RetrogeneDB ID: retro_shar_162

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL834503.1:443654..444244(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MTX2
• Ensembl ID: ENSSHAG00000016381
• Aliases: None
• Description: metaxin 2 [Source:HGNC Symbol;Acc:7506]

Sequence

>retro_shar_162
ATTACCCTCCTGGCCCAGAGAGTAGTCTGCTAGGTCATAGCTACAAAACTTTGGCCTGAAGATGCTATACTTGATCAGCA
TCTGAAAGAGAATAAATTTTGCTTTCTGATAATGCTTCTTCTCTTGCTGTTCAGGCCTTTTTGCAAATGTGCTAGCTCTC
CATCAAAGTGCTTTATAGAGTAATTGCTGAATATATATCTCCATCTGATAAAGTACTTTTTATTCTTATGGGAAAGCAAG
TGGTACCAGAACTTGGTCCAATTAGTATAATTCATAAAAGCCAAGTGCCATTTTCTTAGCAATGGATTGGATGAAATCCA
AAAAGCAGAAATGAAAACCTACATGGAATTAGTGAATAATATGCTATTGACAGCACAGTTGTATCTTCAGTGTTGTGAGG
AAGTTACAGTGAGGGATTTCACTCACTCTCAATATGGATTCCTTATCCTTGGTCTCTGAACTTCATCTTGACTTATCAAA
AACAATAGGAAGTCTAATGTAAGAAGCGTGGGATTGAGATTGGAAGAGATAAGAAGACTCTGGATAAGGTCTTAGAAGAT
GAAGACTAGTATTGTCAAACTCTTTCTCAA

Alignment

ORF - retro_shar_162 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.5 %
• Parental protein coverage: 76.47 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MSLVAEALVSQVAATEPWPEDATLYQQLKGEQ-ILLSDNASSLAVQAFLQMCELPIKVVCRANAEYMSPS
          ..L.A...V..V.AT..WPEDA.L.Q.LK....ILLSDNASSLAVQAFLQMC.L.IKV..R..AEY.SPS
Retrocopy ITLLAQRVVC*VIATKLWPEDAILDQHLKENK<ILLSDNASSLAVQAFLQMC*LSIKVLYRVIAEYISPS

Parental  GKVPFIHVGNQVVSELGPI-VQFVKAKGHSLSDGLDEVQKAEMKAYMELVNNMLLTAELYLQWCDEATVG
          .KV.FI..G.QVV.ELGPI.V.F.KAK.H.LS.GLDE.QKAEMK.YMELVNNMLLTA.LYLQ.C.E.TV.
Retrocopy DKVLFILMGKQVVPELGPI>V*FIKAKCHFLSNGLDEIQKAEMKTYMELVNNMLLTAQLYLQCCEEVTVR

Parental  EITHSRYGF-PYPWPLNHILAYQKQWEV--KRKMKAIGWGNKTLDQVLEDVDQCCQALSQ
          ..THS.YGF.PYPW.LN.IL.YQKQ.EV..K.....IG...KTLD.VLED.D..CQ.LSQ
Retrocopy DFTHSQYGF<PYPWSLNFILTYQKQ*EV*CKKRGIEIGRDKKTLDKVLEDED*YCQTLSQ

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_162 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 8 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000009655	1 retrocopy	retro_chof_2429,
Cavia porcellus	ENSCPOG00000011099	1 retrocopy	retro_cpor_218,
Dipodomys ordii	ENSDORG00000003848	2 retrocopies	retro_dord_159, retro_dord_192,
Homo sapiens	ENSG00000128654	1 retrocopy	retro_hsap_3780,
Macaca mulatta	ENSMMUG00000010185	1 retrocopy	retro_mmul_1643,
Nomascus leucogenys	ENSNLEG00000006020	1 retrocopy	retro_nleu_1117,
Pan troglodytes	ENSPTRG00000012674	1 retrocopy	retro_ptro_2561,
Sarcophilus harrisii	ENSSHAG00000016381	1 retrocopy	retro_shar_162 ,