RetrogeneDB ID: retro_shar_643

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL856908.1:852808..853273(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: JOSD1
• Ensembl ID: ENSSHAG00000015931
• Aliases: None
• Description: Josephin domain containing 1 [Source:HGNC Symbol;Acc:28953]

Sequence

>retro_shar_643
GAATTGTGTGCTTACTACTCATTCAACAACATTTTCCAAGACAGCAATTCCTTCATCTAGGAAACACAATAAGAGATATT
TCAGAGACTGTTTCCAAATACCATGGTGACATCTCATAAGAAGAACATGCTAGGAAATGGGAATTATGATGGAAATATCA
TCATGGCAGCCTTTAAGACCAAAGGCTATGAAACAGTTTTGTGAGACAAATGAAGGGATGTCAGTGTCCTCTCTTACATC
CTGGGTTTCATCATAAATCTCTGCTCTAGCCTCTGCTGGACTCCATTAAAGCTTCCATTCAAAAGGCAGCAGTGGATTTG
TGTCTAAGATGTGAGAAGCATCTAGTACAACCTTGACTCCAAGTTCAAAGTGTCTGAGTTAATAGGAGGTGAGAGTGAGC
TCAGGAAATTTTTGAAACATCAGCTCCAAGGAAATAAGTGTCAATTGCTGCTTGTCATACCAGAG

Alignment

ORF - retro_shar_643 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.34 %
• Parental protein coverage: 77.72 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ELCALHALNNVFQDSNAFTRETLQEIFQRLSPNTMVTPHKKSMLGNGNYDVNVIMAALQTKGYEAVWWDK
          ELCA....NN.FQDSN.F..ET..EIFQRL.PNTMVT.HKK.MLGNGNYD.N.IMAA..TKGYE.V..DK
Retrocopy ELCAYYSFNNIFQDSNSFI*ETQ*EIFQRLFPNTMVTSHKKNMLGNGNYDGNIIMAAFKTKGYETVL*DK

Parental  RRDVSVIALSNVMGFIMNLPSSLCWGPLKLPLKRQHWICVREVGGTYYNLDSKLKVPEWIGGESELRKFL
          .RDVSV..LS...GFI.NL.SSLCW.PLKLP.KRQ.WICV..V....YNLDSK.KV.E.IGGESELRKFL
Retrocopy *RDVSV--LSYILGFIINLCSSLCWTPLKLPFKRQQWICV*DVRSI*YNLDSKFKVSELIGGESELRKFL

Parental  KHQLRGKNCELLLVVPE
          KHQL.G..C.LLLV.PE
Retrocopy KHQLQGNKCQLLLVIPE

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_643 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 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000010171	1 retrocopy	retro_btau_1508,
Canis familiaris	ENSCAFG00000001379	1 retrocopy	retro_cfam_1500,
Choloepus hoffmanni	ENSCHOG00000001723	2 retrocopies	retro_chof_1576, retro_chof_233,
Dasypus novemcinctus	ENSDNOG00000016015	1 retrocopy	retro_dnov_128,
Equus caballus	ENSECAG00000015546	1 retrocopy	retro_ecab_251,
Felis catus	ENSFCAG00000002821	1 retrocopy	retro_fcat_565,
Macropus eugenii	ENSMEUG00000002899	2 retrocopies	retro_meug_1507, retro_meug_531,
Microcebus murinus	ENSMICG00000011798	1 retrocopy	retro_mmur_1202,
Myotis lucifugus	ENSMLUG00000003764	1 retrocopy	retro_mluc_1868,
Mus musculus	ENSMUSG00000022426	1 retrocopy	retro_mmus_3014,
Otolemur garnettii	ENSOGAG00000007520	3 retrocopies	retro_ogar_1462, retro_ogar_2911, retro_ogar_3487,
Pteropus vampyrus	ENSPVAG00000010148	1 retrocopy	retro_pvam_181,
Rattus norvegicus	ENSRNOG00000014440	2 retrocopies	retro_rnor_2954, retro_rnor_906,
Sarcophilus harrisii	ENSSHAG00000015931	1 retrocopy	retro_shar_643 ,
Ictidomys tridecemlineatus	ENSSTOG00000024999	1 retrocopy	retro_itri_193,
Tarsius syrichta	ENSTSYG00000008846	1 retrocopy	retro_tsyr_1076,