RetrogeneDB ID: retro_mmur_1336

Retrocopy location

• Organism: Mouse Lemur (Microcebus murinus)
• Coordinates: scaffold_4573:100809..101526(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ATF1
• Ensembl ID: ENSMICG00000003301
• Aliases: None
• Description: activating transcription factor 1 [Source:HGNC Symbol;Acc:783]

Sequence

>retro_mmur_1336
GTATCATCTTTATCAGAAAGTGAGGAGTCTCAGGACTCATCTGACAGCATAGGCTCCTCACAGAAAGCCCACGGGATCCT
AGCACGGCGCCCATCGTACAGGAAAATTTTTAAAGATCTATCTTCTGAAGATACACGAGGCAGAAAAGGAGATGGAGAAA
ACCCTGGAGTTTCTGCTGTCACTTCTATGTCCGTTCCTACTCCCATCTATCAGACTAGCAGTGGACAGTACATTGCCATT
GCCCCAAATGGAGCCTTACAGTTGGCCAGTCCAGGGACAGATGGAGTACAGGGACTTCAGACATTAACCATGACGAATTC
AGGCAATACTCAGCAAGGTACAACTATTCTCCAGTATGCGCAGACCTCTGATGGACAGCAAATACTTGTGCACAGCAATC
AAGTGGTAGTACAGACGGCATCGGGAGATATGCAGACATATCAGATTCGTACCACACCTTCAGCTACTTCTCTGCCACAA
ACTGTGGTGATGACATCTCCTGTTACTCTTACATCTCAGACAACTAAGACAGATGACCCCCAATTGAAAAGAGAAATAAG
GTTAATGAAAAACAGAGAGGCAGCTCGAGAATGTCGCAGAAAGAAGAAAGAATATGTTAAATGCCTGGAAAATCAAGTTG
CAGTCCTGGAAAATCAAAATAAGACTCTAATAGAAGAGTTAAAAACTTTGAAGGATCTTTATTCCCATAAAAGTGTT

Alignment

ORF - retro_mmur_1336 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.16 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VSSLSESEESQDSSDSIGSSQKAHGILARRPSYRKIFKDLSSEDTRGRKGDGENPGVSAVTSMSVPTPIY
          VSSLSESEESQDSSDSIGSSQKAHGILARRPSYRKIFKDLSSEDTRGRKGDGENPGVSAVTSMSVPTPIY
Retrocopy VSSLSESEESQDSSDSIGSSQKAHGILARRPSYRKIFKDLSSEDTRGRKGDGENPGVSAVTSMSVPTPIY

Parental  QTSSGQYIAIAPNGALQLASPGTDGVQGLQTLTMTNSGNTQQGTTILQYAQTSDGQQILVPSNQVVVQTA
          QTSSGQYIAIAPNGALQLASPGTDGVQGLQTLTMTNSGNTQQGTTILQYAQTSDGQQILV.SNQVVVQTA
Retrocopy QTSSGQYIAIAPNGALQLASPGTDGVQGLQTLTMTNSGNTQQGTTILQYAQTSDGQQILVHSNQVVVQTA

Parental  SGDMQTYQIRTTPSATSLPQTVVMTSPVTLTSQTTKTDDPQLKREIRLMKNREAARECRRKKKEYVKCLE
          SGDMQTYQIRTTPSATSLPQTVVMTSPVTLTSQTTKTDDPQLKREIRLMKNREAARECRRKKKEYVKCLE
Retrocopy SGDMQTYQIRTTPSATSLPQTVVMTSPVTLTSQTTKTDDPQLKREIRLMKNREAARECRRKKKEYVKCLE

Parental  NRVAVLENQNKTLIEELKTLKDLYSHKSV
          N.VAVLENQNKTLIEELKTLKDLYSHKSV
Retrocopy NQVAVLENQNKTLIEELKTLKDLYSHKSV

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_1336 retrocopy.

TSS

Microcebus murinus was not studied using FANTOM5 data.

Lab

retro_mmur_1336 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 4 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000004733	5 retrocopies	retro_chof_1987, retro_chof_2305, retro_chof_27, retro_chof_462, retro_chof_760,
Felis catus	ENSFCAG00000013892	1 retrocopy	retro_fcat_1284,
Microcebus murinus	ENSMICG00000003301	1 retrocopy	retro_mmur_1336 ,
Sarcophilus harrisii	ENSSHAG00000004637	2 retrocopies	retro_shar_221, retro_shar_635,