RetrogeneDB ID: retro_shar_429

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL842496.1:10169..11025(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSHAG00000009835
• Aliases: None
• Description: None

Sequence

>retro_shar_429
CCTGTGACTGAAAAGCTTGACTCTTCAGATCCAAAGGAGAGAAAGGACAAGTCTTTGAATTTGGAAAAAATTACAGATTT
GAATAAGGGGTGCACTCTTTATGGGGTTACATTATCTTCTGTTAAGATGTTACTAGATAATTTGTCTTATGAAATCTTTA
GCCCGAATGCTTGGAAATCCATAGCAAAGACAGGTGTAGAACCTGGACAAAATTTATTGGGGCTTTCAGAGTTTCATGAA
TTATGTAGGATTCAAGCCCAATGCAATAGGCAAACAGGAGCTATTGGAAAAATCCCTTGTGACCAACTAGCTGGTGAAGG
TCAGAATGGTGAGAATTCAGAACAGATTTATTATCCCATAACAGTGTATGTTCAAATTGCTAAGGCTGCAAGAAAAGCTT
AGAATTCTCTTCCTGGACAGAAAGCTCGAAGTCAAACTGACAAAAGTAGAGCAAGGTCCCACTGAACCTTGGGTAGATTT
GGTGGGATGTTTGCAAACAGCGCTAATAAGAACCATTGGAGATAATGGTGCCGCAGAAGTTATGACCAGACATCTGCCTA
AAGAAAATGCCAATGAGGTTTGTAAAATAATTATATGGGGACTAGACAAAGATGCTCCTTTAAAGGATATCACAAGACGC
TGTGCCATAGTGGGTACAAATGCTTATTATGCCCAAACTATGATGAATATAGGAAGACAGGGTCCCTCCTGGCAAGAGAC
TTCTAGAGAAACTCTTGGATGTTTTCATTGTGGAAAAGTTGGACATGTGAGAGCTCAATGCAGATACAGAGATAGAGTGA
GAGGACAGGGTGAGAGAAGAAGGCCCCAGACCCCATGCCCAAAATGGAACCGAGGC

Alignment

ORF - retro_shar_429 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.85 %
• Parental protein coverage: 86.34 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PVVEKLNSSGQERRRYTPFNLEIIKDLKKACILYEATSSYVKMLLQNLAYEILTPSDWKSIARTCLGPGQ
          PV.EKL.SS....R.....NLE.I.DL.K.C.LY..T.S.VKMLL.NL.YEI..P..WKSIA.T...PGQ
Retrocopy PVTEKLDSSDPKERKDKSLNLEKITDLNKGCTLYGVTLSSVKMLLDNLSYEIFSPNAWKSIAKTGVEPGQ

Parental  NLLWLSEHSELCRIQIQQNKQTGVNTPITYDQLTGVSSYADISAQINYPIAAFQEIASAAIEAWGFLPGN
          NLL.LSE..ELCRIQ.Q.N.QTG....I..DQL.G.......S.QI.YPI.....IA.AA..A...LPG.
Retrocopy NLLGLSEFHELCRIQAQCNRQTGAIGKIPCDQLAGEGQNGENSEQIYYPITVYVQIAKAARKA*NSLPGQ

Parental  KT-DEKPSKIEQGPNEPFADFVGPLQTAI----GENAAKEIMIRQLAKENANEVCRRIILGLCKDAPLEE
          K....K..K.EQGP.EP..D.VG.LQTA.....G.N.A.E.M.R.L.KENANEVC..II.GL.KDAPL..
Retrocopy KA>EVKLTKVEQGPTEPWVDLVGCLQTALIRTIGDNGAAEVMTRHLPKENANEVCKIIIWGLDKDAPLKD

Parental  IIRRCATVGTNTFYAQAMMQTS-QDPN-QGTSRETRQCFQCGKVGHLKGQCWHKDRAQQSGD-NHPDSDS
          I.RRCA.VGTN..YAQ.MM....Q.P..Q.TSRET..CF.CGKVGH...QC...DR....G....P....
Retrocopy ITRRCAIVGTNAYYAQTMMNIGRQGPSWQETSRETLGCFHCGKVGHVRAQCRYRDRVRGQGERRRPQTPC

Parental  KQQNPG
          ...N.G
Retrocopy PKWNRG

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_429 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 2 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Sarcophilus harrisii	ENSSHAG00000009835	3 retrocopies	retro_shar_151, retro_shar_195, retro_shar_429 ,
Sarcophilus harrisii	ENSSHAG00000016712	2 retrocopies	retro_shar_169, retro_shar_562,