RetrogeneDB ID: retro_shar_639

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL856894.1:223034..223311(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NDUFB2
• Ensembl ID: ENSSHAG00000015924
• Aliases: None
• Description: NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 2, 8kDa [Source:HGNC Symbol;Acc:7697]

Sequence

>retro_shar_639
GGCTGGCACTTCCTGGAGGGTCCAAGTGAGCAGACTACTGGTTGCACCATAAGAGGAGTATGACATGCTGGAAATGGTGT
ACACATTAAACCCCGCTACCGGCAGTATCCCCAACTGACAAAGTCTCAGGTGTTCCAAGCTGAGTTGTTAGTGCTACAAT
GTGGTTTTGGATTCTCTGCTGATTTTGGCATGACTTGGATGCTGTATTTGTCATTTCCTATATCCAGATCCTTTTAAATG
GACAGATGAAGAATTGGGTATCCCCCCTGATGAAGAG

Alignment

ORF - retro_shar_639 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.67 %
• Parental protein coverage: 92.16 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  GPFFREGGRRFLEGPSERTTDYAIGGVRHAQIRYRQYPQLTKSQVFQAELL-SATMWFWILWQFWHDSDA
          G..F.EG......G...R....A..GV.H...RYRQYPQLTKSQVFQAELL.SATMWFWIL..FWHD.DA
Retrocopy GWHFLEGPSEQTTGCTIRGV*HAGNGV-HIKPRYRQYPQLTKSQVFQAELL<SATMWFWILC*FWHDLDA

Parental  V-LGHFPYPDPSQWTDEELGIPPDEE
          V...HF.YPDP..WTDEELGIPPDEE
Retrocopy V<ICHFLYPDPFKWTDEELGIPPDEE

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_639 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.

---

Parental genes homology:

Parental genes homology involve 12 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000011176	1 retrocopy	retro_acar_138,
Canis familiaris	ENSCAFG00000003930	3 retrocopies	retro_cfam_1673, retro_cfam_2184, retro_cfam_958,
Equus caballus	ENSECAG00000000877	1 retrocopy	retro_ecab_587,
Mustela putorius furo	ENSMPUG00000003423	3 retrocopies	retro_mputfur_132, retro_mputfur_1443, retro_mputfur_207,
Mus musculus	ENSMUSG00000002416	1 retrocopy	retro_mmus_1881,
Otolemur garnettii	ENSOGAG00000009644	1 retrocopy	retro_ogar_1405,
Ochotona princeps	ENSOPRG00000013184	2 retrocopies	retro_opri_1201, retro_opri_143,
Rattus norvegicus	ENSRNOG00000026616	2 retrocopies	retro_rnor_1153, retro_rnor_2449,
Sarcophilus harrisii	ENSSHAG00000015924	1 retrocopy	retro_shar_639 ,
Sus scrofa	ENSSSCG00000016495	1 retrocopy	retro_sscr_1149,
Ictidomys tridecemlineatus	ENSSTOG00000002566	1 retrocopy	retro_itri_1100,
Tursiops truncatus	ENSTTRG00000000547	2 retrocopies	retro_ttru_1567, retro_ttru_1910,