RetrogeneDB ID: retro_shar_519

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL849754.1:582135..583195(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSHAG00000005317
• Aliases: None
• Description: None

Sequence

>retro_shar_519
CTGGAAAAGGCCCCCTCCTCCCTGGTGCTGCCTGCCGTGGGCTGGTCCGCAGCGGCCACCTTGACCTCCTACCTGACCCA
GAAGTTGGGCACGGGGCCTCTGCACGTCGACCAGGCATCCCTGAGGGAGCTGAAGCTGAACGGCACCCAGCCTGTCCTGC
TGCTGGTGTACATACCCTCAGGGGCCAGCGGCGCCCCGGGGGCTCACGAGGAAGCGCTGGCTACTCAAGACAAGGTCCTT
GGGCAGGTGCTGAGCCGGCTCCACGCGGGAGGGAACGCTTACACGGCCTTGCTCACGGCCCTTCGGCCCTCCAGGGCAGC
CCGAGACTTGTCCCTCGCGTCCCGGGGCCCGGCGGCAGCACCTCCTCGGGGAGGGCCAGGAGTACCAAGGCCAGCCGGCC
TGGCCAGCAGCCCTGCCCCCGGTGAGCTACAGCGACACGGCGCCGCGCATCCTGTTCTGGGCCAGGCACTTCTCGGTGAG
TTACCACAGCCAGACCCAGGACCTCACATCGCTCACCTTCGGAGCCCCGGAGCTCAACCTGACTGGCTCCAGCTGGAACG
ACTCCACGGCCCAGCTTGTGATGACCTACAACAATCTCTTCGGGCCCTTCCTGAGGCTGAGGTTCAGTATGATCAATCAC
TTCTACCCGGGGTCCCACCGGAGCTGGTTCACCATGGAGGGGCTGGAGATCAAGACCCACAACTCGACGGCCTTCTTCAG
CTCTGTGCAGGTCATTGCCCCCAGCACCTACTCCTACCACTGCCAGTATGTAAGCAGCGACCCCGCCAAATGGGGCCTTC
TGATGCCTCACGATATTCGCTCCCCCTGGAGTGTAACACTCCAGGATTTCCAGATCCAGGCTTTCAACCTGTCTGGCGGC
AGCTTTTCAGGGGCCAGTGATTGTGCAGCCTTCTTCTCTCCTGCTATCTGGATGGGGCTGGTCTCTTCCCTCTTCATGCT
TTTTTGCATTACCTTTGGGGTACATATCATCTTTAAACTCAAGTCCCTAAACCGTTTTGATGAATACAAAGGGGACCCCC
TCTTTGAGCCCCTTATGGAC

Alignment

ORF - retro_shar_519 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60. %
• Parental protein coverage: 73.7 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LELAPSSLILPSVDWYAASTLTSYLKDKLGASPLHVDQVTLRELKLNDTLPALLLLRLPYTTSSGLMAPK
          LE.APSSL.LP.V.W.AA.TLTSYL..KLG..PLHVDQ..LRELKLN.T.P.LLL...P...S....A..
Retrocopy LEKAPSSLVLPAVGWSAAATLTSYLTQKLGTGPLHVDQASLRELKLNGTQPVLLLVYIPSGASGAPGAHE

Parental  EVLTGNEDEIIGQVMSTLKAEGVPYTAILTAVRPSRVVRDASLVS-GGLGRHLLGEDEGLKPLSPSAPLL
          E.L....D...GQV.S.L.A.G..YTA.LTA.RPSR..RD.SL.S.G....HLLGE.............L
Retrocopy EALA-TQDKVLGQVLSRLHAGGNAYTALLTALRPSRAARDLSLAS>GARRQHLLGEGQEYQGQPAWPAAL

Parental  PPVSYNDTEPRILFWARNFTVTYDSESHDLTHLTFGTSMLNLTGSSWNSSFAQLVLTYENLFGPYLTFKF
          PPVSY.DT.PRILFWAR.F.V.Y.S...DLT.LTFG...LNLTGSSWN.S.AQLV.TY.NLFGP.L...F
Retrocopy PPVSYSDTAPRILFWARHFSVSYHSQTQDLTSLTFGAPELNLTGSSWNDSTAQLVMTYNNLFGPFLRLRF

Parental  ILRNHFYPVSARSWFTMDRLEIHTNNSFVVFNSSHITAPSIYSFHCQSVSTDRSKDGLLMSSP-SSAWRV
          ...NHFYP.S.RSWFTM..LEI.T.NS...F.S....APS.YS.HCQ.VS.D..K.GLLM.....S.W.V
Retrocopy SMINHFYPGSHRSWFTMEGLEIKTHNSTAFFSSVQVIAPSTYSYHCQYVSSDPAKWGLLMPHDIRSPWSV

Parental  NFQNFQIQAFNLSGGNFSYASDCAGFFSPGIWMGLVSSIFMLFTFTYGLHMILNLKTMDRFDDHKGSTLS
          ..Q.FQIQAFNLSGG.FS.ASDCA.FFSP.IWMGLVSS.FMLF..T.G.H.I..LK...RFD..KG..L.
Retrocopy TLQDFQIQAFNLSGGSFSGASDCAAFFSPAIWMGLVSSLFMLFCITFGVHIIFKLKSLNRFDEYKGDPLF

Parental  VPLME
          .PLM.
Retrocopy EPLMD

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_519 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
Mus musculus	ENSMUSG00000019087	1 retrocopy	retro_mmus_1198,
Oryctolagus cuniculus	ENSOCUG00000017631	1 retrocopy	retro_ocun_863,
Sarcophilus harrisii	ENSSHAG00000005317	1 retrocopy	retro_shar_519 ,