RetrogeneDB ID: retro_shar_240

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL834746.1:716066..716371(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: THOC7
• Ensembl ID: ENSSHAG00000011615
• Aliases: None
• Description: THO complex 7 homolog (Drosophila) [Source:HGNC Symbol;Acc:29874]

Sequence

>retro_shar_240
GACATAGAAAATAGCAAAACTGAAGCATCTTTTAAAAATGCTGAGTGCAAAAAGCAGTTTCTTAAAGCAAAATGAACAGA
AAAAAGTGAGTATGATGCTTTAGCCAAAGTGATACAACACTATCCAAACAGTCATGCAACTTTAAAGAAACTAGATGCTT
GGAGGGAAAGAATTACTTCATCTTTCGCATAAAAAAGCAATGTTGAAAATAAGCTGGAATTAAGACAAAAGCAGTTTCAA
AGTCTTAGTACTATCCTCAAAAACTTCAGCAAGCACTAGAAAATGATGAAAAACGCTCAGAAGTT

Alignment

ORF - retro_shar_240 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.49 %
• Parental protein coverage: 50.98 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  DIENSIAGAHEKIAECKKQILQAKRIRKNRQEYDALAKVIQHHPDRHETLKELDAL-GKELQHLSHI-KE
          DIENS...A..K.AECKKQ.L.AK...K...EYDALAKVIQH.P..H.TLK.LDA..GKEL.HLSH..K.
Retrocopy DIENSKTEASFKNAECKKQFLKAK*TEKS--EYDALAKVIQHYPNSHATLKKLDAW>GKELLHLSHK<KS

Parental  NVEDKLELRRKQFHVLLSTI-HELQQTLENDEKLSEV
          NVE.KLELR.KQF..L.......LQQ.LENDEK.SEV
Retrocopy NVENKLELRQKQFQSLSTIL<QKLQQALENDEKRSEV

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_240 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 10 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000034899	2 retrocopies	retro_cjac_354, retro_cjac_398,
Echinops telfairi	ENSETEG00000015076	3 retrocopies	retro_etel_1093, retro_etel_1858, retro_etel_85,
Macropus eugenii	ENSMEUG00000006342	4 retrocopies	retro_meug_1481, retro_meug_1524, retro_meug_1599, retro_meug_1861,
Myotis lucifugus	ENSMLUG00000012060	1 retrocopy	retro_mluc_369,
Monodelphis domestica	ENSMODG00000003009	1 retrocopy	retro_mdom_315,
Oryctolagus cuniculus	ENSOCUG00000021860	1 retrocopy	retro_ocun_124,
Sorex araneus	ENSSARG00000013894	1 retrocopy	retro_sara_41,
Sarcophilus harrisii	ENSSHAG00000011615	1 retrocopy	retro_shar_240 ,
Tupaia belangeri	ENSTBEG00000007069	1 retrocopy	retro_tbel_49,
Tursiops truncatus	ENSTTRG00000013618	3 retrocopies	retro_ttru_1365, retro_ttru_23, retro_ttru_957,