RetrogeneDB ID: retro_shar_423

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL842013.1:34257..35043(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSHAG00000005706
• Aliases: None
• Description: None

Sequence

>retro_shar_423
GAGGTGGTGCTGGTGTACCTCAGCTCCTTATCATCTCAATTCCTCCTTATCTCAGACTTTAGGATGCTCTTTGAGGCTGA
GGAACAGGACATCTTCAAGGACAATCACTCTCTGCCCCAAAATGCCATCCTCAGGAAGCTCATGACCTAATCAATTGGGC
CAGCTGGCCAAGATCCATGCCTACATTATCATCTTCCTCAAGAAGGAAAGGCCCAGCATGTTTGGAAAAGAAAGCAAAGT
AAACAGCTTGGTAAATATCTATTAGAGAATCAAGCATGAACACCAGATCTCTCCCTGGAATTCCTCAAATCTTTGGAATA
TTTGAGAATTTCTGAAGACTCAGGGCTTCAAAAATTCCAGATCCAGAAGCCTAAGCTCTTGGACACCATGGACAGCATGC
CATCCAAAGACATCACTGGGTTGATGGTGACCCAGGAGGAGTTCCTTATGCCCTTACAGTCTCTGAAAGGTGGCCCCTTC
AATAGAACTATGAATGAGCCCTTTGTCCATGGCTACAGAGAAGGGGCCAGAGAGGACACAGATGATATGGAGTGGGTAAT
GGGCAAAGACAAGCCCCCTGATGATGAGATCTTCTGCACTCTTTCATCTGTTAATGGCAAGATTACAAGTGCTAATACCA
AGAAAAAGATGGTAAAATCCAAGCTACCTAATACAGTCCTGGGGAAGATCTGGAAATTGGCCTGTGTGGACAAAATCAGG
CTTCTGGATGAGGAGGAGTTTGCCTTGATCAACCATTTGATCAAGGTCAAATTAGAAGGCCAAAAG

Alignment

ORF - retro_shar_423 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.28 %
• Parental protein coverage: 67.25 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  EVVRVYIGSFWSHPLLIPDNRKLFEAEEQDLFKDIQSLPRNAALRKL-NDLIKRA-RLAKVHAYIISSLK
          EVV.VY..S..S..LLI.D.R.LFEAEEQD.FKD..SLP.NA.LRKL..DLI..A..LAK.HAYII..LK
Retrocopy EVVLVYLSSLSSQFLLISDFRMLFEAEEQDIFKDNHSLPQNAILRKL<HDLINWA<QLAKIHAYIIIFLK

Parental  KEMPNMFGKESKKKELVNNLGDIYQKIEREHQISPGDFPNLRKMQELLQTQDFS-KFQALKPKLLDTVDD
          KE.P.MFGKESK....VN.L..IY..I..EHQISP....NL....E.L.TQ.F..KFQ..KPKLLDT.D.
Retrocopy KERPSMFGKESK----VNSLVNIY*RIKHEHQISPWNSSNLWNI*EFLKTQGFK<KFQIQKPKLLDTMDS

Parental  MLSKDIARLMVMVRQEESLMPSQAVKGGAFDGTMNGPFGHGYGEGAGEGIDDVEWVVGKDKPTYDEIFYT
          M.SKDI..LMV...QEE.LMP.Q..KGG.F..TMN.PF.HGY.EGA.E..DD.EWV.GKDKP..DEIF.T
Retrocopy MPSKDITGLMVT--QEEFLMPLQSLKGGPFNRTMNEPFVHGYREGAREDTDDMEWVMGKDKPPDDEIFCT

Parental  LSPVNGKITGANAKKEMVKSKLPNTVLGKIWKLADVDKDGLLDDEEFALANHLIKVKLEGHE
          LS.VNGKIT.AN.KK.MVKSKLPNTVLGKIWKLA.VDK..LLD.EEFAL.NHLIKVKLEG..
Retrocopy LSSVNGKITSANTKKKMVKSKLPNTVLGKIWKLACVDKIRLLDEEEFALINHLIKVKLEGQK

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_423 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000014128	1 retrocopy	retro_cfam_1713,
Callithrix jacchus	ENSCJAG00000002660	1 retrocopy	retro_cjac_559,
Sarcophilus harrisii	ENSSHAG00000005706	1 retrocopy	retro_shar_423 ,
Sarcophilus harrisii	ENSSHAG00000013011	1 retrocopy	retro_shar_114,