RetrogeneDB ID: retro_shar_676

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL856988.1:2416758..2417265(+)
• Located in intron of: ENSSHAG00000016924

Retrocopy information

• Ensembl ID: ENSSHAG00000016938
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RAB35
• Ensembl ID: ENSSHAG00000018522
• Aliases: None
• Description: RAB35, member RAS oncogene family [Source:HGNC Symbol;Acc:9774]

Sequence

>retro_shar_676
ACACTCTTGGGCAGCCACATCACTACACTTGGGGTGGACTTCAAAATCCAGACTGTGGAGATCAATGGGAAAAGGTCAAA
CTACAGATCTGGGACACGGCTGGGCAGGAACACTTCCGCATCATCACCTCCAGGTGTTACCAAGGGACCCCCGGGGTCAT
TGTTGTGTACAATGTCACCAGCGCAGTCTTTCGTCAATGTCAAGCTGTGGCTCCATGAAATCAACCAGAACTGTGATGAC
GTGTGCAGGATATTAGTGGGAAACAAGAATGATGACCCAGAGCAGAAGGTGGTAGAGACGGAAGACGCCTACAAGTTTGC
TGGGAAGATGGGGATCCAGCGGTTTAAGACCAGCGCCAAAGAGAACGTCAACGTGGAAGAGATGTTCAACTGCATCACAG
AGCTGGTTCTCCGAGCAAAGAAAGAAAATTTAGTAAAGGGGCAGCAGCAGCAACAGAATGATGTGGTCAAGCTCACAAAG
AACAGTAACCGGAAGAAGCGGTGCTGC

Alignment

ORF - retro_shar_676 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.56 %
• Parental protein coverage: 91.89 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  TFSGSYITTIGVDFKIRTVEING-EKVKLQIWDTAGQERFRTITSTYYRGTHGVIVVY-DVTSAESFVNV
          T..GS.ITT.GVDFKI.TVEING.EKVKLQIWDTAGQE.FR.ITS..Y.GT.G...V......A.SFVNV
Retrocopy TLLGSHITTLGVDFKIQTVEING<EKVKLQIWDTAGQEHFRIITSRCYQGTPG-VIVV>TMSPAQSFVNV

Parental  KRWLHEINQNCDDVCRILVGNKNDDPERKVVETEDAYKFAGQMGIQLFETSAKENVNVEEMFNCITELVL
          K.WLHEINQNCDDVCRILVGNKNDDPE.KVVETEDAYKFAG.MGIQ.F.TSAKENVNVEEMFNCITELVL
Retrocopy KLWLHEINQNCDDVCRILVGNKNDDPEQKVVETEDAYKFAGKMGIQRFKTSAKENVNVEEMFNCITELVL

Parental  RAKKENLAKQQQQQQNDVVKLTKNSKRKKRCC
          RAKKENL.K.QQQQQNDVVKLTKNS.RKKRCC
Retrocopy RAKKENLVKGQQQQQNDVVKLTKNSNRKKRCC

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_676 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.

---

Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Microcebus murinus	ENSMICG00000012472	1 retrocopy	retro_mmur_1173,
Sarcophilus harrisii	ENSSHAG00000010376	1 retrocopy	retro_shar_68,
Sarcophilus harrisii	ENSSHAG00000018522	1 retrocopy	retro_shar_676 ,