLELIKETGVPIAGKHAVVAGRSKIVGAPVH

Parental  DLLLWNNATVTTCHSKTANLGEEVNKGDILVVATGQPE-MVKGEWIKPGAIVIDCGINYIPDNTKSNGRR
          DLLLWNNATVTTCHSKTANLGEEVNKGDILVVATGQPE.MVKGEWIKPGAIVIDCGINYIPD.TKSNGRR
Retrocopy DLLLWNNATVTTCHSKTANLGEEVNKGDILVVATGQPE<MVKGEWIKPGAIVIDCGINYIPDDTKSNGRR

Parental  IVGDVAYNEAKERAGFITPVPGGVGPMTVAMLMQSTVESARGFLEKYKPGKWSIQYNNLNLKTPVPSDIA
          IVGDVAY.EAKERAGFITPVPGGVGPMTVAMLMQSTVESARGFLEKYKPGKWSIQYNNLNLKTPVPSDIA
Retrocopy IVGDVAYKEAKERAGFITPVPGGVGPMTVAMLMQSTVESARGFLEKYKPGKWSIQYNNLNLKTPVPSDIA

Parental  ISRSCKLKPIGTLAREIGLLSEEVELYGETKAKVLLSALERLKHQPDGKYVVVTGITPTPLGEGKSTTTI
          ISRSCK.K.I.TLAREIGL.SEEVE.YGETKAKVLLSALERLKHQPDGKYVVVTGITP.PLGEGKSTTTI
Retrocopy ISRSCKPKRISTLAREIGLFSEEVE*YGETKAKVLLSALERLKHQPDGKYVVVTGITPVPLGEGKSTTTI

Parental  GLVQ-ALGAHLFQNVFACVRQPSQG-PTFGIKGGAAGGGYSQVIPMEEFNLHLTGDIHAITAANNLVAAA
          GLVQ..LGAHLFQNVFACVRQPSQG.PTFGIKGGAAGGGYSQVIP.EEFNLHLTGDIHAITAANNL.AAA
Retrocopy GLVQ<TLGAHLFQNVFACVRQPSQG>PTFGIKGGAAGGGYSQVIPREEFNLHLTGDIHAITAANNLLAAA

Parental  IDARIFHELTQTDKALFNRLVPSVNGVRKFSDIQIRRLRRLGIEKTDPTTLTDEEINRFARLDIDPETIT
          IDARIFHELTQTDKALFNRLVPSVNGVRKFSDIQ.RRLRRLGIEKTDPTTLTDEEINRFARLDIDPETIT
Retrocopy IDARIFHELTQTDKALFNRLVPSVNGVRKFSDIQTRRLRRLGIEKTDPTTLTDEEINRFARLDIDPETIT

Parental  WQRVLDTNDRFLRKITIGQAPTEKGHTRTTQFDISVASEIMAVLALTSSLEDMRERLGKMVVASSKKGEP
          WQRVLDTNDRFLRKITIGQAPTEKGHTRTTQFDISVASEIMAVLALTSSLEDMRERLGKMVVASSKKGEP
Retrocopy WQRVLDTNDRFLRKITIGQAPTEKGHTRTTQFDISVASEIMAVLALTSSLEDMRERLGKMVVASSKKGEP

Parental  ISAEDLGVSGALTVLMKDAIKPNLMQTLEGTPVFVHAGPFANIAHGNSSIIADRVALKLVGPEGFVVTE
          ISA.DLGVSGALTVLMKDAIKPNLMQ.LEGTPVFVHAGPFANIAHGNSSIIADRVALKLV.PEGFVVTE
Retrocopy ISAKDLGVSGALTVLMKDAIKPNLMQMLEGTPVFVHAGPFANIAHGNSSIIADRVALKLVSPEGFVVTE

Legend:

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

Expression

RNA-Seq

Microcebus murinus was not studied using RNA-Seq expression data.

ChIP-Seq

Microcebus murinus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmur_1462 retrocopy.

TSS

Microcebus murinus was not studied using FANTOM5 data.

Lab

retro_mmur_1462 was not experimentally validated.

Homology

Retrocopy orthology:

Microcebus murinus 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 6 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000015967	1 retrocopy	retro_cfam_300,
Homo sapiens	ENSG00000100714	1 retrocopy	retro_hsap_4839,
Gorilla gorilla	ENSGGOG00000005251	1 retrocopy	retro_ggor_3018,
Microcebus murinus	ENSMICG00000013011	6 retrocopies	retro_mmur_1069, retro_mmur_1250, retro_mmur_1462 , retro_mmur_451, retro_mmur_777, retro_mmur_993,
Macaca mulatta	ENSMMUG00000001319	1 retrocopy	retro_mmul_2583,
Pan troglodytes	ENSPTRG00000006435	1 retrocopy	retro_ptro_3223,