RetrogeneDB ID: retro_shar_687

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL857066.1:119014..119443(+)
• Located in intron of: ENSSHAG00000004551

Retrocopy information

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

Parental gene information

• Parental gene symbol: AGPAT5
• Ensembl ID: ENSSHAG00000000051
• Aliases: None
• Description: 1-acylglycerol-3-phosphate O-acyltransferase 5 [Source:HGNC Symbol;Acc:20886]

Sequence

>retro_shar_687
ATAAAAAATTACTTAGATGAAATTTATGATGTTACATGAACTTATGTAGATACAATGGGAAAGAGAAAAGAAGCACCATC
TATGGCAAAATTTCTTTGCATAGAATATCCAAAAGTTCACATTCACATTGATCACATAGATAAAAAGAGGCCCAGAAAAA
TAGATATGAGAAGGTGGTTTCATGACCTCTTTGAAATAAAAAGTAAGTTGCTGATAGAGTTCTATGATTCACTGGATTTC
CAAAGAAGAAACAAGTTTTCTGGAAATAATATTAATTTCAAATCAAGCCTCTAGAAAACTTTATATTCTTTACTGTTCTT
AGGTGATCTGACTGTTAGTAGATTCATGACAGATTCTGAAAAGAAATTTTATGTGAAATCTTGAATATATGGAGCTTTAA
TTAGTTGCCTGCTGGTTAGTATTAAAGTG

Alignment

ORF - retro_shar_687 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.92 %
• Parental protein coverage: 74.0 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MKNYLDAIYDVTVAYEGTVDQTGKRKEAPSMAEFLCKECPKVHIHIDRIDKKDVPEEQLSMRRWLHDRFE
          .KNYLD.IYDVT..Y...VD..GKRKEAPSMA.FLC.E.PKVHIHID.IDKK........MRRW.HD.FE
Retrocopy IKNYLDEIYDVT*TY---VDTMGKRKEAPSMAKFLCIEYPKVHIHIDHIDKKR--PRKIDMRRWFHDLFE

Parental  IKDKLLIEFYDSPDSQRRNKFPGKCINSKLSLKKTLPSLLFLGGLTASMLMTESGRKLYVKTWIYGTVIG
          IK.KLLIEFYDS.D.QRRNKF.G..IN.K.SL.KTL.SLLFLG.LT.S..MT.S..K.YVK..IYG..I.
Retrocopy IKSKLLIEFYDSLDFQRRNKFSGNNINFKSSL*KTLYSLLFLGDLTVSRFMTDSEKKFYVKS*IYGALIS

Parental  CLLVSIKV
          CLLVSIKV
Retrocopy CLLVSIKV

Legend:

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

Expression

RNA-Seq

Sarcophilus harrisii was not studied using RNA-Seq expression data.

ChIP-Seq

Sarcophilus harrisii was not studied using ChIP-Seq data.

EST

Sarcophilus harrisii was not studied using EST data.

TSS

Sarcophilus harrisii was not studied using FANTOM5 data.

Lab

retro_shar_687 was not experimentally validated.

Homology

Retrocopy orthology:

Sarcophilus harrisii 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 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000005142	1 retrocopy	retro_chof_376,
Dasypus novemcinctus	ENSDNOG00000004979	1 retrocopy	retro_dnov_823,
Dipodomys ordii	ENSDORG00000008708	1 retrocopy	retro_dord_523,
Otolemur garnettii	ENSOGAG00000008958	1 retrocopy	retro_ogar_3477,
Ochotona princeps	ENSOPRG00000014343	3 retrocopies	retro_opri_343, retro_opri_829, retro_opri_935,
Pongo abelii	ENSPPYG00000018320	1 retrocopy	retro_pabe_3671,
Sarcophilus harrisii	ENSSHAG00000000051	1 retrocopy	retro_shar_687 ,
Sarcophilus harrisii	ENSSHAG00000008796	1 retrocopy	retro_shar_1,
Tupaia belangeri	ENSTBEG00000013084	1 retrocopy	retro_tbel_2948,