RetrogeneDB ID: retro_shar_832

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL867714.1:9717..10145(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: UBE2C
• Ensembl ID: ENSSHAG00000002117
• Aliases: None
• Description: ubiquitin-conjugating enzyme E2C [Source:HGNC Symbol;Acc:15937]

Sequence

>retro_shar_832
TTGATGACCCTAATGATGTCTGGAGACAATGGAATTTTTGCCTTCTCAGAATCAGACAGTCTCTTCAAATGGATTGGGAC
CATCCATTGGGCAGCTGGGACAGTATATGAAGACCTAAGGTACAAACTGTCCCTGGAGTTTCCCAGAGGTTACTCATATA
ATGCTCCCACTGTGAAATTTGTCACCACCACTTGTTACCATCTTAATGTGGATACCCAAGGCAATATCTGTGTGGACATC
CTAAAGGACAAGTGGTTAGCTCTGTATGATGTCAGGACCATCCTACTGTCTATTCAGAGCCTGCTGGGAGAACCCAACAT
CAAGAGCCCACTGAATACACACGCTGCTGAACTTTTTGGACAAACCCCACAGCCTTTAAAAAGTACCTTCTGAAAATCTA
CATGAAGCAGGTGACTAGCCAAGAGCCC

Alignment

ORF - retro_shar_832 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.56 %
• Parental protein coverage: 71.94 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ILPLQMSGDKGISAFPESDNLFKWVGTIHGAAGTVYEDLRYKLSLEFPSGYPYNAPTVKFV-TPCYHPNV
          ...L.MSGD.GI.AF.ESD.LFKW.GTIH.AAGTVYEDLRYKLSLEFP.GY.YNAPTVKFV.T.CYH.NV
Retrocopy LMTLMMSGDNGIFAFSESDSLFKWIGTIHWAAGTVYEDLRYKLSLEFPRGYSYNAPTVKFVTTTCYHLNV

Parental  DTQGNICLDILKDKWSALYDVRTILLSIQSLLGEPNIDSPLNTHAAELW-TNPTAFK-KYLLETYMKQVT
          DTQGNIC.DILKDKW.ALYDVRTILLSIQSLLGEPNI.SPLNTHAAEL....P...K.KYLL..YMKQVT
Retrocopy DTQGNICVDILKDKWLALYDVRTILLSIQSLLGEPNIKSPLNTHAAELFGQTPQPLK<KYLLKIYMKQVT

Parental  SQEP
          SQEP
Retrocopy SQEP

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_832 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 8 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000005054	1 retrocopy	retro_chof_902,
Cavia porcellus	ENSCPOG00000014102	2 retrocopies	retro_cpor_1007, retro_cpor_211,
Loxodonta africana	ENSLAFG00000003164	1 retrocopy	retro_lafr_73,
Macaca mulatta	ENSMMUG00000021023	4 retrocopies	retro_mmul_1345, retro_mmul_170, retro_mmul_1951, retro_mmul_777,
Mustela putorius furo	ENSMPUG00000017619	2 retrocopies	retro_mputfur_103, retro_mputfur_189,
Otolemur garnettii	ENSOGAG00000004989	3 retrocopies	retro_ogar_2347, retro_ogar_249, retro_ogar_3067,
Pan troglodytes	ENSPTRG00000013564	1 retrocopy	retro_ptro_38,
Sarcophilus harrisii	ENSSHAG00000002117	1 retrocopy	retro_shar_832 ,