RetrogeneDB ID: retro_mmur_1364

Retrocopy location

• Organism: Mouse Lemur (Microcebus murinus)
• Coordinates: scaffold_49282:3373..4221(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: IDH1
• Ensembl ID: ENSMICG00000009797
• Aliases: None
• Description: isocitrate dehydrogenase 1 (NADP+), soluble [Source:HGNC Symbol;Acc:5382]

Sequence

>retro_mmur_1364
ATGTCCAAAAAAATCAGTGGTGGTTCTGTGGTAGAGATGCAAGGAGATGAAATGACACGAATCATTTGGGAATTGATTAA
AGAAAAACTCATTTTTTCCTATGTGGAATTGGATCTGCATAGCTATGATTTAGGCATAGAGAATCGTGATGCCACCCATG
ACCAAGTCACCAAGGATGCTGCAGAGGCCATAAAGAAATATAATGTGGGTGTCAAGTGTGCTACTATCACCCCCGATGAG
AAGAGGGTTGAGGAGTTCAAGTTGAAACAAATGTGGAAATCACCAAACGGCACCATCCGAAATATTCTGGGCGGCACTGT
CTTCAGGGAAGCTATTATCTGCAAAAATATCCCCCGACTTGTGAGTGGATGGGTAAAACCCATCATCATAGGTCGTCATG
CTTATGGGGACCAATACAGAGCAACCGATTTTGTTGTTCCTGGGCCAGGAAAAGTAGAGATAACCTACACACCAAGTGAT
GGAACCAAAAGGTGACATACTTGGTACATAACTTTGAAGATGGTGGCGGTGTTGCCATGGGTATGTACAATCAAGATAAG
TCAATTGAAGATTTTGCACACAGTTCCTTCCAAATGGCTCTGTCTAAGGGTTGGCCTTTGTATCTGAGCACCAAAAACAC
TATTCTGAAGAAATATGATGGACGTTTTAAAGACATCTTTCAGGAGATATATGACAAGCAGTACAAATCCCAATTTGAAG
CCCAGAAGATCTGGTATGAGCATAGGCTCATCGATGACATGGTGGCCCAAGCTATGAAATCAGAAGGAGGCTTCATCTGG
GCCTGCAAAAACTATGATGGTGATGTGCAGTTGGACTCCATGGCCCAA

Alignment

ORF - retro_mmur_1364 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.55 %
• Parental protein coverage: 68.36 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSKKISGGSVVEMQGDEMTRIIWELIKEKLIFPYVELDLHSYDLGIENRDATHDQVTKDAAEAIKKYNVG
          MSKKISGGSVVEMQGDEMTRIIWELIKEKLIF.YVELDLHSYDLGIENRDATHDQVTKDAAEAIKKYNVG
Retrocopy MSKKISGGSVVEMQGDEMTRIIWELIKEKLIFSYVELDLHSYDLGIENRDATHDQVTKDAAEAIKKYNVG

Parental  VKCATITPDEKRVEEFKLKQMWKSPNGTIRNILGGTVFREAIICKNIPRLVSGWVKPIIIGRHAYGDQYR
          VKCATITPDEKRVEEFKLKQMWKSPNGTIRNILGGTVFREAIICKNIPRLVSGWVKPIIIGRHAYGDQYR
Retrocopy VKCATITPDEKRVEEFKLKQMWKSPNGTIRNILGGTVFREAIICKNIPRLVSGWVKPIIIGRHAYGDQYR

Parental  ATDFVVPGPGKVEITYTPSDGT-QKVTYLVHNFEXXXXXXXXXXXXXXXXXXXAHSSFQMALSKSWPLYL
          ATDFVVPGPGKVEITYTPSDGT.QKVTYLVHNFE...................AHSSFQMALSK.WPLYL
Retrocopy ATDFVVPGPGKVEITYTPSDGT<QKVTYLVHNFEDGGGVAMGMYNQDKSIEDFAHSSFQMALSKGWPLYL

Parental  STKNTILKKYDGRFKDIFQEIYDKQYKSQFEAQKIWYEHRLIDDMVAQAMKSEGGFIWACKNYDGDVQSD
          STKNTILKKYDGRFKDIFQEIYDKQYKSQFEAQKIWYEHRLIDDMVAQAMKSEGGFIWACKNYDGDVQ.D
Retrocopy STKNTILKKYDGRFKDIFQEIYDKQYKSQFEAQKIWYEHRLIDDMVAQAMKSEGGFIWACKNYDGDVQLD

Parental  SVAQ
          S.AQ
Retrocopy SMAQ

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_1364 retrocopy.

TSS

Microcebus murinus was not studied using FANTOM5 data.

Lab

retro_mmur_1364 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 12 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000020527	1 retrocopy	retro_btau_1235,
Choloepus hoffmanni	ENSCHOG00000004574	2 retrocopies	retro_chof_2158, retro_chof_897,
Cavia porcellus	ENSCPOG00000013587	1 retrocopy	retro_cpor_1010,
Homo sapiens	ENSG00000138413	1 retrocopy	retro_hsap_3554,
Gorilla gorilla	ENSGGOG00000012619	1 retrocopy	retro_ggor_2400,
Microcebus murinus	ENSMICG00000009797	1 retrocopy	retro_mmur_1364 ,
Macaca mulatta	ENSMMUG00000016077	1 retrocopy	retro_mmul_1817,
Nomascus leucogenys	ENSNLEG00000007143	3 retrocopies	retro_nleu_1169, retro_nleu_2328, retro_nleu_3117,
Otolemur garnettii	ENSOGAG00000014848	4 retrocopies	retro_ogar_1488, retro_ogar_2270, retro_ogar_2925, retro_ogar_3057,
Pongo abelii	ENSPPYG00000013125	2 retrocopies	retro_pabe_2935, retro_pabe_926,
Pan troglodytes	ENSPTRG00000012865	1 retrocopy	retro_ptro_2415,
Sus scrofa	ENSSSCG00000023264	1 retrocopy	retro_sscr_549,