RetrogeneDB ID: retro_shar_198

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL834625.1:2475433..2475851(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NDUFA8
• Ensembl ID: ENSSHAG00000011368
• Aliases: None
• Description: NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 8, 19kDa [Source:HGNC Symbol;Acc:7692]

Sequence

>retro_shar_198
ATGCCAGGTGTGGTGGAGCTGCCTACCTTGGATGACCTCAGTGTTCAGGAGGTGAATGTCTGTTCTGTTAAGCTAAAAAC
TGCAGCCCATCAGTAAGGCACACAGTGTGATAAAGTCAAAAAGAATTTACGCTTTGCCACTGGGAAGAGAAGGATCCAAG
GTGATATTTAAGCAAAGGAAGATTTGTCAATCAGTGTGCTCTGGATTTCTTCAGGAGTATAAAGAAACACTGCGCTGATC
CCTTTATTGAGTGTTGATCCTGTATTAATTATTCTGAGCTTTAAAAGCTTTGCCAATATCACAAGATACAGGCAAAATTT
GACAAAAGTGTGCTGAACAAACCAGACTGGGTTTATTCTGACTTGGAAGAAATGTCAAACATTACAAAATAAGCACAACC
CAATCGCTACCTGAGAAT

Alignment

ORF - retro_shar_198 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.75 %
• Parental protein coverage: 81.4 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MPGVVELPTLVELDIRSVNVNSAVLKAAAHHYGSQCDKINK-KFMLCRWEEKDPRRCLKEGKLVNECALH
          MPGVVELPTL..L....VNV.S..LK.AAH..G.QCDK..K..F.LC.WEEKDPR..L..G..VN.CAL.
Retrocopy MPGVVELPTLDDLSVQEVNVCSVKLKTAAHQ*GTQCDKVKK<EFTLCHWEEKDPR*YLSKGRFVNQCALD

Parental  FFRNIKTHCAEPFTEYWTCVDYSELQELRRCRKEQAKFDDCVLKKLGWVRPDLGELSKTT-KVHTTRPEP
          FFR.IK.HCA.PF.E...C..YSEL..L....K.QAKFD..VL.K..WV..DL.E.S..T.K..TT...P
Retrocopy FFRSIKKHCADPFIEC*SCINYSEL*KLCQYHKIQAKFDKSVLNKPDWVYSDLEEMSNIT<KISTTQSLP

Parental  EN
          EN
Retrocopy EN

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_198 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Otolemur garnettii	ENSOGAG00000015093	1 retrocopy	retro_ogar_1487,
Rattus norvegicus	ENSRNOG00000005668	1 retrocopy	retro_rnor_2583,
Sarcophilus harrisii	ENSSHAG00000011368	1 retrocopy	retro_shar_198 ,
Sus scrofa	ENSSSCG00000005528	1 retrocopy	retro_sscr_477,