RetrogeneDB ID: retro_shar_462

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL849566.1:864687..865126(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ARF1
• Ensembl ID: ENSSHAG00000014599
• Aliases: None
• Description: ADP-ribosylation factor 1 [Source:HGNC Symbol;Acc:652]

Sequence

>retro_shar_462
CTATTCAAACTGAAGTTGGGTGCAATTGTAACTACTATTCCCACTGTAAGTTACAACATAAAAATTGTAGAATATAAATA
CATTAGCTTCACAGTGTGGGATGTAGGTGTCTAGAACAAGAGCCAAGTCCTATGGCACCATTACTTTCAGAACACACAAG
GGCAGATTTTTTGTGGTTGACAGTAATGACAGAGAATAAATGAATGAGGCCCAAGAACTGATGAGAATGTTGGCAGAGGA
TGAGCTTAGAGATGCCATCTTATTAGTGTTTGTTAACAGATAGGATCTTTCCAGTGCCACGAATGCAGCCAAATTTGTAG
ATAAATTCAGACTGCATTCTTTTCATCACAGAAACTGGTACATCTAAGCCACCTGTGTCACTAATGGGGATGGTCTTTAT
GAAGCACTGGACTAGTTGTCCAATCAATTCTGAAATCAA

Alignment

ORF - retro_shar_462 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.95 %
• Parental protein coverage: 81.22 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LYKLKLGEIVTTIPTIGFNVETVEYKNISFTVWDVGGQDKIRPLWRHYFQNTQGLIF-VVDSNDRERVNE
          L.KLKLG.IVTTIPT...N...VEYK.ISFTVWDVG...K...LW.HYFQNTQG.IF.VVDSNDRE..NE
Retrocopy LFKLKLGAIVTTIPTVSYNIKIVEYKYISFTVWDVGV*NKSQVLWHHYFQNTQGQIF>VVDSNDRE*MNE

Parental  AREELMRMLAEDELRDAVLLVFANKQDLPNAMNAAEITDKLGLHSLRHRNWYIQATCATSGDGLYEGLDW
          A..ELMRMLAEDELRDA.LLVF.N..DL..A.NAA...DK..LHS..HRNWYI.ATC.T.GDGLYE.LD.
Retrocopy A-QELMRMLAEDELRDAILLVFVNR*DLSSATNAAKFVDKFRLHSFHHRNWYI*ATCVTNGDGLYEALD*

Parental  LSNQLRNQ
          LSNQ..NQ
Retrocopy LSNQF*NQ

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_462 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 19 parental genes, and 51 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000007725	2 retrocopies	retro_btau_1257, retro_btau_1390,
Callithrix jacchus	ENSCJAG00000016671	10 retrocopies	retro_cjac_1295, retro_cjac_1691, retro_cjac_1719, retro_cjac_2189, retro_cjac_2896, retro_cjac_300, retro_cjac_3181, retro_cjac_3311, retro_cjac_3335, retro_cjac_390,
Ciona savignyi	ENSCSAVG00000007011	1 retrocopy	retro_csav_2,
Ficedula albicollis	ENSFALG00000001088	1 retrocopy	retro_falb_2,
Gallus gallus	ENSGALG00000005393	1 retrocopy	retro_ggal_7,
Latimeria chalumnae	ENSLACG00000019009	1 retrocopy	retro_lcha_10,
Myotis lucifugus	ENSMLUG00000007020	6 retrocopies	retro_mluc_1631, retro_mluc_242, retro_mluc_2605, retro_mluc_428, retro_mluc_511, retro_mluc_876,
Macaca mulatta	ENSMMUG00000002792	3 retrocopies	retro_mmul_237, retro_mmul_541, retro_mmul_810,
Oryctolagus cuniculus	ENSOCUG00000023645	2 retrocopies	retro_ocun_1137, retro_ocun_247,
Otolemur garnettii	ENSOGAG00000010974	4 retrocopies	retro_ogar_2431, retro_ogar_295, retro_ogar_3353, retro_ogar_974,
Procavia capensis	ENSPCAG00000014202	2 retrocopies	retro_pcap_15, retro_pcap_23,
Pongo abelii	ENSPPYG00000000148	3 retrocopies	retro_pabe_3159, retro_pabe_849, retro_pabe_965,
Pelodiscus sinensis	ENSPSIG00000009767	1 retrocopy	retro_psin_12,
Sarcophilus harrisii	ENSSHAG00000003635	2 retrocopies	retro_shar_25, retro_shar_364,
Sarcophilus harrisii	ENSSHAG00000014599	3 retrocopies	retro_shar_106, retro_shar_462 , retro_shar_725,
Ictidomys tridecemlineatus	ENSSTOG00000009288	3 retrocopies	retro_itri_1754, retro_itri_273, retro_itri_363,
Taeniopygia guttata	ENSTGUG00000000233	1 retrocopy	retro_tgut_2,
Tetraodon nigroviridis	ENSTNIG00000011685	1 retrocopy	retro_tnig_19,
Vicugna pacos	ENSVPAG00000003224	4 retrocopies	retro_vpac_281, retro_vpac_328, retro_vpac_6, retro_vpac_78,