RetrogeneDB ID: retro_mmur_571

Retrocopy location

• Organism: Mouse Lemur (Microcebus murinus)
• Coordinates: GeneScaffold_3960:566278..566916(+)
• Located in intron of: ENSMICG00000002231

Retrocopy information

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

Parental gene information

• Parental gene symbol: STOML2
• Ensembl ID: ENSMICG00000005517
• Aliases: None
• Description: stomatin (EPB72)-like 2 [Source:HGNC Symbol;Acc:14559]

Sequence

>retro_mmur_571
ACTCTGGATAAAGTCTTCCAGGAGTGGGAGTCCCTGAATGCCAGCACTGTGTATGCAGTCAACCAGGCTGCTGTCTGCTG
GGGCATCCACTGCCTTCATTATGAGATCAAGGATATCCATATGCCACCCTGCCTGAATGGGTTCGTACATATGCAGGTGG
AGACAGAGTGGTGGAAACAGGCCACAGTTCTAGAGTCTGAGGGGACCTGATAGTCGGCCATCAAGTGGCAGCGGGGATGG
AACAGGGCCAGATACTGGTCTCTAAAGCAGAAAAGGCTGAACAAATAAATCAGATAGTGGGAGAGGGCAGTGTAGTTCTG
GCTGGGGCCAAGGCCAAAGCTATTCATATCCTGGCTGCATCTCTGACACAACATAATGGAGATGCAGCAGCTTGACTGAC
TGTGACCAAGCAGTGTGTCAATGCATTCTCCAAACTGGCCAAGGACTCCATCACTATCCTATTGCCCTCCATTCCCAGTG
ATGTCACCAGTACGGTTGCTCAGGTCATGGGTGTATGTGGGGCCCTCACCAAAGCCCTGGGCACGGACCTAGGACTCTTG
GTGTATAGCAGGAGCAGCAGAGCTGTCCAGGGTACAGATGCAAGTCTTGATGAGGAACTTGATGGAGTCAAGCTGAGT

Alignment

ORF - retro_mmur_571 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.06 %
• Parental protein coverage: 60.56 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SLDRVFRERESLNASIVDAINQAADCWGIRCLRYEIKDIHVPPRVKESMQMQVEAERRKRATVLESEGTR
          .LD.VF.E.ESLNAS.V.A.NQAA.CWGI.CL.YEIKDIH.PP.......MQVE.E..K.ATVLESEGT.
Retrocopy TLDKVFQEWESLNASTVYAVNQAAVCWGIHCLHYEIKDIHMPPCLNGFVHMQVETEWWKQATVLESEGT*

Parental  ESAIN-VAEGKKQAQILASEAEKAEQINQAAGEASAVLAKAKAKAEAIRILAAALTQHNGDAAASLTVAE
          .SAI..VA.G..Q.QIL.S.AEKAEQINQ..GE.S.VLA.AKAKA..I.ILAA.LTQHNGDAAA.LTV..
Retrocopy *SAIK<VAAGMEQGQILVSKAEKAEQINQIVGEGSVVLAGAKAKA--IHILAASLTQHNGDAAA*LTVTK

Parental  QYVSAFSKLAKDSNTILLPSNPGDVTSMVAQXXXXXGALTKAPMPGAQDSVSSGSSRDDQGTDASLDEEL
          Q.V.AFSKLAKDS.TILLPS.P.DVTS.VAQ.....GALTKA........V.S.SSR..QGTDASLDEEL
Retrocopy QCVNAFSKLAKDSITILLPSIPSDVTSTVAQVMGVCGALTKALGTDLGLLVYSRSSRAVQGTDASLDEEL

Parental  DRFKLS
          D..KLS
Retrocopy DGVKLS

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_571 retrocopy.

TSS

Microcebus murinus was not studied using FANTOM5 data.

Lab

retro_mmur_571 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 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Ciona intestinalis	ENSCING00000000485	1 retrocopy	retro_cint_6,
Callithrix jacchus	ENSCJAG00000009137	1 retrocopy	retro_cjac_440,
Ciona savignyi	ENSCSAVG00000000950	1 retrocopy	retro_csav_5,
Microcebus murinus	ENSMICG00000005517	1 retrocopy	retro_mmur_571 ,
Mus musculus	ENSMUSG00000028455	1 retrocopy	retro_mmus_1034,
Oryctolagus cuniculus	ENSOCUG00000006451	1 retrocopy	retro_ocun_695,