RetrogeneDB ID: retro_shar_360

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL841475.1:446867..447490(+)
• Located in intron of: ENSSHAG00000008637

Retrocopy information

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

Parental gene information

• Parental gene symbol: ERP44
• Ensembl ID: ENSSHAG00000012181
• Aliases: None
• Description: endoplasmic reticulum protein 44 [Source:HGNC Symbol;Acc:18311]

Sequence

>retro_shar_360
TTTGGATCTACTTCAAACCAGAAAGATTTAGTGGAGACAATATAATCTACAAATCATTAGGGGAAAATGTTCCAGATATG
GTATGCCTGGGATCTCTAACAAATTTTGACTTGGCTTATGCTTGGACTCAAGATAACTGTGTCCCTCTTATTCAGGAAAT
AACTTTTGAAAATGGAGAACTGACCAAACTATCTTTTCTTATACTTTTCTATACAAAAGAGGATACAATGAGTTTAGATG
TATTCCAAAATGAAGTATCACATCAATTAATAAGTGAAAAAGGTACAATACACTTTTTACATCTGATTGTGATAAATGTA
GACACCCATTTCTGCATATACGAAAAACGCCAGCAGATTGCCCTGTAACAACCATTGACAGCTTCAGGAACATGTATGTC
TTTCCAGACTTCAAGGATTTATCAATTCCAAACAAGCTTAAGCAATCTATATTAGACTTGCATTCAAGAAAATTGCACTA
GAATTCCATCATGGTCCCGATCCCACTTATGTTGTCCAGTGACAGCACACTCAAGATGTACCAAGTAATCCACCAGAGAA
TTCTTCCAGAAACTTACACCCAGCAAATATAGCTTTACCTTATTGAGGGATCGAGATAAGCTT

Alignment

ORF - retro_shar_360 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.7 %
• Parental protein coverage: 53.54 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  FGSVS-KPERFSGDNIIYKPPGENAPDMVYLGSLTNFDLAYAWTQDKCVPLVREITFENGEELTEEGLPF
          FGS.S.KPERFSGDNIIYK..GEN.PDMV.LGSLTNFDLAYAWTQD.CVPL..EITFENGE.LT...L.F
Retrocopy FGSTS<KPERFSGDNIIYKSLGENVPDMVCLGSLTNFDLAYAWTQDNCVPLIQEITFENGE-LTK--LSF

Parental  LILFHMKEDTMSLDVFQNEVARQLISEKGTINFLH-ADCDKFRHPLLHIQKTPADCPVIAIDSFRHMYVF
          LILF..KEDTMSLDVFQNEV..QLISEKGTI.FLH..DCDK.RHP.LHI.KTPADCPV..IDSFR.MYVF
Retrocopy LILFYTKEDTMSLDVFQNEVSHQLISEKGTIHFLH<SDCDKCRHPFLHIRKTPADCPVTTIDSFRNMYVF

Parental  PDFKDLSIPNKLKQFVLDLHSGKLH-REFHHGPDPTDVAPGQHIQDVASSPPESS-FQKLAPSEYRYTLL
          PDFKDLSIPNKLKQ..LDLHS.KLH..EFHHGPDPT.V...QH.QDV.S.PPE.S.FQKL.PS.Y..TLL
Retrocopy PDFKDLSIPNKLKQSILDLHSRKLH<LEFHHGPDPTYVVQ*QHTQDVPSNPPENS<FQKLTPSKYSFTLL

Parental  RDRDEL
          RDRD.L
Retrocopy RDRDKL

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_360 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
Oryctolagus cuniculus	ENSOCUG00000004220	1 retrocopy	retro_ocun_592,
Ochotona princeps	ENSOPRG00000000004	1 retrocopy	retro_opri_852,
Sarcophilus harrisii	ENSSHAG00000012181	1 retrocopy	retro_shar_360 ,