RetrogeneDB ID: retro_shar_774

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL864774.1:3311734..3312395(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DHPS
• Ensembl ID: ENSSHAG00000015920
• Aliases: None
• Description: deoxyhypusine synthase [Source:HGNC Symbol;Acc:2869]

Sequence

>retro_shar_774
TATCAGGGTGAATTTATATTGAAGGGGTAATACCTGAGGTAAATATTATTATTAGGACTGCAAACCTGCTTGTTCCTAAT
GACAGTTGCTACAAGTTTGAGGGCTGACTGATATCATTTCTGGAGCAGTTCTTCTGGAGCAAAATACAAATGGAATGAGA
TGGACAACTTTGAAGCTGATTCCAAAATTGGAAAAGGAAATCAATAATCCTGAGTGTATTTATATTAATGAACACAGAGG
AACAACTTCCCAGGGCTAAATCCATCTCTAACAGAAGGCTTTCTTGGAGATATGGTTTTCCATTCATATAAGACCCTTTG
GCTGATGCTAGACATCATGGAGAACTTACAGCTCATTAAGACTCAGGACATCCTTGCCAAACACACAAGCATGATCATTG
TCAAAGGAGGCCTGAAAAACATCACATTGCCAGTGCCAAACTCATGAAAAATGGGATTGATTATACTGTCATATGAACGT
GGCCCAAGAGTTTGGCGACTCAAAATTAGGTGTGAGGCCAGATGACTCTGTGTCCTGGAACAAGATTTATATGAATTCTG
GGCCAGTCAATGTATATACTGATACCCTTCCTGGCTTTCTTTTGCTTATGGCAGAGACTTTTGCCCAGAAAATTAGCACC
TTCACTCTTGAGAAAAGTAAC

Alignment

ORF - retro_shar_774 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.9 %
• Parental protein coverage: 59.36 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  YLGEFSLKGKDLR-QNGINRIGNLLVPNDNYCKFETWLMPILDQ-MVLEQDTEGVKWTPSKMI-ARLGKE
          Y.GEF.LKG..LR..N.I.R..NLLVPND...KFE..L...L.Q...LEQ.T.G..WT..K.I....GK.
Retrocopy YQGEFILKG*YLR<VNIIIRTANLLVPNDSCYKFEG*LISFLEQ<VLLEQNTNGMRWTTLKLI<SKIGKG

Parental  INNPESVYYW--AQKNNIPVLSPALTDGSLGDMIFFHSYKKPGLVLDIVEDLQLINTQALFAKRTGMIIL
          .N....VY.....Q.NN.P.L.P.LT.G.LGDM.F.HSYK...L.LDI.E.LQLI.TQ...AK.T.MII.
Retrocopy -NQ*S*VYLY**TQRNNFPGLNPSLTEGFLGDMVF-HSYKTLWLMLDIMENLQLIKTQDILAKHTSMIIV

Parental  GGGLV-KHHIANANLMRNGADYAV-YINTAQEFDGSDSGARPDEAVSWGKIRMDAKPVKVYADASLVFPL
          .GGL..KHHIA.A.LM.NG.DY.V...N.AQEF..S..G.RPD..VSW.KI.M...PV.VY.D....F.L
Retrocopy KGGLK<KHHIASAKLMKNGIDYTV<HMNVAQEFGDSKLGVRPDDSVSWNKIYMNSGPVNVYTDTLPGFLL

Parental  LVAETFAQKISAFTPEKSD
          L.AETFAQKIS.FT.EKS.
Retrocopy LMAETFAQKISTFTLEKSN

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_774 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
Felis catus	ENSFCAG00000000465	1 retrocopy	retro_fcat_1573,
Monodelphis domestica	ENSMODG00000006807	2 retrocopies	retro_mdom_731, retro_mdom_753,
Sarcophilus harrisii	ENSSHAG00000015920	1 retrocopy	retro_shar_774 ,