RetrogeneDB ID: retro_shar_551

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL849899.1:292042..292313(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: UBXN6
• Ensembl ID: ENSSHAG00000000301
• Aliases: None
• Description: UBX domain protein 6 [Source:HGNC Symbol;Acc:14928]

Sequence

>retro_shar_551
CTATCTGTGACTGGGGTTTATTTTACTTACCCATTCACTGAAGCCACCTTGAGAAAAGACCAACGGGATGCCTATATGAA
AGAGGCCATTAACAAGCACTCGAAAAAAGACCCAGTGACTGCTTCCATCATGAAGATCCATACGTTCAACAGGAACCGAG
AGAAAGTGAAATTGGGGATGAACACCATTTGACAAGTATCTAGATAACATCCATCTTCACCCAGAAGAGGAGAAATATAG
GAAAATCAAGTTGTAAAATAAAGTGTTTCAG

Alignment

ORF - retro_shar_551 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.81 %
• Parental protein coverage: 72.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LSVSGVYFTCPFTGATLRKDQRDAHIKEAINKHSKKDPVAASIMKIHTFNRDREKVKLGVDTI-AKYLDN
          LSV.GVYFT.PFT.ATLRKDQRDA..KEAINKHSKKDPV.ASIMKIHTFNR.REKVKLG..TI..KYLDN
Retrocopy LSVTGVYFTYPFTEATLRKDQRDAYMKEAINKHSKKDPVTASIMKIHTFNRNREKVKLGMNTI>DKYLDN

Parental  IHLHPEEEKYRKIKLQNKVFQ
          IHLHPEEEKYRKIKL.NKVFQ
Retrocopy IHLHPEEEKYRKIKL*NKVFQ

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_551 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000000967	1 retrocopy	retro_mdom_249,
Mustela putorius furo	ENSMPUG00000005027	1 retrocopy	retro_mputfur_1648,
Sarcophilus harrisii	ENSSHAG00000000301	1 retrocopy	retro_shar_551 ,