RetrogeneDB ID: retro_mmur_777

Retrocopy location

• Organism: Mouse Lemur (Microcebus murinus)
• Coordinates: GeneScaffold_81:90700..92774(+)
• 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_777
GTTGGCGACAGAGATGATTCCAATCTTTATATAAATGTGAAGCTGAAGGCTGCTGAAGAGGTTGGGATCAAAGCCATTCA
CGGTAAATTACCAAGAACAGCCACAGAATCTGAGGCGTTAAAGTACATTAGATCTTTGAATGAAGACTCTACTGTACATG
GATTCATACTGCAGCTACCTTTAGATTCAGAAAATGTTATTAACACTGAAGCAGTGATCAGTGCTATCACACCCGAAAAG
GATGTGGATGGATCGACTAGTATCAGTGCTGGGAAACTCGCTAGAGGTGATCTAAATGACTGTTTCATTCCTTGTACACC
TAAAGGATGCTTGGAACTCATCAAAGAGACAGGGGTGCAGATCGCAGGAAAGCACGCCGTGGTGGTTGGGCGCAGTAAAA
TAGTAGGAGCCCCAATGCATGACTTGATTCTGTGGAACAATGCCACAGTGACCACCTGCCACTCCAAGACTGCCAATCTG
GGCGAGGATGTAAACAAAGGTGACATCCTGATGGTTGCAACTGGTCAGCCTGAAATGGTGAAAGGAGAGTGGATCAAACC
TGGGGCAATAGTCATCGACTGTGGGATCAATTATGTCCCAGATGATACAAAATCAAATGCGAGAAGGATTGTGGGTGATG
TGGCATACAACGAGGCCAAAGAGCGGGCGGGCTTCATCACTCCTGTTCCTGGTGGCATCGGGCCCATGACAGTGGCAATG
CTGATGCAGAGCATGGTAGAGAGTGCAAGGCATTTCCTGGAGAAATACAGGCAAGGAAAGTGGAGTATTCAGTATAACAA
CCTTAACCTGAAGACACCTGTTCCAAGTGACATTGCTATATCACGATCTTGCAAACCAAAGCCCATTAGTACACTGGCTC
GAGAAATTGGCCTGTTCTCTGAAGAGGTGGAATAGTATGGTGAGACAAAGGCCAAAGTCCTGCTGTCAGCACTGGAACGC
CTGAAACACCAGCCTGACGGGAAATACGTGGTGGTGACTGCAATAACTCCAATGCCCCTGGGAGAAGGGAAAAGTACAAC
CACAATCGGGCTGGTGCAAGCCCTGGGTGCCCATCTTTTCCAGAACGTTTTTGCGTGTGTGCAACAGCCTTCCCAGGGCC
CCACCTTTGGAATAAAAGGTGGTGCTGCAGGAGGCGGCTACTCCCAGGTCATTCCTATGGAAGAGTTTAATCTCCACCTC
ACTGGTGACATCCATGCCATCACTGCAGCTAATAACCTGGTTGCCGCAGCCATTGATGCCCGGATATTCCATGAACTGAC
CCAGACAGACAAGGCTCTCTTTAATCGTTTGGTGCCCTCAGTAAATGGAGTGAGAAAGTTCTCTGATATCCAAATCCGAA
GGTTAAGGAGACTAGGCATTGAAAAGACTGACCCTACCACACTGACAGACGAAGAGATAAACAGATTTGCAAGATTGGAT
ATTGATCCAGAAACCATAACTTGGCAAAGAGTGTTGGATACCAATGATAGATTCCTGCGGAAGATCACAATTGGACAGGC
TCCAACGGAGAAAGGGCACACACGGACGACCCAGTTTGATATCTCAGTTGCCAGTGAGATCATGGCTGTCCTGGCCCTCA
CCAGTTCTCTGGAAGACATGAGAGAGAGACTGGGCAAAATGGTGGTGGCCTCCAGCAAGAAAGGGGAGCCCATCAGTGCC
GAAGACCTGGGGGTGAGTGGCTCATTGACAGTGCTTATGAAGGATACGATCAAGCCTAACCTCATGCAGACGTTAGAGGG
CACTCCGGTGTTCGTCCACGCCGGCCCCTTCGCCAACATCTCACATGGCAATTTTGTTTATCATCGCAGACCGGATCGCA
CTCAAACTTGTCAGCCCAAAAGAGTCTGTAGTGACCGAAGCAGAATTCGGAGCAGACATTGGAATGGAAAAGTTTTTAAA
CATCAAATGCAGGTACTCTGGCCTCCGCCCTCATGTGGTGGTGCTCGTTGCTACTGTCAGGGCTCTTAAAATGCACGGGG
GCGTCCCCACGGTCCTGGCTGGATTGCCTCTTCCCAAGGCTTGCATAGAGGAGAATCTGGAGCTGGTTGAAAAG

Alignment

ORF - retro_mmur_777 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.5 %
• Parental protein coverage: 76.22 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VGDRDDSNLYINVKLKAAEEVGIKATHVKLPRTATESE-VKYIRSL-EDSTIHGFILQLPLDSENAINTE
          VGDRDDSNLYINVKLKAAEEVGIKA.H.KLPRTATESE..KYIRSL.EDST.HGFILQLPLDSEN.INTE
Retrocopy VGDRDDSNLYINVKLKAAEEVGIKAIHGKLPRTATESEALKYIRSLNEDSTVHGFILQLPLDSENVINTE

Parental  AVINAIAPEKDVDGLTSISAGKLSRGDLNDCFIPCTPKGCLELIKETGVQIAGKHAVVVGRSKIVGAPMH
          AVI.AI.PEKDVDG.TSISAGKL.RGDLNDCFIPCTPKGCLELIKETGVQIAGKHAVVVGRSKIVGAPMH
Retrocopy AVISAITPEKDVDGSTSISAGKLARGDLNDCFIPCTPKGCLELIKETGVQIAGKHAVVVGRSKIVGAPMH

Parental  DLLLWNNATVTTCHSKTANLGEEVNKGDILVVATGQPEMVKGEWIKPGAIVIDCGINYIPDNTKSNGRRI
          DL.LWNNATVTTCHSKTANLGE.VNKGDIL.VATGQPEMVKGEWIKPGAIVIDCGINY.PD.TKSN.RRI
Retrocopy DLILWNNATVTTCHSKTANLGEDVNKGDILMVATGQPEMVKGEWIKPGAIVIDCGINYVPDDTKSNARRI

Parental  VGDVAYNEAKERAGFITPVPGGVGPMTVAMLMQSTVESARGFLEKYKPGKWSIQYNNLNLKTPVPSDIAI
          VGDVAYNEAKERAGFITPVPGG.GPMTVAMLMQS.VESAR.FLEKY..GKWSIQYNNLNLKTPVPSDIAI
Retrocopy VGDVAYNEAKERAGFITPVPGGIGPMTVAMLMQSMVESARHFLEKYRQGKWSIQYNNLNLKTPVPSDIAI

Parental  SRSCKLKPIGTLAREIGLLSEEVELYGETKAKVLLSALERLKHQPDGKYVVVTGITPTPLGEGKSTTTIG
          SRSCK.KPI.TLAREIGL.SEEVE.YGETKAKVLLSALERLKHQPDGKYVVVT.ITP.PLGEGKSTTTIG
Retrocopy SRSCKPKPISTLAREIGLFSEEVE*YGETKAKVLLSALERLKHQPDGKYVVVTAITPMPLGEGKSTTTIG

Parental  LVQALGAHLFQNVFACVRQPSQGPTFGIKGGAAGGGYSQVIPMEEFNLHLTGDIHAITAANNLVAAAIDA
          LVQALGAHLFQNVFACV.QPSQGPTFGIKGGAAGGGYSQVIPMEEFNLHLTGDIHAITAANNLVAAAIDA
Retrocopy LVQALGAHLFQNVFACVQQPSQGPTFGIKGGAAGGGYSQVIPMEEFNLHLTGDIHAITAANNLVAAAIDA

Parental  RIFHELTQTDKALFNRLVPSVNGVRKFSDIQIRRLRRLGIEKTDPTTLTDEEINRFARLDIDPETITWQR
          RIFHELTQTDKALFNRLVPSVNGVRKFSDIQIRRLRRLGIEKTDPTTLTDEEINRFARLDIDPETITWQR
Retrocopy RIFHELTQTDKALFNRLVPSVNGVRKFSDIQIRRLRRLGIEKTDPTTLTDEEINRFARLDIDPETITWQR

Parental  VLDTNDRFLRKITIGQAPTEKGHTRTTQFDISVASEIMAVLALTSSLEDMRERLGKMVVASSKKGEPISA
          VLDTNDRFLRKITIGQAPTEKGHTRTTQFDISVASEIMAVLALTSSLEDMRERLGKMVVASSKKGEPISA
Retrocopy VLDTNDRFLRKITIGQAPTEKGHTRTTQFDISVASEIMAVLALTSSLEDMRERLGKMVVASSKKGEPISA

Parental  EDLGVSGALTVLMKDAIKPNLMQTLEGTPVFVHAGPFANIAHGN-SSIIADRVALKLVGPEGFVVTEAGF
          EDLGVSG.LTVLMKD.IKPNLMQTLEGTPVFVHAGPFANI.HGN...IIADR.ALKLV.P...VVTEA.F
Retrocopy EDLGVSGSLTVLMKDTIKPNLMQTLEGTPVFVHAGPFANISHGN>LFIIADRIALKLVSPKESVVTEAEF

Parental  GADIGMEKFFNIKCRYSGLRPHVVVLVATVRALKMHGGGPTVTAGLPLPKAYIEENLELVEK
          GADIGMEKF.NIKCRYSGLRPHVVVLVATVRALKMHGG.PTV.AGLPLPKA.IEENLELVEK
Retrocopy GADIGMEKFLNIKCRYSGLRPHVVVLVATVRALKMHGGVPTVLAGLPLPKACIEENLELVEK

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_777 retrocopy.

TSS

Microcebus murinus was not studied using FANTOM5 data.

Lab

retro_mmur_777 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,