RetrogeneDB ID: retro_mmur_1069

Retrocopy location

• Organism: Mouse Lemur (Microcebus murinus)
• Coordinates: scaffold_18908:3877..6025(+)
• 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_1069
GTTGGTGACAGAGATGATTCCAATCTTTATATAAATGTGAAGCTGAAGGCTGCTGAAGAGGTTGGGGTCAAAGCCACTCA
CATTAAATTACCAAGAACAGCCACAGAATCTGAGGTGTGAAAGTACATTAGATCTTTGCATGAAGACTCTACTGTACATG
GATTCATACTGCAGCTACCTTTAGATTCAGAAAATGCTGTTAACACTGAAGCAGTGATCAAAGCTATCGCACCCGAAAAG
GATGTGGATGGATTGACTAGTATCAGTGCTGGGAAACTCGCTAGAGGTGATCTAAATGACTATTTCATCCCTTGTACGCC
TAAAGGATGCTTGGAACTCATCAAAGAGACAGGGGCGCAGATCGCCGGAAAGCGCGCCGTGGTGGTTGGGCGCAGTAAAA
TAGTAGGAGCCCCAGTGCATGGCTTGCTTCTGTGGAACAATGCCACAGTGGCCACCTGCCACTCCAAGACTGCCAACCTG
GGCCAGGAGGTAAATAAAGGTGACATCCTGGTGGTTGCAACTGGTCAGCCTGAAATGGTGAAAGGAGAGTGGATCAAACT
GGGGCAATACTCATCGACTGTGGGACCAATTATGTCCCAGATGATACAAAATCAAATGGGAGAAGGATCGTGGGTGATGT
GGCATAAAACGGGGCCAAAGAGCGGGCGGGCTTCATCCCTCCTGTTCCTGGCGACGTCGGGCCCATGACGGTGGCCATGC
TGATGCAGGGCACGGTAGAGAGCGCAAGGGGTTTCCTGGAGAAATACAAGCCAGGAAAGTATTAACCTTAAGTATTAAAA
TTAACCTGAAGACACCTGTTCCAAGTGACATTGCTATATCACGATCTTGCAAACCAAAGCCCATTGGTACGCTGGCTCGA
GAAATTGGCCTGTTCTCTGAAGAGGTGGAATCGTATGGTGAGACAAAGGCCAAAGTCCTGCCATCAGCACTGGCACGACT
GAAACGCCAGCCTGACGGGAAATACGTGGTGGTGACTGGAGTAACTCCAGCTCCCCTGGGAGAGGGGGAAATACAACCAC
AGTCGGGCTGGTGCAAGCCCTGGGCGCCCATCTTTCCCAGGACGTCTTCGCGTGTGTGCGACAGCCTTCCCAGGGCCCCA
CCTTTGGAATAAAAGGTGGTGCTGCAGGAGGTGGCTACTCCCAGGTCATTCCTACGGAAGAGTTTAATCTCCACCTCACT
GGTGACATCCATGCCATCACTGCAGCTAATAACCCGGTTGCTGCGGCCACTGATGCCCGGATATTCCATGAACTGACCCA
GACAGACAAGGCTCTCTTTAATCGTTTGGTGCCCTCAGCAAATGGAGTGAGAAAGTTCTCTGATATCCAAATCCGAAGGT
TAAGGAGACTAGGCATTGGAAAGACTGACCCGACCACACTGACAGACGAATAGATAAACAGATTTGCAAGATTGGATATT
GATCCAGAAACCATAACTTGGCAAAGAGTGTAGGATACCAATGATAGATTCCTGCGGAAGATCACAACTGGACAGGCTCC
AACGGAGAAAGGGCACACACGGACGACCCAGTTTGATAGCTCAGTGGCCAGTGCAATCATGGCTGTCCTGGCCCTCACCA
GTTCTCTGGAAGACATGAGAGAGGGACTGGGCAAAATGGTGGTGGCCTCCTGCAAGAAAGGGGAGCCCATCAGTGCGGAA
GATCTGGGGGTGAGTGGCGCGTTGACAGTGCTTATGAAGGACGCGATCAAGCCTAACCTCATGCAGACGTTGGAGGGCAC
TCCGGTGTTTGTCCACGCCGGCCTGTTCGCCAACATCGTGCATGGGAATTCATCTGTCATGGCAGACCCGGTCGCACTCA
AGCTTGTCGGCCCAGAAGGGATGGTAGTGACCGAAGCCGGATTCGGAGCAGACATTGGAATGGAAAAGTTTTTTAACATT
AAATGCCGGTACTCTGGCCTCCTCCCTCACGTGGTGGTGCTGGTTGCTACTGTCAGGGCTCTTAAAATGCACGGGGGCGG
CCCCACGCTCACCGCTGGACTGCCTGTTCCCAAGGCTTACAGAGAGGAGAACCTGGAGCTGGTTGAAAAAGGCTTCAGTA
ACTTGAAGAAGCAAATTGAAAATGCCAGAATGTTTGGAGTTCCAGTTGCAGTGGCTGTGAATGCGTTC

Alignment

ORF - retro_mmur_1069 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.89 %
• Parental protein coverage: 79.09 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  VGDRDDSNLYINVKLKAAEEVGIKATHVKLPRTATESEV-KYIRSL-EDSTIHGFILQLPLDSENAINTE
          VGDRDDSNLYINVKLKAAEEVG.KATH.KLPRTATESEV.KYIRSL.EDST.HGFILQLPLDSENA.NTE
Retrocopy VGDRDDSNLYINVKLKAAEEVGVKATHIKLPRTATESEV*KYIRSLHEDSTVHGFILQLPLDSENAVNTE

Parental  AVINAIAPEKDVDGLTSISAGKLSRGDLNDCFIPCTPKGCLELIKETGVQIAGKHAVVVGRSKIVGAPMH
          AVI.AIAPEKDVDGLTSISAGKL.RGDLND.FIPCTPKGCLELIKETG.QIAGK.AVVVGRSKIVGAP.H
Retrocopy AVIKAIAPEKDVDGLTSISAGKLARGDLNDYFIPCTPKGCLELIKETGAQIAGKRAVVVGRSKIVGAPVH

Parental  DLLLWNNATVTTCHSKTANLGEEVNKGDILVVATGQPEMVKGEWIK-PGAIVIDCGINYIPDNTKSNGRR
          .LLLWNNATV.TCHSKTANLG.EVNKGDILVVATGQPEMVKGEWIK..GAI.IDCG.NY.PD.TKSNGRR
Retrocopy GLLLWNNATVATCHSKTANLGQEVNKGDILVVATGQPEMVKGEWIK<TGAILIDCGTNYVPDDTKSNGRR

Parental  IVGDVAYNEAKERAGFITPVPGGVGPMTVAMLMQSTVESAR-GFLEKYKPGKWSIQYNNLNLKTPVPSDI
          IVGDVA.N.AKERAGFI.PVPG.VGPMTVAMLMQ.TVESAR.GF.......K........NLKTPVPSDI
Retrocopy IVGDVA*NGAKERAGFIPPVPGDVGPMTVAMLMQGTVESAR<GFPGEIQARKVLTLSIKINLKTPVPSDI

Parental  AISRSCKLKPIGTLAREIGLLSEEVELYGETKAKVLLSALERLKHQPDGKYVVVTGITPTPLGEGK-STT
          AISRSCK.KPIGTLAREIGL.SEEVE.YGETKAKVL.SAL.RLK.QPDGKYVVVTG.TP.PLGEG...TT
Retrocopy AISRSCKPKPIGTLAREIGLFSEEVESYGETKAKVLPSALARLKRQPDGKYVVVTGVTPAPLGEGE<NTT

Parental  TIGLVQALGAHLFQNVFACVRQPSQGPTFGIKGGAAGGGYSQVIPMEEFNLHLTGDIHAITAANNLVAAA
          T.GLVQALGAHL.Q.VFACVRQPSQGPTFGIKGGAAGGGYSQVIP.EEFNLHLTGDIHAITAANN.VAAA
Retrocopy TVGLVQALGAHLSQDVFACVRQPSQGPTFGIKGGAAGGGYSQVIPTEEFNLHLTGDIHAITAANNPVAAA

Parental  IDARIFHELTQTDKALFNRLVPSVNGVRKFSDIQIRRLRRLGIEKTDPTTLTDEEINRFARLDIDPETIT
          .DARIFHELTQTDKALFNRLVPS.NGVRKFSDIQIRRLRRLGI.KTDPTTLTDE.INRFARLDIDPETIT
Retrocopy TDARIFHELTQTDKALFNRLVPSANGVRKFSDIQIRRLRRLGIGKTDPTTLTDE*INRFARLDIDPETIT

Parental  WQRVLDTNDRFLRKITIGQAPTEKGHTRTTQFDISVASEIMAVLALTSSLEDMRERLGKMVVASSKKGEP
          WQRV.DTNDRFLRKIT.GQAPTEKGHTRTTQFD.SVAS.IMAVLALTSSLEDMRE.LGKMVVAS.KKGEP
Retrocopy WQRV*DTNDRFLRKITTGQAPTEKGHTRTTQFDSSVASAIMAVLALTSSLEDMREGLGKMVVASCKKGEP

Parental  ISAEDLGVSGALTVLMKDAIKPNLMQTLEGTPVFVHAGPFANIAHGNSSIIADRVALKLVGPEGFVVTEA
          ISAEDLGVSGALTVLMKDAIKPNLMQTLEGTPVFVHAG.FANI.HGNSS..AD.VALKLVGPEG.VVTEA
Retrocopy ISAEDLGVSGALTVLMKDAIKPNLMQTLEGTPVFVHAGLFANIVHGNSSVMADPVALKLVGPEGMVVTEA

Parental  GFGADIGMEKFFNIKCRYSGLRPHVVVLVATVRALKMHGGGPTVTAGLPLPKAYIEENLELVEKGFSNLK
          GFGADIGMEKFFNIKCRYSGL.PHVVVLVATVRALKMHGGGPT.TAGLP.PKAY.EENLELVEKGFSNLK
Retrocopy GFGADIGMEKFFNIKCRYSGLLPHVVVLVATVRALKMHGGGPTLTAGLPVPKAYREENLELVEKGFSNLK

Parental  KQIENARMFGVPVVVAVNVF
          KQIENARMFGVPV.VAVN.F
Retrocopy KQIENARMFGVPVAVAVNAF

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_1069 retrocopy.

TSS

Microcebus murinus was not studied using FANTOM5 data.

Lab

retro_mmur_1069 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,