RetrogeneDB ID: retro_mmur_368

Retrocopy location

• Organism: Mouse Lemur (Microcebus murinus)
• Coordinates: GeneScaffold_2637:164937..165460(+)
• Located in intron of: ENSMICG00000014413

Retrocopy information

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

Parental gene information

• Parental gene symbol: GTF3A
• Ensembl ID: ENSMICG00000014763
• Aliases: None
• Description: general transcription factor IIIA [Source:HGNC Symbol;Acc:4662]

Sequence

>retro_mmur_368
TGTCAAAAGAGATGCTCCTTTGTGGCAAAAACACGGAGGGAATTTCTGAAACACGTGAGAGAAAGCCCTAAGGGGGGAGT
AACACGCGGAGCATTCCAGAAGACATGTACATGGGGAGAGTATCTTAAGCAACATGTAAGAACTCCTGCCCCAGAAAGGG
ACGTATGTCAATGTCCAAGAGAAGGAAGTGGCAGGACCTACACAACTGTGTTTAATCTCCAGGGCCGCAGTCTTTCTTTT
CAAGATGAAACCACCCTTTTGGGTGAGCACACCCTGGCTGCAGCAAACTCTCTGCAATGAAACACAGTCTCACTAGCCCG
GTTGCGCATGAAACTAACAAGAAGAAAATGAAGCTCCAAGTAAAAGCATCTTGCGAAAAAAGGAAGTTTGGCCTCTTGGC
TCAGTGGGTATGTCTCTCTTCAAAGGAAACCAAAAGAGCAGGCTTATCTCTGCCTAAAACAGAGAGTTGCTGAACTGTAT
GGGCGAGGAGATGCTCTCAAAACTTGGACTACTAACCATCAAC

Alignment

ORF - retro_mmur_368 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.11 %
• Parental protein coverage: 59.66 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  CQKGCSFVAKTWTELLKHVRETHREEITCEVCQKTFKHKDHLKQHMKAHAPERDVYRCPRDGCGRTYTTV
          CQK.CSFVAKT..E.LKHVRE......T....QKT......LKQH....APERDV..CPR.G.GRTYTTV
Retrocopy CQKRCSFVAKTRREFLKHVRESPKGGVTRGAFQKTCTWGEYLKQHVRTPAPERDVCQCPREGSGRTYTTV

Parental  FNLQSHVLSFHEE-RRPFVCEHAGCGKTFAMKQSLSRHAVVHDPDKKKMKLKVKKSREKR-SLASRLSGY
          FNLQ...LSF..E...PF...H.GC.K..AMK.SL....V.H...KKKMKL.VK.S.EKR.SLAS.LSGY
Retrocopy FNLQGRSLSFQDE<NHPFG*AHPGCSKLSAMKHSLT-SPVAHETNKKKMKLQVKASCEKR>SLASWLSGY

Parental  IPPKRKQEKQ-GLSLSK-NGELLNCVKDQVLTTVAILTRN
          ....RK...Q.GLSL.K.N.ELLNC.....L.....LT.N
Retrocopy VSLQRKPKEQ<GLSLPK<NRELLNCMGEEMLSKLGLLTIN

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_368 retrocopy.

TSS

Microcebus murinus was not studied using FANTOM5 data.

Lab

retro_mmur_368 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 10 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000019373	1 retrocopy	retro_cjac_3066,
Equus caballus	ENSECAG00000014803	1 retrocopy	retro_ecab_866,
Felis catus	ENSFCAG00000006982	1 retrocopy	retro_fcat_426,
Gasterosteus aculeatus	ENSGACG00000003107	1 retrocopy	retro_gacu_6,
Gorilla gorilla	ENSGGOG00000008407	1 retrocopy	retro_ggor_2622,
Microcebus murinus	ENSMICG00000014763	1 retrocopy	retro_mmur_368 ,
Macaca mulatta	ENSMMUG00000009029	1 retrocopy	retro_mmul_1632,
Nomascus leucogenys	ENSNLEG00000000331	2 retrocopies	retro_nleu_1134, retro_nleu_214,
Oreochromis niloticus	ENSONIG00000014134	1 retrocopy	retro_onil_8,
Vicugna pacos	ENSVPAG00000004995	1 retrocopy	retro_vpac_456,