RetrogeneDB ID: retro_shar_652

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL856934.1:2624063..2624582(+)
• Located in intron of: ENSSHAG00000017079

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSHAG00000013955
• Aliases: None
• Description: None

Sequence

>retro_shar_652
GGAAAGTGCCTCAAGACTTTACCTGCTCATTCTGACTTTATTTCAACTGTTCATTTTAATCGTGATGAATCCTTGATAGT
ATCAAGTAGTTACAATGGTCTCTGTTGAACCTGGGATTATAGCATCAGGTCAATATCTAAAAACACTTATTGATGATGAT
AACTCTCCTGTGTCTTTTGTGAATTCTCTCCAAATGGTAAATACATTCTTGCTGCAATTCTGCACAACACTCTTAAGCTA
TGGGACTATAGCAAAGGGAAGTGCCTGAAGACATACACTGGTCACAAGAATGAGAAATACTGCATTTTTGCTAATTTTTC
AGTCATTGATGAAAAGTGGATTGTGTCTGGATCAGAAGATAACCTGGTTTACATTTGGAACCTCCAGACAAAAGAGATTG
TACAGAAATTACAAGGTCATACAGATGTGATTTCAATAGTTTGTTACCCTACAGAAAGCCTCATTGTATCAGCTGCATTA
GAAAATGACAAAACAATTAAACTCTGGAAGAGTGACTGT

Alignment

ORF - retro_shar_652 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.8 %
• Parental protein coverage: 52.1 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  GKCLKTLPAHSDPVSAVHFNRDGSLIVSSSYDGLCRIWD-TASGQCLKTLIDDDNPPVSFV-KFSPNGKY
          GKCLKTLPAHSD..S.VHFNRD.SLIVSSSY.GLC..WD..ASGQ.LKTLIDDDN.PVSFV..FSPNGKY
Retrocopy GKCLKTLPAHSDFISTVHFNRDESLIVSSSYNGLC*TWD>IASGQYLKTLIDDDNSPVSFV<EFSPNGKY

Parental  ILAATLDNTLKLWDYSKGKCLKTYTGHKNEKYCIFANFSVTGGKWIVSGSEDNLVYIWNLQTKEIVQKLQ
          ILAA.L.NTLKLWDYSKGKCLKTYTGHKNEKYCIFANFSV...KWIVSGSEDNLVYIWNLQTKEIVQKLQ
Retrocopy ILAAILHNTLKLWDYSKGKCLKTYTGHKNEKYCIFANFSVIDEKWIVSGSEDNLVYIWNLQTKEIVQKLQ

Parental  GHTDVVISTACHPTENIIASAALENDKTIKLWKSDC
          GHTD.VIS..C.PTE..I.SAALENDKTIKLWKSDC
Retrocopy GHTD-VISIVCYPTESLIVSAALENDKTIKLWKSDC

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_652 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 2 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Sarcophilus harrisii	ENSSHAG00000013955	3 retrocopies	retro_shar_34, retro_shar_45, retro_shar_652 ,
Drosophila melanogaster	FBgn0040066	1 retrocopy	retro_dmel_69,