RetrogeneDB ID: retro_shar_681

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL857000.1:3259853..3260309(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSHAG00000011279
• Aliases: None
• Description: None

Sequence

>retro_shar_681
ATGGCATTAGTGTCAGCAGACTCCAGAATAGCTGAATTACTCACAAAGCTTTATCAACTGATGGAACGAACTCAGGACAA
ATGCTTCTGAACTGAATGTAGCCTGATCAATATTCAGAAGACACATGGGAGAATTCAGACAGAAAATAAAATCTCTCCTT
ATTACCGGACAAAGCTTCGAGGTCTGTATACCATGACCAAGGCAGATGCAGAGGAAGAATGCAATATAATGTACAAAGCT
CTGAATAAGATTGCTGAGAGTAAGACTTCACTGGAAGAAAAGTGAATTGAGGCTAAAATTGCATGTTTGTACGATGATTC
AGAATCTCCACAGAAAACTATGTGCCTAGGGGTACTGATGAGTCTATTGCAACAATCAGTCATGACATTGCCTCTGTGAA
TTGGGAAACCTAGAGACAAGCCTCCACCCCTATGTGGGACTAATTTAGCTTCAGGG

Alignment

ORF - retro_shar_681 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.68 %
• Parental protein coverage: 51.88 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MALVSADSRIAELLTELHQLIKQTQEERSRSEHNLINIQKTHERMQTENKISPYYRTKLRGLYTTAKADA
          MALVSADSRIAELLT.L.QL...TQ......E..LINIQKTH.R.QTENKISPYYRTKLRGLYT..KADA
Retrocopy MALVSADSRIAELLTKLYQLMERTQDKCF*TECSLINIQKTHGRIQTENKISPYYRTKLRGLYTMTKADA

Parental  EAECNILRRALDKIAEIKTLLEERRIAAKIAGLYNDSEPPRKTMRRGVLMTLLQQSAMTLPLWIGKPGDK
          E.ECNI...AL.KIAE.KT.LEE..I.AKIA.LY.DSE.P.KTM..GVLM.LLQQS.MTLPL.IGKP.DK
Retrocopy EEECNIMYKALNKIAESKTSLEEK*IEAKIACLYDDSESPQKTMCLGVLMSLLQQSVMTLPL*IGKPRDK

Parental  PPPLCGAIPASG
          PPPLCG...ASG
Retrocopy PPPLCGTNLASG

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_681 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	ENSMODG00000015642	1 retrocopy	retro_mdom_939,
Sarcophilus harrisii	ENSSHAG00000011279	1 retrocopy	retro_shar_681 ,
Tarsius syrichta	ENSTSYG00000009894	1 retrocopy	retro_tsyr_2,