RetrogeneDB ID: retro_mmur_554

Retrocopy location

• Organism: Mouse Lemur (Microcebus murinus)
• Coordinates: GeneScaffold_3827:166129..166651(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TAF8
• Ensembl ID: ENSMICG00000011353
• Aliases: None
• Description: TAF8 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 43kDa [Source:HGNC Symbol;Acc:17300]

Sequence

>retro_mmur_554
CTCACTGCAGGGCAGAACCGACCCCGCCCGCCACACGTCCCCAGACATTTTCCTGAGTTCCCCGATCCCCACACCTACAT
CAGAACTCCGACTTTCCGAGAGCCTGTGTCGGACTCCCAGGGCCTGCGGGAGAAGGCTGCATCCCAGAGGCGCGATGTGG
AGCGGGCACTCGCCCGTTTCATGGCCAAGACAGGAGAGACCCAGAGTCTTTTCAAAGATGATGTCAGCACATTTCCATCG
ATTGCTGCCAGACCTTTCAGCATCCCCTACCTGACAGCTCTTCTTCCGTCTAAGCTGGAGATGCAACAAATGGAAGACAC
GGATTCCTCGGAGCAGGAAGAGCAGACAGACACACAGAACCTCACTCTTCATAGCAGTACGGACGATTCTGGAGTTGAGA
AGGAGAACACTTCTGTCCTGCAGCAGAAGCCCGCCTTGTTGGGAAGCCGCAACGGGGAAGAGAGCATCATTGATAACCCT
TATCTGCGACCTGTGAAGAAACCCAAGCTCCGCAGGAAGAAG

Alignment

ORF - retro_mmur_554 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.51 %
• Parental protein coverage: 61.92 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ITARQNRPHPPHIPSHFPEFPDPHTYIKTPTYREPVSDYQVLREKAASQRRDVERALTRFMAKTGETQSL
          .TA.QNRP.PPH.P.HFPEFPDPHTYI.TPT.REPVSD.Q.LREKAASQRRDVERAL.RFMAKTGETQSL
Retrocopy LTAGQNRPRPPHVPRHFPEFPDPHTYIRTPTFREPVSDSQGLREKAASQRRDVERALARFMAKTGETQSL

Parental  FKDDVSTFPLIAARPFSIPYLTALLPSELEMQQMEETDSSEQDEQTDTENLTLHISTDDSGAEKENTSVL
          FKDDVSTFP.IAARPFSIPYLTALLPS.LEMQQME.TDSSEQ.EQTDT.NLTLH.STDDSG.EKENTSVL
Retrocopy FKDDVSTFPSIAARPFSIPYLTALLPSKLEMQQMEDTDSSEQEEQTDTQNLTLHSSTDDSGVEKENTSVL

Parental  QQNPALSGSRNGEESIIDNPYLRPVKKPKIRRKK
          QQ.PAL.GSRNGEESIIDNPYLRPVKKPK.RRKK
Retrocopy QQKPALLGSRNGEESIIDNPYLRPVKKPKLRRKK

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_554 retrocopy.

TSS

Microcebus murinus was not studied using FANTOM5 data.

Lab

retro_mmur_554 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 7 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000010516	1 retrocopy	retro_chof_661,
Macropus eugenii	ENSMEUG00000006952	1 retrocopy	retro_meug_150,
Microcebus murinus	ENSMICG00000011353	6 retrocopies	retro_mmur_112, retro_mmur_1455, retro_mmur_443, retro_mmur_455, retro_mmur_554 , retro_mmur_555,
Monodelphis domestica	ENSMODG00000012785	2 retrocopies	retro_mdom_1206, retro_mdom_1357,
Mus musculus	ENSMUSG00000023980	1 retrocopy	retro_mmus_436,
Otolemur garnettii	ENSOGAG00000016885	1 retrocopy	retro_ogar_759,
Rattus norvegicus	ENSRNOG00000015249	1 retrocopy	retro_rnor_2317,