RetrogeneDB ID: retro_meug_150

Retrocopy location

• Organism: Wallaby (Macropus eugenii)
• Coordinates: GeneScaffold_4433:51030..51523(+)
• Located in intron of: ENSMEUG00000009001

Retrocopy information

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

Parental gene information

• Parental gene symbol: TAF8
• Ensembl ID: ENSMEUG00000006952
• Aliases: None
• Description: TAF8 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 43kDa [Source:HGNC Symbol;Acc:17300]

Sequence

>retro_meug_150
ACACTTGCTGAGATGGGTTTCAAAGTGGAAACTCTTCCTGCATATGCTAAATGGTCCCAGAAGATGGTCATCACAGCACC
TCCAGTCACCCATCAGCCTGTGTGACTCCCAAAGCCCTGACTGCTGGACAGAACAAGTTCATCCACCTCATATCCCCAGC
CATTTTCCTGAATTCTCCAATCCCCACACCTACATCAAAACACCGACATACCAGCAAGCTTGTCTCAGATTACCAGGTCC
TTAGTGAAAGGCTGCATCACAGAGGCGTAATGTGGAACAGGCACTTACTCGTTTTATGACCAAGACAAGTGAGACACGGA
GTCTTTTCAAAGATGATGCCAGCACATTTCCATTGATTGCTGCCCGGCTGTTTACCCTTCCCTATCTGACAGCCCTTCTC
CTGTCTCAATTGGAGATGAAGCAGATGGAAGAGCCTCATTCGTCTGAGCAGGATGAACAGACAGACACAGGGAACCTTCC
TTTCCACATTAGT

Alignment

ORF - retro_meug_150 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.07 %
• Parental protein coverage: 63.08 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  TLVEMGFNVETLPAYAKRSQRMVITAPPVTNQPV-TPK-ALTAGQNK-SHPPHIPSHFPEFPDPHTYIKT
          TL.EMGF.VETLPAYAK.SQ.MVITAPPVT.QPV..PK.ALTAGQNK..HPPHIPSHFPEF..PHTYIKT
Retrocopy TLAEMGFKVETLPAYAKWSQKMVITAPPVTHQPV*LPK<ALTAGQNK<VHPPHIPSHFPEFSNPHTYIKT

Parental  PTYRE-LVSDYQVLRE-KAASQRRDVERALTRFMAKTGETQSLFKDDVSTFPLIAARPFTIPYLTALLPS
          PTY...LVSDYQVL.E.KAASQRR.VE.ALTRFM.KT.ET.SLFKDD.STFPLIAAR.FT.PYLTALL.S
Retrocopy PTYQQ>LVSDYQVLSE<KAASQRRNVEQALTRFMTKTSETRSLFKDDASTFPLIAARLFTLPYLTALLLS

Parental  ELEMQQMEETDSSEQDEQTDTENLPLHIS
          .LEM.QMEE..SSEQDEQTDT.NLP.HIS
Retrocopy QLEMKQMEEPHSSEQDEQTDTGNLPFHIS

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Macropus eugenii was not studied using RNA-Seq expression data.

ChIP-Seq

Macropus eugenii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_meug_150 retrocopy.

TSS

Macropus eugenii was not studied using FANTOM5 data.

Lab

retro_meug_150 was not experimentally validated.

Homology

Retrocopy orthology:

Macropus eugenii 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 11 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,
Mus musculus	ENSMUSG00000023980	1 retrocopy	retro_mmus_436,
Otolemur garnettii	ENSOGAG00000016885	1 retrocopy	retro_ogar_759,
Rattus norvegicus	ENSRNOG00000015249	1 retrocopy	retro_rnor_2317,