RetrogeneDB ID: retro_shar_38

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL864871.1:59739..60459(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSHAG00000003330
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSHAG00000002679
• Aliases: None
• Description: None

Sequence

>retro_shar_38
ATGGGATACGACAGAGCCCGTTTCTTGGGGGATGTAGATGAAGACCTCATCTGCCCCATCTGCTGTGGCGTTCTTGAGGA
GCCTGTTCAAGCTCCTAACTGCGAGCATGCCTTCTGCAACACCTGCGTGAGCCAGGGGTCCTCCTGGCAGCAAACATGCC
CCGTGGACGGCAGCGTGGTGACAGTCCCCCACCTGCGCCCCATCCCTCGAATCATGAGGAACATGCTGTCCAAACTCCAG
ATCACGTGCGACAACGCCGTGGCCGGCTGCAACGCCATCCTGAGGCTGGACAATCTCATGGCTCACCTCCTCAACTGCGA
GCACAGCCCCAAGTGCCCCGTGGCCTGCAAACACGGCTGCGGCCTGGAGATGTCCAATGGAGAGCTGCCCAATCACAACT
GCATCGAGCACCTGCACTCCATGGTCCAGCAGCAAGAGACCCACATCACGGAGCTGGAGAAGACATCGGCCGAGCAGAAG
TTCCAGCTGGAGGAACAGCAGCGAGACATCCAGCTGCTGAAGGCCTACGTCCACGCTCTCCACAACGACAAGCCCAAGCT
CCGTCCCGAGAGCAGCGAGATCATCCAGTGGGTCAACTCCCTGCATCCAGAAGGGGTGCCGAGCGGGGAGGATGGAAGCT
CCAGCCCGGGGCCCACTCAACCACCGGTGCCGAAGACTTCAGCGGAAAGTGCCTGCTCGGTGTCCTCCCCAACGAGCTGA

Alignment

ORF - retro_shar_38 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.6 %
• Parental protein coverage: 59.43 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGYDVARFQGDVDEDLICPICSGVLEEPVQAPHCEHAFCNACITQWFSQQQTCPVDRSVVTVAHLRPVPR
          MGYD.ARF.GDVDEDLICPIC.GVLEEPVQAP.CEHAFCN.C..Q..S.QQTCPVD.SVVTV.HLRP.PR
Retrocopy MGYDRARFLGDVDEDLICPICCGVLEEPVQAPNCEHAFCNTCVSQGSSWQQTCPVDGSVVTVPHLRPIPR

Parental  IMRNMLSKLQIACDNAVFGCSAVVRLDNLMSHLSDCEHNPKRPVTCEQGCGLEMPKDELPNHNCIKHLRS
          IMRNMLSKLQI.CDNAV.GC.A..RLDNLM.HL..CEH.PK.PV.C..GCGLEM...ELPNHNCI.HL.S
Retrocopy IMRNMLSKLQITCDNAVAGCNAILRLDNLMAHLLNCEHSPKCPVACKHGCGLEMSNGELPNHNCIEHLHS

Parental  VVQQQQTRIAELEKTSAEHKHQLAEQQKRDIQLLKAYMRAIRSVNPNLQ
          .VQQQ.T.I.ELEKTSAE.K.QL.EQQ.RDIQLLKAY..A.....P.L.
Retrocopy MVQQQETHITELEKTSAEQKFQLEEQQ-RDIQLLKAYVHALHNDKPKLR

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_38 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 8 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Macropus eugenii	ENSMEUG00000001320	1 retrocopy	retro_meug_901,
Meleagris gallopavo	ENSMGAG00000006916	1 retrocopy	retro_mgal_15,
Myotis lucifugus	ENSMLUG00000006057	1 retrocopy	retro_mluc_300,
Mus musculus	ENSMUSG00000025373	2 retrocopies	retro_mmus_3645, retro_mmus_3648,
Otolemur garnettii	ENSOGAG00000001525	4 retrocopies	retro_ogar_2365, retro_ogar_2487, retro_ogar_3113, retro_ogar_3228,
Ochotona princeps	ENSOPRG00000001348	1 retrocopy	retro_opri_528,
Rattus norvegicus	ENSRNOG00000023456	1 retrocopy	retro_rnor_2918,
Sarcophilus harrisii	ENSSHAG00000002679	1 retrocopy	retro_shar_38 ,