RetrogeneDB ID: retro_shar_27

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL841443.1:713625..715338(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSHAG00000010597
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSHAG00000002842
• Aliases: None
• Description: None

Sequence

>retro_shar_27
GCTGCCGCCATGTCGGAAGACTTCACAAAATGGGACTACATGGTGTTCATACTCATGTTGCTCATTTCAGCCGCTATTGG
AGTCTACTACGCTTGGAAAGAAAGAGGCAAGCAGACGGAAACGGAATTCCTGATGGGGGGCCGCCAGATGTCAGGGGTCC
CTGTGTCATTGTCCCTCACGGCCAGCTTCATGTCCGCAGTCACCGTGTTGGGCACCCCGGCTGAGGTCTACCGCTTTGGG
GCCATGTTCTCGCTCTTCTGCATCACCTACACCCTGGTGGTAATCATCACCACGGAGCTCTACATGCCCGTGTTCTACCG
GCTCCGGATCAGCAGCACCTACGAGTACCTGGAGCTTCGATTTAATAAGTTAGTCCGTCTCCTCGGAACGGTTTTCTTTA
TCACCCAGACGATCCTCTACACCGGAATCGTCATTTATGCTCCGGCTCTCGCTTTGAATCAAGTCACGGGTTTCGAACTC
TGGGGTGCGGTGGTGACTACGGGACTCGTCTGTACCTTCTACTGCGCGCTGGGAGGCCTCAAAGCCGTCATCTGGACGGA
TGTGTTCCAATCCGTGGTTATGGTGGCCGGGTTTTCTTCAGTTATCATACAGACAGCGCAACTTCAAGGTGGAATAAGTA
ACGTCATGCAACACGCCGAGGAAGGAGGAAGATTAAGAATATGGGACTTTAACCTGAATCCTTTACAGAGACACACTTTC
TGGACAATTATAATAGGCGGTACCTTCACGTGGACCAGCATTTATGGCGTCAACCAGTCCCAAGTGCAGAGATACCTGGC
CTGTAAAAGCAAAGGCCACGCAAGACTAGCGCTTTATTTAAATCTCCTGGGCCTCTGGATAATTCTCGCCTGCGCGGTTC
TAAGCGGCTTGTCCCTCTACTCGATGTTTCGCGACTGCGATCCGTGGACGTCTCACAAGGTCAGAGCCCCGGATCAGCTC
ATGCCCTACCTGGCCGTGCTGATCCTCAACGAGTTCCCGGGCCTGCCCGGGCTTTTCGTGTCCAGCGCTTACAGCGGAAC
GTTGAGCACCGTGTCCTCCAGCATCACCGCTCTAGCCGCAGTAACTGTAGAAGATCTCATCAAACCGCAGTTAGTTTCAC
CTTCACAGAGGACTCTGTCTCTTCTTTCTCAAGGAATAAGCGTGTTCTTCGGGATACTTTGTATCGGGATGGCTGCCCTG
GCCTCCTTAATGGGAGGCCTGTTACAGGCGGCCCTCAGCATATTCGGGATGATCGGAGGACCTCTGTTGGGATTGTTTAC
TCTGGGACTTTTAAATCCTTACGCCAACTCGATGGGTTCGTTTATCGGTCTGATGTTTGGATTTTCTTTCTCCATATGGA
CTGGAGTTGGGGCTTATTTTTACCCTCCACCTTCTTCCAGGACATTGCCTTTACCTCTTTCTGTGGCAAATTGTACCCTG
ACTAGAAGCTTGCCTCTGAATTTCACTGGCTTAATCGAATACTCAGTCTTGATGCCCTGGAAAACAGCTTTCAGAAGAAA
TTTTCTAATGAATAATTTATATTCCCTTTCTTACCTCTACCTAAGCACTTTGGGGACATTGATGACAATACTCATGGGAT
CAGTTTTCAGCTTTCTAACAGGTGGACACGAACAGTCTATTGATCCCAAGTACCTCTGGACCAAAGAAGATATGTCACTG
GGTCAATATTTAACAAAGAAAAAAGAAGAAGTT

Alignment

ORF - retro_shar_27 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.55 %
• Parental protein coverage: 77.36 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  FVVWDYLVFAAMLLISAAIGVYYAFAGGGQQTSKDFLMGGRKMTAVPVALSLTASFMSAVTVLGTPSEVY
          F..WDY.VF..MLLISAAIGVYYA....G.QT...FLMGGR.M..VPV.LSLTASFMSAVTVLGTP.EVY
Retrocopy FTKWDYMVFILMLLISAAIGVYYAWKERGKQTETEFLMGGRQMSGVPVSLSLTASFMSAVTVLGTPAEVY

Parental  RFGAIFCIFAITYALVVIVSAEVFLPVFYKLGITSTYEYLEVAYSRVMGC-NSEFFLFNSLLFTGYIHRK
          RFGA.F..F.ITY.LVVI...E...PVFY.L.I.STYEYLE.............FF.....L.TG.....
Retrocopy RFGAMFSLFCITYTLVVIITTELYMPVFYRLRISSTYEYLELRFNKLVRLLGTVFFITQTILYTGIVI--

Parental  FSESFSVFAVTGFDLWGAVVATGVVCTFYCTMGGLKAVVWTDVFQVGIMVAGFASVIIQATVVQGGINNI
          .........VTGF.LWGAVV.TG.VCTFYC..GGLKAV.WTDVFQ...MVAGF.SVIIQ....QGGI.N.
Retrocopy YAPALALNQVTGFELWGAVVTTGLVCTFYCALGGLKAVIWTDVFQSVVMVAGFSSVIIQTAQLQGGISNV

Parental  LNDSYYGGRLNFWDFNPNPLQRHSFWTIIIGGTFTWTTIYGVNQSQVQRYISCKNRFHAKMSLYINLVGL
          ......GGRL..WDFN.NPLQRH.FWTIIIGGTFTWT.IYGVNQSQVQRY..CK...HA...LY.NL.GL
Retrocopy MQHAEEGGRLRIWDFNLNPLQRHTFWTIIIGGTFTWTSIYGVNQSQVQRYLACKSKGHARLALYLNLLGL

Parental  WAILTCAVFCGLALYSRYHDCDPWTAKKVSALDQLMPYLVLDILQDYPGLPGLFVACAYSGTLSTVSSSI
          W.IL.CAV..GL.LYS...DCDPWT..KV.A.DQLMPYL...IL...PGLPGLFV..AYSGTLSTVSSSI
Retrocopy WIILACAVLSGLSLYSMFRDCDPWTSHKVRAPDQLMPYLAVLILNEFPGLPGLFVSSAYSGTLSTVSSSI

Parental  NALAAVTIEDLVKPYFPSLSEKTLSWLSKGTSVLYGALCIGMAALASLMGALLQAALSIFGMIGGPLLGL
          .ALAAVT.EDL.KP...S.S..TLS.LS.G.SV..G.LCIGMAALASLMG.LLQAALSIFGMIGGPLLGL
Retrocopy TALAAVTVEDLIKPQLVSPSQRTLSLLSQGISVFFGILCIGMAALASLMGGLLQAALSIFGMIGGPLLGL

Parental  FSLGILVPIANSLGAFVGLIAGFAISLWVGIGAQLYPPLPERTLPLSLVTDGCNIT
          F.LG.L.P.ANS.G.F.GL..GF..S.W.G.GA..YPP...RTLPL.L....C..T
Retrocopy FTLGLLNPYANSMGSFIGLMFGFSFSIWTGVGAYFYPPPSSRTLPLPLSVANCTLT

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_27 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Sarcophilus harrisii	ENSSHAG00000002842	1 retrocopy	retro_shar_27 ,