RetrogeneDB ID: retro_shar_318

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL841308.1:778372..778815(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• 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]

Sequence

>retro_shar_318
TGTGACTTCATAGAAGATCAGGCAGAGGAGTTCAAGGCGGTTTTCCAGCTGTTTGACCCAACAAGAGATGGAAAGATCTT
ATACAGTCGGTGTGGGGTCGTGATATGAGCCCTGGGCCAGAGCCCCACCAATGCTGAGGTGCTCAGTGTTTGAGGGAATC
CCAAGACTGGTGAGATGAATGTGAAGGTGCTGGACTTTGAACATTTCCTGCAAATGCTGCAAACTGTAGCAAAGAATAAG
GACCAGGGCACATTTGAGGACTATGTTGAGGGGCTTTGGGTGTTTGATAAGAAAGGGACTGGTACAGTCATGGGAGCTGA
AATATGACACATCCTCAGTACCCTGGGTGAGAAGATGACAGAAGTAGAAGTGTTAGGGGAGGGCATGAGGACAGCAAAGG
TTGTATCAGCTATGAAGAGCTAGTTTGGGTGGTGCTAAATGGC

Alignment

ORF - retro_shar_318 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.15 %
• Parental protein coverage: 99.34 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  CDFTEDQTAEFKEAFQLFDRTGDGKILYSQCGDVMRALGQNPTNAEVLKVLGNPKSDEMNVKVLDFEHFL
          CDF.EDQ..EFK..FQLFD.T.DGKILYS.CG.V..ALGQ.PTNAEVL.V.GNPK..EMNVKVLDFEHFL
Retrocopy CDFIEDQAEEFKAVFQLFDPTRDGKILYSRCGVVI*ALGQSPTNAEVLSV*GNPKTGEMNVKVLDFEHFL

Parental  PMLQTVAKNKDQGTYEDYVEGLRVFDKEGNGTVMGAEIRHVLITLGEKMTEEEVEVLVAG-HEDSNGCIN
          .MLQTVAKNKDQGT.EDYVEGL.VFDK.G.GTVMGAEI.H.L.TLGEKMT..EVEVL..G.HEDS.GCI.
Retrocopy QMLQTVAKNKDQGTFEDYVEGLWVFDKKGTGTVMGAEI*HILSTLGEKMT--EVEVLGEG<HEDSKGCIS

Parental  YEELVRMVLNG
          YEELV..VLNG
Retrocopy YEELVWVVLNG

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_318 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 13 parental genes, and 41 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000092841	2 retrocopies	retro_hsap_1786, retro_hsap_2533,
Macropus eugenii	ENSMEUG00000001272	1 retrocopy	retro_meug_2172,
Macaca mulatta	ENSMMUG00000031838	6 retrocopies	retro_mmul_1633, retro_mmul_1663, retro_mmul_211, retro_mmul_2221, retro_mmul_2410, retro_mmul_96,
Mus musculus	ENSMUSG00000090841	7 retrocopies	retro_mmus_1281, retro_mmus_1504, retro_mmus_2328, retro_mmus_3231, retro_mmus_3333, retro_mmus_3358, retro_mmus_434,
Nomascus leucogenys	ENSNLEG00000000205	2 retrocopies	retro_nleu_2736, retro_nleu_779,
Oryctolagus cuniculus	ENSOCUG00000017371	1 retrocopy	retro_ocun_1300,
Otolemur garnettii	ENSOGAG00000034596	1 retrocopy	retro_ogar_2549,
Pongo abelii	ENSPPYG00000004647	3 retrocopies	retro_pabe_1467, retro_pabe_1864, retro_pabe_538,
Pan troglodytes	ENSPTRG00000005080	2 retrocopies	retro_ptro_1196, retro_ptro_1476,
Sarcophilus harrisii	ENSSHAG00000004472	6 retrocopies	retro_shar_137, retro_shar_318 , retro_shar_452, retro_shar_510, retro_shar_719, retro_shar_765,
Sus scrofa	ENSSSCG00000025467	1 retrocopy	retro_sscr_829,
Ictidomys tridecemlineatus	ENSSTOG00000023318	1 retrocopy	retro_itri_1478,
Tupaia belangeri	ENSTBEG00000000485	8 retrocopies	retro_tbel_130, retro_tbel_1715, retro_tbel_2980, retro_tbel_332, retro_tbel_3515, retro_tbel_3545, retro_tbel_3707, retro_tbel_4075,