RetrogeneDB ID: retro_shar_704

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL858642.1:10251..10678(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRRF
• Ensembl ID: ENSSHAG00000012469
• Aliases: None
• Description: mitochondrial ribosome recycling factor [Source:HGNC Symbol;Acc:7234]

Sequence

>retro_shar_704
GTTTCAGAAGTTAGGCTAAGGATTACATACATAACATGGAATGACTATCAGCAATATGGGGCCTATCCAACTGTCTATCT
GACATTTTGCTACCAAGAACACCAAAGCCAAGGGCAAAGGACATCTCCAGCCCAGAGTCATCATTAATGCATCCTTGGTG
GAGGACACAATCCATCTGGAAGAGGTAGATGGGGAAATGAAGTCTGTGATTAAGAATAATTTCAATAAAAATCTCAATAT
AGGGACTTCTCCAGGGTCCCTGGATCACTTAACTGTGACAACTGATGATGGGAAGTTTGATCTAAATCAGATTGGCCAAA
TTTCCCTGAAATAGCCTCAGCTAATTTTACTAAACATGACCAATTTCCCAGAGTGTACTGCTGCAGCTATCAAGACCATA
AAAGAAAATAGAATGAAAGTGGAACCA

Alignment

ORF - retro_shar_704 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.07 %
• Parental protein coverage: 55.73 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VSGVRLNSANITWNDCQQCGAFPIVPIRHFATKKAKAKG-KGHSQPRVNINASLVEDIIRLEEVDGEMKS
          VS.VRL....ITWND.QQ.GA.P.V....F........G.KGH.QPRV.INASLVED.I.LEEVDGEMKS
Retrocopy VSEVRLRITYITWNDYQQYGAYPTVYLT-FCYQEHQSQG>KGHLQPRVIINASLVEDTIHLEEVDGEMKS

Parental  VVEALKDNFNKNLNIRTSPGSLDHITVTTADGKFALNQIGQISLKSPQLILVNMTNFPECTAAAIKAIRE
          V....K.NFNKNLNI.TSPGSLDH.TVTT.DGKF.LNQIGQISLK.PQLIL.NMTNFPECTAAAIK.I.E
Retrocopy VI---KNNFNKNLNIGTSPGSLDHLTVTTDDGKFDLNQIGQISLK*PQLILLNMTNFPECTAAAIKTIKE

Parental  SGMNLNP
          ..M...P
Retrocopy NRMKVEP

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_704 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 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000007351	1 retrocopy	retro_cpor_877,
Homo sapiens	ENSG00000148187	1 retrocopy	retro_hsap_4897,
Gorilla gorilla	ENSGGOG00000023499	1 retrocopy	retro_ggor_98,
Mus musculus	ENSMUSG00000026887	1 retrocopy	retro_mmus_340,
Nomascus leucogenys	ENSNLEG00000017177	1 retrocopy	retro_nleu_1263,
Pongo abelii	ENSPPYG00000019570	1 retrocopy	retro_pabe_80,
Pan troglodytes	ENSPTRG00000021324	1 retrocopy	retro_ptro_3265,
Rattus norvegicus	ENSRNOG00000025997	2 retrocopies	retro_rnor_1477, retro_rnor_2654,
Sarcophilus harrisii	ENSSHAG00000012469	2 retrocopies	retro_shar_610, retro_shar_704 ,
Tupaia belangeri	ENSTBEG00000016569	1 retrocopy	retro_tbel_4411,