RetrogeneDB ID: retro_shar_244

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL834792.1:1746745..1747056(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSHAG00000001103
• Aliases: None
• Description: None

Sequence

>retro_shar_244
GAGTTACTAAGAATTACAACTAAAGAAAATGTACATATATTTATTCAAAATTTTTTTGGAAAAAACTGAAAATAAGGCAA
ATAACATTATAGAAATCATCCAACTGAAGGTGCTGGTGTCTGTCAAAGAAAAATTTCATCAAGTGATAGTGTAAAGGGTC
CATGAGCTGTATGATCTGGAAGAGACTCCAATAGGGTGGCAGGAAGGCATTGAGAGAACCAACAGACTAATGTTGATAGG
CAGAAACTTAGATGAGGAAATCCTTAAAATACCTATACAATGATACAATGACTGAGAAATAAATAAACAAT

Alignment

ORF - retro_shar_244 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.89 %
• Parental protein coverage: 50.24 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  EVLGSTTEENLNIFIQNLL-W-EKTVKNKADNTMEVIRLKGLVSIKDKPHQVIVQAVHELYDLEETPVKW
          E.L..TT.EN..IFIQN...W.EKT..NKA.N..E.I.LK.LVS.K.K.HQVIV..VHELYDLEETP..W
Retrocopy ELLRITTKENVHIFIQNFF<W<EKT-ENKANNIIEIIQLKVLVSVKEKFHQVIV*RVHELYDLEETPIGW

Parental  KEDTERTNRLVLIGRNLDKEI-LKHLFIDTVTEKQVSS
          .E..ERTNRL.LIGRNLD.EI.LK.L..DT.TEK....
Retrocopy QEGIERTNRLMLIGRNLDEEI>LKYLYNDTMTEK*INN

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_244 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
Canis familiaris	ENSCAFG00000001943	1 retrocopy	retro_cfam_354,
Sarcophilus harrisii	ENSSHAG00000001103	1 retrocopy	retro_shar_244 ,
Tupaia belangeri	ENSTBEG00000001371	1 retrocopy	retro_tbel_1641,