RetrogeneDB ID: retro_shar_760

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL863862.1:1708..2226(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RWDD4
• Ensembl ID: ENSSHAG00000011971
• Aliases: None
• Description: RWD domain containing 4 [Source:HGNC Symbol;Acc:23750]

Sequence

>retro_shar_760
TCTATTTTTAAAGGTGATGAAAATTTCCAAGAACTAAGTCCAGTTTCATGTGATATGGGATAGGTGCAAAAAGATGATCC
TAACACCTTCTTGATAGAAGTTTCTTGAACCAAAACACACCCACAAACAATTCCAATCATATTTATAATTTTTTTCAACA
ATATTATATCATTAGTGGTAAAGTAAAGTATTCTGGCGAAATTATAGGAAGAAGTTGAAATTAATTTTGCAACTGCTCTG
ACATATATATTGTTTGAATATGCAAAGGAGAATAAAGAACAATTCAAGGAGAATCATCATCCTGTTAATCCTATCACATC
AACAAACAATATTGTTTCAGTTGAAACTTCTAAGATGACTCCATCAGATAAGAAAAATTAAAAAAAAAAAAAAAACTTTT
CCAAAACTCAGAAATGAAAGCTGGCAGACAAGATGGCTCACAAAAGTGAATTCAATAAGGCTGGACGTAGGTCAATGTGG
TTAAGCATTTAACCAAAACTGGCTCTCAGGATGATGAA

Alignment

ORF - retro_shar_760 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.57 %
• Parental protein coverage: 92.02 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SIYEGDESFRELSPVSFQYRIGENGDPKAFLIEVSWTETYPQTAPIISMNAFFNNTISSAVKQSILAKLQ
          SI..GDE.F.ELSPVS.........DP..FLIEVS.T.T.PQT.PII....FFNN.IS..VK.SILAKL.
Retrocopy SIFKGDENFQELSPVSCDMG*VQKDDPNTFLIEVS*TKTHPQTIPIIFI-IFFNNIISLVVK*SILAKL*

Parental  EEVEVNLGTAMTYTLFEYAKDNKEQFMENHHPVNNVTSISNIISAETPNTVPSIK-KKDKKEQLSKTQKR
          EEVE.N..TA.TY.LFEYAK.NKEQF.ENHHPVN..TS..NI.S.ET....PS.K.........SKTQK.
Retrocopy EEVEINFATALTYILFEYAKENKEQFKENHHPVNPITSTNNIVSVETSKMTPSDKXXXXXXXXFSKTQK*

Parental  KLADKTDHKGELPR-GWNWVDVIKHLSKTGSKDDE
          KLADK..HK.E....GW..V.V.KHL.KTGS.DDE
Retrocopy KLADKMAHKSEFNK<GWT*VNVVKHLTKTGSQDDE

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_760 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 20 parental genes, and 30 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000003081	1 retrocopy	retro_btau_603,
Canis familiaris	ENSCAFG00000007880	1 retrocopy	retro_cfam_1281,
Choloepus hoffmanni	ENSCHOG00000005290	3 retrocopies	retro_chof_1477, retro_chof_441, retro_chof_887,
Dasypus novemcinctus	ENSDNOG00000015132	1 retrocopy	retro_dnov_968,
Felis catus	ENSFCAG00000024337	1 retrocopy	retro_fcat_1156,
Homo sapiens	ENSG00000182552	2 retrocopies	retro_hsap_3770, retro_hsap_3841,
Gorilla gorilla	ENSGGOG00000011982	1 retrocopy	retro_ggor_2536,
Myotis lucifugus	ENSMLUG00000006800	1 retrocopy	retro_mluc_545,
Monodelphis domestica	ENSMODG00000004223	2 retrocopies	retro_mdom_1015, retro_mdom_251,
Nomascus leucogenys	ENSNLEG00000010733	1 retrocopy	retro_nleu_1898,
Otolemur garnettii	ENSOGAG00000016709	5 retrocopies	retro_ogar_1084, retro_ogar_1171, retro_ogar_1228, retro_ogar_2652, retro_ogar_2789,
Ochotona princeps	ENSOPRG00000015147	1 retrocopy	retro_opri_1002,
Pongo abelii	ENSPPYG00000015230	1 retrocopy	retro_pabe_3082,
Pan troglodytes	ENSPTRG00000016632	2 retrocopies	retro_ptro_1456, retro_ptro_2556,
Rattus norvegicus	ENSRNOG00000022500	1 retrocopy	retro_rnor_2930,
Sarcophilus harrisii	ENSSHAG00000011971	1 retrocopy	retro_shar_760 ,
Sus scrofa	ENSSSCG00000015776	2 retrocopies	retro_sscr_1019, retro_sscr_1051,
Ictidomys tridecemlineatus	ENSSTOG00000013086	1 retrocopy	retro_itri_533,
Tarsius syrichta	ENSTSYG00000006599	1 retrocopy	retro_tsyr_1898,
Vicugna pacos	ENSVPAG00000005743	1 retrocopy	retro_vpac_341,