RetrogeneDB ID: retro_shar_578

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL850399.1:48330..48957(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TAZ
• Ensembl ID: ENSSHAG00000001896
• Aliases: None
• Description: tafazzin [Source:HGNC Symbol;Acc:11577]

Sequence

>retro_shar_578
ATCATCGAGAATCGAGATCCTGGCACGCTGCAAATTATTGTCTCCAATCACCAGTCTTGTATGGATGACCCACACCTCTG
GGGGATCCTGAAACTCCACCACATCTGGAACTTGAAGCTGATGAGGTGGACCCAGTAGCTGCAAATATCTATTTTACCAA
GGAGCTGCATTCTCATTTCTTCAGTTTGGAAAAGTGTGTCCCTGTGTGCTGAGGGGATGGCGTCTACCAGAAAGTGATGC
ATTTTGCCCTGGAGAAACTCAACAACAGGGCCTGAGTCCACATCTTCCCTGAAGGAAAAGTGCACATGAGCCAGGAGTTT
CTTCGCTTTAAGTGGGAAATAGGGTGCCTGGTTGCTGAGTGTCACCTCAACCCCATTATCCTTCCACTCTGGCACATTGG
GATGAGTGATGTGCTTCCTAACGCTCCGCCCTATTTCTCCGAATTTGCCCAGAAAAGTCACCGTTCTCATTGGGAAGCCA
TTCAATGCCATGCCTGTTCTTGAACATCTCCAATCTGAGAATAAGTCAGCAGTGCAAATGCGCAAAGCCCTGACGAATTT
TATCCGGGATGAGTTTCAGAGCCTCAAAGCACCAGCAGAATCACTGCACAACCACTTCGAGCCCTCG

Alignment

ORF - retro_shar_578 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.46 %
• Parental protein coverage: 79.77 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LIENRDPGTPLITVSNHQSCMDDPHLWGILKLRHIWNLRLMRWT-PAAADICFTKELHSHFFSLGKCVPV
          .IENRDPGT..I.VSNHQSCMDDPHLWGILKL.HIWNL.LMRWT.P.AA.I.FTKELHSHFFSL.KCVPV
Retrocopy IIENRDPGTLQIIVSNHQSCMDDPHLWGILKLHHIWNLKLMRWT<PVAANIYFTKELHSHFFSLEKCVPV

Parental  CRGDGVYQRGMDFILEKLNNGDWVHIFPEGKVNMSQEFLRFKWGIGRLVAECHLNPIILPLWHIGMSDVL
          C.GDGVYQ..M.F.LEKLNN...VHIFPEGKV.MSQEFLRFKW.IG.LVAECHLNPIILPLWHIGMSDVL
Retrocopy C*GDGVYQKVMHFALEKLNNRA*VHIFPEGKVHMSQEFLRFKWEIGCLVAECHLNPIILPLWHIGMSDVL

Parental  PNAPPYFPRFGQ-KITVLIGKPFSAMPVLERLRSENKSAVEMRKALTDFIQDEFQSLKAQAESLHSHFQP
          PNAPPYF..F.Q.K.TVLIGKPF.AMPVLE.L.SENKSAV.MRKALT.FI.DEFQSLKA.AESLH.HF.P
Retrocopy PNAPPYFSEFAQ>KVTVLIGKPFNAMPVLEHLQSENKSAVQMRKALTNFIRDEFQSLKAPAESLHNHFEP

Parental  A
          .
Retrocopy S

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_578 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 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000007456	1 retrocopy	retro_btau_1427,
Macropus eugenii	ENSMEUG00000012657	2 retrocopies	retro_meug_325, retro_meug_459,
Sarcophilus harrisii	ENSSHAG00000001896	1 retrocopy	retro_shar_578 ,