RetrogeneDB ID: retro_shar_712

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL861582.1:799306..799718(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: UBE2E1
• Ensembl ID: ENSSHAG00000001416
• Aliases: None
• Description: ubiquitin-conjugating enzyme E2E 1 [Source:HGNC Symbol;Acc:12477]

Sequence

>retro_shar_712
CTCAAAATTCAGAAGGAACTGGTCAACATTACATTAGACTCACCTCCCAACTACAATGCTATTTCCAAAGGTGATAACAT
CTATGAATGGAGCTCAACTACTCTGGGGCCTTTCAGATTAGTCTAATGAAGGGGGGTGTTCTTTTTTTGACATAACCTTT
ATGCCCGAATATTCCTTCAAGTTTCCAAAGGTTATCTTTCATACAAAAATTTATCACTGTGACATCAATAGCTAAGGGGT
AATCTGTTTGAATATTCTGAAGGACAACTAAAGGCCAACCCTCACCATAGCTAATGTATTCCTTCCCATCTGCTCCCTGC
TCACTGATTGCAACTCTGCCTAACCCTTAAGGGGAAGGATCAGTATTCATCTACAGAGCAGAACAAGGCAGAATGGCCAG
GCAGTGGACCAA

Alignment

ORF - retro_shar_712 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.14 %
• Parental protein coverage: 95.14 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MRIQKELADITLDPPPNCSAGPKGDNIYEWRSTILGPPGSVYEGGVF-FLDITFTPEYPFKPPKVTFRTR
          ..IQKEL..ITLD.PPN..A..KGDNIYEW.ST.LGP...V...GVF.F.DITF.PEY.FK.PKV.F.T.
Retrocopy LKIQKELVNITLDSPPNYNAISKGDNIYEWSSTTLGPFRLV**RGVF>FFDITFMPEYSFKFPKVIFHTK

Parental  IYHCNINSQGVICLDILKDNWSPALTISKVLLSICSLLTDCNPADPLVGSIATQYMTNRAEHDRMARQ
          IYHC.INS.GVICL.ILKDN..P.LTI..V.L.ICSLLTDCN.A.PL.G.I................Q
Retrocopy IYHCDINS*GVICLNILKDN*RPTLTIANVFLPICSLLTDCNSA*PLRGRISIHLQSRTRQNGQAVDQ

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_712 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 17 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000003515	2 retrocopies	retro_amel_1117, retro_amel_483,
Ciona intestinalis	ENSCING00000006860	1 retrocopy	retro_cint_33,
Cavia porcellus	ENSCPOG00000002251	2 retrocopies	retro_cpor_1036, retro_cpor_52,
Dipodomys ordii	ENSDORG00000015441	1 retrocopy	retro_dord_785,
Felis catus	ENSFCAG00000024719	1 retrocopy	retro_fcat_623,
Gorilla gorilla	ENSGGOG00000008393	1 retrocopy	retro_ggor_76,
Loxodonta africana	ENSLAFG00000004150	1 retrocopy	retro_lafr_320,
Macropus eugenii	ENSMEUG00000014517	1 retrocopy	retro_meug_2089,
Mus musculus	ENSMUSG00000021774	3 retrocopies	retro_mmus_2493, retro_mmus_2600, retro_mmus_537,
Oryctolagus cuniculus	ENSOCUG00000006026	2 retrocopies	retro_ocun_134, retro_ocun_243,
Otolemur garnettii	ENSOGAG00000007527	3 retrocopies	retro_ogar_2029, retro_ogar_2566, retro_ogar_626,
Pan troglodytes	ENSPTRG00000014693	1 retrocopy	retro_ptro_68,
Pteropus vampyrus	ENSPVAG00000001773	1 retrocopy	retro_pvam_1451,
Rattus norvegicus	ENSRNOG00000008794	3 retrocopies	retro_rnor_1632, retro_rnor_2291, retro_rnor_2343,
Sarcophilus harrisii	ENSSHAG00000001416	1 retrocopy	retro_shar_712 ,
Sarcophilus harrisii	ENSSHAG00000010481	1 retrocopy	retro_shar_714,
Ictidomys tridecemlineatus	ENSSTOG00000025799	2 retrocopies	retro_itri_1371, retro_itri_645,