RetrogeneDB ID: retro_shar_367

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL841498.1:1925593..1926046(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPL24
• Ensembl ID: ENSSHAG00000015996
• Aliases: None
• Description: mitochondrial ribosomal protein L24 [Source:HGNC Symbol;Acc:14037]

Sequence

>retro_shar_367
TTGCTAGCCCAGGCAGCTAAGGCCAACTTGTCTCATAACTACCCCTATGGAATGAGCCTACCTGGATCTATGGCGGACAA
GAGGAGAAACCCAACCTGGAACAGATAGCATTCAATCCTTATCGAGCCTATACCTGAGGATTCCTGGAATGTGTTTTGTG
GGGTACAATTGAGATCCTGGAGAGTGAAGATGCTGGGAAGCAGGTCAAGGAAGTTCAGATCATCAGGAAGAAGAACTAGG
TTGTCTTGGAACGACTGAACACAAATTTCTGATATGTTGGCAGGAGCAAGAATTAGTGGGGGACCAGGCTCCCCCAGTGA
TTTCCCCAATTTTCCACCAGGTCAAGCTTGTGTCTGTCACTGACAGGAAGCCAACCAGACTGGAATGGAGGTTACAGAGG
AAAGCAAGCATGTACAAGTCTCCCTGAGAGCAGGGGGAACCATTCAAGTTCCC

Alignment

ORF - retro_shar_367 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.35 %
• Parental protein coverage: 70.37 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  LLAMAVKADLPRNYRYGMSRPGTMAEKKRNPPWKRPRPVLVEPIPEDSWNVYCG-DMVEILEGKDAGKQG
          LLA.A.KA.L..NY.YGMS.PG.MA.K.RNP.W.R....L.EPIPEDSWNV.CG....EILE..DAGKQ.
Retrocopy LLAQAAKANLSHNYPYGMSLPGSMADKRRNPTWNR*HSILIEPIPEDSWNVFCG<GTIEILESEDAGKQV

Parental  KVVQIIRERNWVILEGLNTHFRIVGNYKDFRGTMVPSEAPL-LFRQVKLVDPTDRKPTEVEWRF-TEEGE
          K.VQIIR..N.V.LE.LNT.F..VG..K...GT..P...P...F.QVKLV..TDRKPT..EWR..TEE..
Retrocopy KEVQIIRKKN*VVLERLNTNF*YVGRSKN*WGTRLPQ*FPQ<IFHQVKLVSVTDRKPTRLEWRL<TEESK

Parental  RVRVSLRTGRIIPKP
          .V.VSLR.G..I..P
Retrocopy HVQVSLRAGGTIQVP

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_367 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Sarcophilus harrisii	ENSSHAG00000015996	1 retrocopy	retro_shar_367 ,