RetrogeneDB ID: retro_shar_610

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL856751.1:2331202..2331603(-)
• 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_610
CCAACTGTGCCAATCTGACATTTTGCTACCAAGAGAGCCAATGCCAAAGATAAAGGACATTACCAATCTTGAGTCAACAT
TAATGCATCCTTGGTAGAGCACATAATCCATCTGGAACAGGAAGACATGGAAATGAAGTCTGTGGTTTTAGAAGCCCTTG
GGATAATTTCTACAAAAATCTCAATGTAAGGTCCTTTCCTGGATCCCTGGATCACATACCTGTAACAATTGGTGATGGAA
AGTTTGCTTTAAATGAGATCAGCCAAATCTCCCTGAAATTTCCTCAGCTGAATATAGTAAACACCACCAATTTCCTAGAT
TATACAGCTGCAGCTATCAAGGCCATAAGAGAAAATGGAATTAATCTGAACCCTGAAGTTGATGGGTCAATTCTTGAAGT
T

Alignment

ORF - retro_shar_610 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.85 %
• Parental protein coverage: 50.76 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PIVPIRHFATKKAKAKGKGHSQPRVNINASLVEDIIRLEEVDGEMKSVV-EALK-DNFNKNLNIRTSPGS
          P.VPI.HFATK.A.AK.KGH.Q..VNINASLVE.II.LE..D.EMKSVV.EAL..DNF.KNLN.R..PGS
Retrocopy PTVPI*HFATKRANAKDKGHYQS*VNINASLVEHIIHLEQEDMEMKSVVLEALG<DNFYKNLNVRSFPGS

Parental  LDHITVTTADGKFALNQIGQISLKSPQLILVNMTNFPECTAAAIKAIRESGMNLNPEVDGTVIRV
          LDHI.VT..DGKFALN.I.QISLK.PQL..VN.TNF...TAAAIKAIRE.G.NLNPEVDG....V
Retrocopy LDHIPVTIGDGKFALNEISQISLKFPQLNIVNTTNFLDYTAAAIKAIRENGINLNPEVDGSILEV

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_610 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,