RetrogeneDB ID:

retro_shar_452

Retrocopy
location
Organism:Tasmanian devil (Sarcophilus harrisii)
Coordinates:GL849535.1:303410..303853(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:MYL6
Ensembl ID:ENSSHAG00000004472
Aliases:None
Description:myosin, light chain 6, alkali, smooth muscle and non-muscle [Source:HGNC Symbol;Acc:7587]


Retrocopy-Parental alignment summary:






>retro_shar_452
TGTGACTTCACGAAAGATCAGATAACAGAGTTTGAGGCATTCCAGATGTTTGACTGAATAGGAGATGGAAAGATCTTATA
CAGCCAGCCTGGGGATGTGATGTAAACCCTGGGCCAAAATCCTACCAATGGTAAAGTGCTCAAAGTCTTTGGGGATCCCA
AGAGTGATGAGATGAGTGTGAAGGTGCTAGACTTTGAATCCTTTCTGCAATGCTGCAGACTGTAGCAAAAAATAAGGCCT
AGAACCTCTATAAAGACTTTGTAGAAGGGCTCTGGGTGTTTGATAGATAAGGGAATGGTACTGTCAACAGAAATGAAATA
CATTATATCCTCATCATCCTAGGTGAAAAGATGACAGAGGAAGAAATGGAAGTGTTGATGGGAGGGCATGATAACAGCAG
TGGTTATGTCATTTATGAAGACCTAGTCTAAATGGTGCTTAAT

ORF - retro_shar_452 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 70. %
Parental protein coverage: 98.68 %
Number of stop codons detected: 5
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalCDFTEDQTAEFKEAFQLFDRTGDGKILYSQCGDVMRALGQNPTNAEVLKVLGNPKSDEMNVKVLDFEHFL
CDFT.DQ..EF.EAFQ.FD..GDGKILYSQ.GDVM..LGQNPTN..VLKV.G.PKSDEM.VKVLDFE.FL
RetrocopyCDFTKDQITEF-EAFQMFD*IGDGKILYSQPGDVM*TLGQNPTNGKVLKVFGDPKSDEMSVKVLDFESFL
ParentalP-MLQTVAKNKDQGTYEDYVEGLRVFDKEGNGTVMGAEIRHVLITLGEKMTEEEVEVLVAGHEDSNGCIN
..MLQTVAKNK....Y.D.VEGL.VFD..GNGTV...EI...LI.LGEKMTEEE.EVL..GH..S.G...
RetrocopyQ<MLQTVAKNKA*NLYKDFVEGLWVFDR*GNGTVNRNEIHYILIILGEKMTEEEMEVLMGGHDNSSGYVI
ParentalYEELVRMVLN
YE.LV.MVLN
RetrocopyYEDLV*MVLN

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






Sarcophilus harrisii was not studied using RNA-Seq expression data.
Sarcophilus harrisii was not studied using ChIP-Seq data.
Sarcophilus harrisii was not studied using EST data.
Sarcophilus harrisii was not studied using FANTOM5 data.
retro_shar_452 was not experimentally validated.

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.

Parental genes homology:
Parental genes homology involve 13 parental genes, and 41 retrocopies.

Species Parental gene accession Retrocopies number
Homo sapiens ENSG000000928412 retrocopies
Macropus eugenii ENSMEUG000000012721 retrocopy
Macaca mulatta ENSMMUG000000318386 retrocopies
Mus musculus ENSMUSG000000908417 retrocopies
Nomascus leucogenys ENSNLEG000000002052 retrocopies
Oryctolagus cuniculus ENSOCUG000000173711 retrocopy
Otolemur garnettii ENSOGAG000000345961 retrocopy
Pongo abelii ENSPPYG000000046473 retrocopies
Pan troglodytes ENSPTRG000000050802 retrocopies
Sarcophilus harrisii ENSSHAG00000004472 6 retrocopies
Sus scrofa ENSSSCG000000254671 retrocopy
Ictidomys tridecemlineatus ENSSTOG000000233181 retrocopy
Tupaia belangeri ENSTBEG000000004858 retrocopies



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