RetrogeneDB ID: retro_mmur_1389

Retrocopy location

• Organism: Mouse Lemur (Microcebus murinus)
• Coordinates: scaffold_52753:571..1211(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMICG00000010342
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CASP3
• Ensembl ID: ENSMICG00000004809
• Aliases: None
• Description: caspase 3, apoptosis-related cysteine peptidase [Source:HGNC Symbol;Acc:1504]

Sequence

>retro_mmur_1389
TCAGGTACAGATGTAGATGCAGCAAACCTCAGGGAAACATTCGTGAACTTGAAACAGCAAGTCCAGAATAAAAATGATCT
GACGCGTGAAGAAATTGTGGAATTGATGCGCCATGTTTCTAAAGAAGATCATAGCAAAAAGAAAAGTTTTATTTGCATGC
TTCTAAGCCATGGTGGAGAAGGAATAATTTGGGGGACAAATGGACCTGTTGACCTAAAAAAAAAAAAAATAACAAGTTTC
TCCAGAGGGGATTATTGTAGACATCTAACTGGAAAGCCCAAACTTTTCATTATTCAGGCCTGTGGAGGTATGGAACCAGA
CTGTGGCATTGAGACAGACAGCAGTATTGATGATGACGTGGCGGTGTCAGAAAACACCAGTTGAGGCCAACTCTTATACA
CGTTCTCCACAGCACCTGGTTACTACTCCTGGCGAAATTCAAAGGATGTTCCTGGTTCGGCCAGTCACTTTTGTGCTGTA
CTGAAACTGTACGCTCACAACCTTAAGTTTATGCACATTCCTACCTGGGTTAAGGTGGCAAGAGAATTTGAGTCCTTTTC
CTTTGACTCTACTTTTCATACAAAAAAAACAGATTACATGTATTGTGTCCATGCTCACAAAAGAACTATATTTTTATCAC

Alignment

ORF - retro_mmur_1389 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.45 %
• Parental protein coverage: 76.9 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  SGTDVDAANLRETFMNLKYEVRNKNDLTREEIVELMHNVSKEDHSKRSSFICVLLSHGEEGIIFGTNGPV
          SGTDVDAANLRETF.NLK..V.NKNDLTREEIVELM..VSKEDHSK..SFIC.LLSHG.EGII.GTNGPV
Retrocopy SGTDVDAANLRETFVNLKQQVQNKNDLTREEIVELMRHVSKEDHSKKKSFICMLLSHGGEGIIWGTNGPV

Parental  DLKKI--TSFFRGDYCRSLTGKPKLFIIQXXXXXELDCGIETDSSADDDMA-CQKIPVEAD-FLYAYSTA
          D......TSF.RGDYCR.LTGKPKLFIIQ.....E.DCGIETDSS.DDD.A.CQK.PVEA...LY..STA
Retrocopy DXXXXXXTSFSRGDYCRHLTGKPKLFIIQACGGMEPDCGIETDSSIDDDVA>CQKTPVEAN<LLYTFSTA

Parental  PGYYSWRNSKD-GSWFIQSL-CAMLKLYAHKLEFMHILTRVNRKVATEFESFSLEATFH-AKKQIPCIVS
          PGYYSWRNSKD..SWF.QSL.CA.LKLYAH.L.FMHI.T.V..KVA.EFESFS...TFH....QI.CIVS
Retrocopy PGYYSWRNSKD<CSWFGQSL>CAVLKLYAHNLKFMHIPTWV--KVAREFESFSFDSTFH>XXXQITCIVS

Parental  MLTKELYFYH
          MLTKELYFYH
Retrocopy MLTKELYFYH

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_1389 retrocopy.

TSS

Microcebus murinus was not studied using FANTOM5 data.

Lab

retro_mmur_1389 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 9 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000012511	2 retrocopies	retro_cpor_1203, retro_cpor_1450,
Dasypus novemcinctus	ENSDNOG00000013931	1 retrocopy	retro_dnov_1013,
Microcebus murinus	ENSMICG00000004809	2 retrocopies	retro_mmur_1389 , retro_mmur_691,
Microcebus murinus	ENSMICG00000010297	2 retrocopies	retro_mmur_709, retro_mmur_844,
Macaca mulatta	ENSMMUG00000012053	1 retrocopy	retro_mmul_114,
Otolemur garnettii	ENSOGAG00000005985	2 retrocopies	retro_ogar_1756, retro_ogar_3263,
Rattus norvegicus	ENSRNOG00000010475	1 retrocopy	retro_rnor_2747,
Sarcophilus harrisii	ENSSHAG00000009178	1 retrocopy	retro_shar_404,
Ictidomys tridecemlineatus	ENSSTOG00000003865	2 retrocopies	retro_itri_172, retro_itri_586,