RetrogeneDB ID: retro_shar_540

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL849865.1:2..409(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSHAG00000010906
• Aliases: None
• Description: None

Sequence

>retro_shar_540
AAAGTATACGATGTGAAAGAGCTTGTCCTGGACAACTGTAGGTCATATGATGGTGAAATTGAAGGCCTCACAGATGAATT
TAAAGAACTGGAGTTCTTAAGTACAATCAATGTAGGCCTTTCCTCAGTTGCAAACTTACCAACGTTAAATAAACTTAAGA
ATCCTGAACTAAAGTGATAACAGAATCTCCAGAGGATTTGGAAGTATTGGCAGAAAAGTGCCTGAAACTCACACATCTAA
ATCTAAGCAGAAGCAAATTTAAAAACCTCAGTACAATAAACCTACTGAAAAAGTTAGAAAACCTCAAAAGCTTAGATCTT
TTTAATTGTGAGGTAACTAACTTGAATGACTACAGAGAAAATGTATTCAAACTCCTCCCCCAACTCACATACCTTGATGG
CTATGAC

Alignment

ORF - retro_shar_540 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.86 %
• Parental protein coverage: 54.66 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KPSDVKELVLDNCRSYDGKIEGLTDEFEELEFLSTINVGLSSVANLPKLNKLKKLEL-SDNRISGG-LEV
          K..DVKELVLDNCRSYDG.IEGLTDEF.ELEFLSTINVGLSSVANLP.LNKLK..EL.SDNRIS.G.LEV
Retrocopy KVYDVKELVLDNCRSYDGEIEGLTDEFKELEFLSTINVGLSSVANLPTLNKLKNPEL>SDNRISRG>LEV

Parental  LAEKCPNLTHLNLSGNKIKDLSTIDPLKKLENLKSLDLFNCEVTNLNDYRENVFKLLPQLTYLDGYD
          LAEKC..LTHLNLS..K.K.LSTI..LKKLENLKSLDLFNCEVTNLNDYRENVFKLLPQLTYLDGYD
Retrocopy LAEKCLKLTHLNLSRSKFKNLSTINLLKKLENLKSLDLFNCEVTNLNDYRENVFKLLPQLTYLDGYD

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_540 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 16 parental genes, and 28 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000002339	2 retrocopies	retro_cjac_3305, retro_cjac_3799,
Dasypus novemcinctus	ENSDNOG00000015360	5 retrocopies	retro_dnov_1199, retro_dnov_1250, retro_dnov_1696, retro_dnov_836, retro_dnov_956,
Dipodomys ordii	ENSDORG00000008611	1 retrocopy	retro_dord_240,
Felis catus	ENSFCAG00000015773	1 retrocopy	retro_fcat_1188,
Homo sapiens	ENSG00000140350	3 retrocopies	retro_hsap_1479, retro_hsap_3117, retro_hsap_48,
Gorilla gorilla	ENSGGOG00000015417	1 retrocopy	retro_ggor_1134,
Loxodonta africana	ENSLAFG00000022560	1 retrocopy	retro_lafr_679,
Macaca mulatta	ENSMMUG00000022717	1 retrocopy	retro_mmul_1985,
Nomascus leucogenys	ENSNLEG00000013347	2 retrocopies	retro_nleu_15, retro_nleu_2383,
Otolemur garnettii	ENSOGAG00000003058	1 retrocopy	retro_ogar_2596,
Ochotona princeps	ENSOPRG00000015394	2 retrocopies	retro_opri_302, retro_opri_563,
Pongo abelii	ENSPPYG00000006595	2 retrocopies	retro_pabe_210, retro_pabe_2575,
Pan troglodytes	ENSPTRG00000007219	2 retrocopies	retro_ptro_2108, retro_ptro_758,
Rattus norvegicus	ENSRNOG00000045651	1 retrocopy	retro_rnor_1043,
Sarcophilus harrisii	ENSSHAG00000010906	1 retrocopy	retro_shar_540 ,
Tupaia belangeri	ENSTBEG00000016417	2 retrocopies	retro_tbel_4078, retro_tbel_4595,