RetrogeneDB ID: retro_shar_463

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL849573.1:221653..222111(+)
• Located in intron of: ENSSHAG00000003050

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSHAG00000002993
• Aliases: None
• Description: None

Sequence

>retro_shar_463
ATGACTCACCATTGGGATTATTTGACGATTTTGGCACAGGAGTCATTCCCTCAGTTTTCTTTCAAAAGTATAAACTTCAT
CCAAGACCTGATAAATCAGGAGCTCAGAATCAATCTCCAGCCAATAAAATGTTCTAAGAAGGGTAGGTTACTTACCCAAA
CCCTATGCATTGAAAATGTATTCAATGACCTCAGCAACTTCCCAGAAGCCATGTCGCAGCTGTTGGAGCATCCCCAAGAG
CTGGCTTGGATTAACTTGTTCTTCAGTGATCTCTACAGTACTGACCACATGCTGACCCTGTCTTTAACTTTGCTGTACTT
TCTCTGCAGTGCAACTACATTCAGCACATAACAGAAATAGATATACTATCAAAACTTCACAAGCATGGATACTTGACCTT
CCATGGGAACCTCATAGAGGAAAGGAAGGGATACAGGCAACGCATGCTATCCATTATA

Alignment

ORF - retro_shar_463 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.13 %
• Parental protein coverage: 79.79 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MTDNWDYVKTLAQEPPLDFSFKSINFIQDLISEEPRAGLRPVKRSTQGKSLTQAVRINNNVLNDLTDFSQ
          MT..WDY...LAQE....FSFKSINFIQDLI..E.R..L.P.K.S..G..LTQ...I..NV.NDL..F..
Retrocopy MTHHWDYLTILAQESFPQFSFKSINFIQDLINQELRINLQPIKCSKKGRLLTQTLCI-ENVFNDLSNFPE

Parental  TMSQLLEHPQNLAWIDLSFNDLPNIDPVLT-TFHNLSVLYLHGNCIHRLTEVDKLSSLPKLRSLTLHGNP
          .MSQLLEHPQ.LAWI.L.F.DL...D..LT....N..VL.L..N.I...TE.D.LS.L.K...LT.HGN.
Retrocopy AMSQLLEHPQELAWINLFFSDLYSTDHMLT<PVFNFAVLSLQCNYIQHITEIDILSKLHKHGYLTFHGNL

Parental  IEDEKGYRQYVLSIL
          IE..KGYRQ..LSI.
Retrocopy IEERKGYRQRMLSII

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_463 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 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000005109	1 retrocopy	retro_cpor_512,
Sarcophilus harrisii	ENSSHAG00000002993	1 retrocopy	retro_shar_463 ,