RetrogeneDB ID: retro_shar_388

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL841573.1:857428..857874(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CENPO
• Ensembl ID: ENSSHAG00000005861
• Aliases: None
• Description: centromere protein O [Source:HGNC Symbol;Acc:28152]

Sequence

>retro_shar_388
CCAGTCTTCATGTCTTTGGAATAGATAGCTTTAAAGTACTTGCTGACTAATTTCCAACACTTTGTGTGCAGTCTCAGTGA
ATACCTAAATGCACATTCTAGAGGAAAGTACCAGGCACATCAATTTCAGTGTGACTTTTCAACTTTCCTAAGTAGGTTCT
TGTAGAAAAATTTACCATGCACTTTGCTTTCATTCTCATACACTGTGCACTCCAGTAGAGCATCTTTCACTTTTGTACCA
GTCTTGTTCAATAGAACTTTATAACAACTCTTTTTACCAATGTCACAATCATGTACCAAGGGATAAGAGCAACTCCTGCC
TCTTTGGAGGATCAATGAGCAATCTGTGAGACTTTATTCTTCAAAAATGCCCTTCCTAAGGTGCTTGAATCCTTTTTAAG
AGTTAAAGAGAACTTAGATTTTATATCCAGTGTAACCAGAAGCAGA

Alignment

ORF - retro_shar_388 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60. %
• Parental protein coverage: 50.51 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PVFIPLEQIAAKYLQTNFQNFVYSLSEHLNAYSGRKYQADQVQSGFSAFLARPLQRNSLCTLLSFTYTMD
          PVF..LE.IA.KYL.TNFQ.FV.SLSE.LNA.S..KYQA.Q.Q..FS.FL.R.L..N..CTLLSF.YT..
Retrocopy PVFMSLE*IALKYLLTNFQHFVCSLSEYLNAHSRGKYQAHQFQCDFSTFLSRFL*KNLPCTLLSFSYTVH

Parental  PNEESFP-FCARLLYHDLTITLPTSVTITYQGTGATPASWEDQRAVHVTLFYKNALHKVFESFLRVEKNF
          ....SF..FC..L.......TL.T.VTI.YQG..ATPAS.EDQ.A...TLF.KNAL.KV.ESFLRV..N.
Retrocopy SSRASFT<FCTSLVQ*NFITTLFTNVTIMYQGIRATPASLEDQ*AICETLFFKNALPKVLESFLRVKENL

Parental  DCLSSIPRSR
          D..SS..RSR
Retrocopy DFISSVTRSR

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_388 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Macropus eugenii	ENSMEUG00000010491	1 retrocopy	retro_meug_568,
Pongo abelii	ENSPPYG00000012596	1 retrocopy	retro_pabe_2764,
Rattus norvegicus	ENSRNOG00000050111	1 retrocopy	retro_rnor_1069,
Sarcophilus harrisii	ENSSHAG00000005861	1 retrocopy	retro_shar_388 ,