RetrogeneDB ID: retro_shar_612

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL856756.1:729494..730240(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: STK11
• Ensembl ID: ENSSHAG00000007173
• Aliases: None
• Description: serine/threonine kinase 11 [Source:HGNC Symbol;Acc:11389]

Sequence

>retro_shar_612
TATGCAGTGATGGAGTACTGAGTGTGAAGAGTGTAGAAAATGCTGGACAGCATTCCAGAGAAAAGATTTCCTGTCTTTCG
GGCTCATGGGTACTTTTGCCAGCTGATAGATGGGTTAGAATATTTGAATAGCCAAGTAATTGTTCATAAAGATATAAAAC
TAGGGAAACTGTTGCTTATAATCAATGAGACACTAAAAATATCTGACTTAGGAGTAGCAAAAGCATTGCATTCTTTTGCA
GAAGATGATGCATGTTGAACGAGCCATGTATCATTTACATCCCAGTCACCAAAATGGCCAATGGCTTATACACCTTTTCA
GTCTTTAAATGAACATTTGGTTGGCTAGGGTCATGCTTTACAATGCCACAACAGGTCTTTATTCCTTTAAAGGGTACAAT
ATCCATAAATTATTTGAAAATGTTGAGAAAGGAGACCACAATTCCAGGGGATTGTAGTCCTCCACTTTCTGATATGCTGG
AAGGTATTTTGAATATGAACCATTAGGAGATTTTTTCAATACAGCAGCTATGGCAGCACAACCACTTTCATAAGAAATAA
TACCAGGCAGAGGTTCTGGTCTCCATTTTTCCTCACCCAGAAATCAAGGACATGTGGCAAAGTATGACAGTGGTGCCTTA
TCTGGAGGATCTGTTTGGCTGCAATAAGAAAAAAAAAAAAGGCAATGACCTCTTTGGCATTGAGAATAAAATCATTTACA
CTCCAGATTTCATAGTATGAGGACAG

Alignment

ORF - retro_shar_612 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.96 %
• Parental protein coverage: 99.21 %
• Number of stop codons detected: 7
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  YMVMEYCVCGMQEMLDSVPEKRFPVFQAHGYFCQLIDGLEYLHSQGIVHKDIKPGNLLLTTNGTLKISDL
          Y.VMEY.V.....MLDS.PEKRFPVF.AHGYFCQLIDGLEYL.SQ.IVHKDIK.G.LLL..N.TLKISDL
Retrocopy YAVMEY*V*RV*KMLDSIPEKRFPVFRAHGYFCQLIDGLEYLNSQVIVHKDIKLGKLLLIINETLKISDL

Parental  GVAEALHPFAEDDTCRTSQGSPAFQPPE-IANGLDTFSGFK-VDIWSAGVTLSRYNITTGLY-PFEGDNI
          GVA.ALH.FAEDD.C.TS..S...Q.P...ANGL.TFS.FK...IW.A.V.L..YN.TTGLY.P..G...
Retrocopy GVAKALHSFAEDDAC*TSHVSFTSQSPK<MANGLYTFSVFK<MNIWLARVML--YNATTGLY>PLKGTIS

Parental  YKLFENIGKGDYTIPGDCGPPLSDLLKGMLEYEPSKRFSIQQIRQHNWFRKKHPQAEALVPIPPSPETKD
          ........K...TIPGDC.PPLSD.L.G.L.......FSIQQ..QHN.F.KK..QAE.LV.I.P.PE.KD
Retrocopy INYLKMLRK-ETTIPGDCSPPLSDMLEGILNMNH*EIFSIQQLWQHNHFHKK*YQAEVLVSIFPHPEIKD

Parental  RWRSMTVVPYLEDLHGYNE--EEDDDLFDIEDDIIYTQDFTVPGK
          .W.SMTVVPYLEDL.G.N.......DLF.IE..IIYT.DF.V.G.
Retrocopy MWQSMTVVPYLEDLFGCNKXXXXGNDLFGIENKIIYTPDFIV*GQ

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_612 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 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Loxodonta africana	ENSLAFG00000011567	1 retrocopy	retro_lafr_32,
Procavia capensis	ENSPCAG00000008434	1 retrocopy	retro_pcap_190,
Sarcophilus harrisii	ENSSHAG00000007173	1 retrocopy	retro_shar_612 ,