RetrogeneDB ID: retro_shar_358

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL841471.1:486463..487021(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: BUB3
• Ensembl ID: ENSSHAG00000010372
• Aliases: None
• Description: BUB3 mitotic checkpoint protein [Source:HGNC Symbol;Acc:1151]

Sequence

>retro_shar_358
CAACACATTGACTTCCCTTTCAACTGTGTTTTCTATGATCCCACACATCCTTGGAGTGGGGGATTAGATCATAAGTTGAA
AATGCATGACTGAAATACTAATCAAGAAAATCTTGTTGAAACCCATGATGTACCTATTAGATATTTTGGATATTATCCAG
AAGTGAATGTTATGGTTACTGGAATTTGGGATCAAACAGTTAATTGTAGGATCCCAGAACACCTTGTAATGCAGTTACCT
TTTCTCAGTCAGAAAAGGTTTACATATTCTCTGTGTCTGGTGGCAGATTAATTGTGGGGATAGCTGGATGGAGAGTGTTT
GGTATGGGATTTAAAGAATATGGGCTATGTGCATTATACTTTAAAATACCAGACTCATTGCATAGGAGCATTTTTAAAGA
AGCAGGGTTATATGTTAAGCTCTATTGAAGGCCAAATGGCAGTTGAATATTTGCACCCAAGTCCTGAGGTATAGAAGAAG
AAATGTGCATTCAAATATCACAGACTAAAAGAAAATAATATTAAGCAGATTTATCCTGTCAATGCCATTTCCTTTCAT

Alignment

ORF - retro_shar_358 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.48 %
• Parental protein coverage: 57.93 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  QHTGAVLDCAFYDPTHAWSGGLDHQLKMHDLNTDQENLVGTHDAPIRCVEYCPEVNVMVTGSWDQTVK-L
          QH......C.FYDPTH.WSGGLDH.LKMHD.NT.QENLV.THD.PIR...Y.PEVNVMVTG.WDQTV..L
Retrocopy QHIDFPFNCVFYDPTHPWSGGLDHKLKMHD*NTNQENLVETHDVPIRYFGYYPEVNVMVTGIWDQTVN<L

Parental  WDPRTPCNAGTFSQPEKVYTLSVSGDRLIVGTAGRRV-LVWDLRNMGYVQQRRESSLKYQTRCIRAFPNK
          .DPRTPCNA.TFSQ.EKVY..SVSG.RLIVG.AG.RV.LVWDL.NMGYV.......LKYQT.CI.AF..K
Retrocopy *DPRTPCNAVTFSQSEKVYIFSVSGGRLIVGIAGWRV>LVWDLKNMGYVHY----TLKYQTHCIGAFLKK

Parental  QGYVLSSIEGRVAVEYLDPSPEVQKKKYAFKCHRLKENNIEQIYPVNAISFH
          QGY.LSSIEG..AVEYL.PSPEV.KKK.AFK.HRLKENNI.QIYPVNAISFH
Retrocopy QGYMLSSIEGQMAVEYLHPSPEV*KKKCAFKYHRLKENNIKQIYPVNAISFH

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_358 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 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000010213	1 retrocopy	retro_chof_1339,
Macaca mulatta	ENSMMUG00000003092	1 retrocopy	retro_mmul_1729,
Sarcophilus harrisii	ENSSHAG00000000550	1 retrocopy	retro_shar_812,
Sarcophilus harrisii	ENSSHAG00000002438	1 retrocopy	retro_shar_811,
Sarcophilus harrisii	ENSSHAG00000010372	1 retrocopy	retro_shar_358 ,