RetrogeneDB ID: retro_shar_411

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL841711.1:61863..62302(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPL23
• Ensembl ID: ENSSHAG00000002716
• Aliases: None
• Description: mitochondrial ribosomal protein L23 [Source:HGNC Symbol;Acc:10322]

Sequence

>retro_shar_411
CATACCCTGTGCCAGGCAGGAATCCCCCAGCTGTGCATCTATCAGACCAACTTCTTCATCTAGTTGGCGTGAACTGGCAC
AAGCCAGCCAAAGAACACTGTGCAATTCCAGGTCCCAATGGAGATGACCAGGGTCAACCCCAAGAATTATCTGCAGAGCA
TCTATAATGTGTTGGTGGCTGCAATCAGAATTGGGATATAGCATGGGTCCAACAAGAAGCAGGATCATAGAAATGTGTAC
ATCAAGCAACCAGATTACAAGGTCACCTCCATCCAGCTGGTTTACTGACAGGCCTTCAAGTTCCCAGATCAGTTTCCTGA
GAAAGAAACAAGTCCTGAATTCAGCTCCTTTGAAAAAATCCAAAATCAGTTTATAGATGATGAAAGAAAAGGCAGAAAGA
CAACCCCAGCATGGGGAAGTCCCTGACAGGTTTGGCTTG

Alignment

ORF - retro_shar_411 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.44 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  YPLYQAGNPQLRIFRTNFFIQLVRPGTVQPEDTVQFRIPMEMTRVDLKNYLQSIYNVPVAAVRTRVQHGS
          ..L.QAG.PQL.I..TNFFI.L...GT.QP..TVQF..PMEMTRV..KNYLQSIYNV.VAA.R....HGS
Retrocopy HTLCQAGIPQLCIYQTNFFI*LA*TGTSQPKNTVQFQVPMEMTRVNPKNYLQSIYNVLVAAIRIGI*HGS

Parental  NKKRDHRNVRIKQPDYKVAYVQLAYGQTFTFPDLFPEKETSPDTVSFEGIQNEFMDKER-ERQKGD-PRR
          NKK.DHRNV.IKQPDYKV...QL.Y.Q.F.FPD.FPEKETSP...SFE.IQN.F.D.ER..RQK...P..
Retrocopy NKKQDHRNVYIKQPDYKVTSIQLVY*QAFKFPDQFPEKETSPEFSSFEKIQNQFIDDER<KRQKDN<PQH

Parental  GGVPDWFGL
          G.VPD.FGL
Retrocopy GEVPDRFGL

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_411 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 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000000103	1 retrocopy	retro_btau_329,
Macaca mulatta	ENSMMUG00000031268	1 retrocopy	retro_mmul_1226,
Mus musculus	ENSMUSG00000037772	1 retrocopy	retro_mmus_2046,
Nomascus leucogenys	ENSNLEG00000026950	1 retrocopy	retro_nleu_1043,
Otolemur garnettii	ENSOGAG00000029988	1 retrocopy	retro_ogar_372,
Sarcophilus harrisii	ENSSHAG00000002716	1 retrocopy	retro_shar_411 ,