RetrogeneDB ID: retro_shar_821

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL867584.1:3345460..3346332(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LYAR
• Ensembl ID: ENSSHAG00000008286
• Aliases: None
• Description: Ly1 antibody reactive [Source:HGNC Symbol;Acc:26021]

Sequence

>retro_shar_821
TTTACATGCAATGAATGTGGAGAATCAGTGAAGAAAGGCCAAGTAAAGAAACACGTGGAAATGTTCAACAAATGTCAATA
CATTTCCTGTGGCAAGGATTTCTGGAATGATGAATTCAAAAACCTGAGAAGTTTATCAGTGACAATCAGAAATATTATCA
CAAAAGTTATGAGATAAAAAACAACAAAGAACTGAAACAGCAGAAATGGATTCAGAAGGTTCATGAATTAATGAAGAAAA
CCAGTATTAGCTTCAAATTGCAGGAGATTTTAGAAAAAGGTAGTAGTTTTGATAGCATTACAGAAAAAAAGGCCAAGTTT
CAGAATTGGATGAAGAACAGTTTAAAAAATTATAACTGTCTTCAGGAACAGGTGTGGAATATCTTGTGGGATATTTTTTT
CTGAAATGAATGAATGAATGAATCAAATAAAAAAGAACAATAGACATGACCTCTTAACCAAGTAGGCAATCAGCATTCAG
AAAACAAAGTCAAGACAACCCACCCTGAAGTCAGTGAAAACCAGTTGGACAATAGAAGGGGAAAGAGAACAATAGTAAAT
GCAGGGAAGGGCAACAGAAGAACACGAAAAAGCAAAAGAACTAAAGTTAGAAAAGTCAAGAACATTCAGGTGATCCAAAA
TCCAAAAAGGACAAGAGGGCCCAGGAAGAAATAGATGTCAAAAGGAAAGGAAAGCCAAAATCATCAATGCAGGAAAAAGG
GGAAATTTTTTTAAAACGCTAAGAAGGAATATTCAGTGGAGTCAGAAAGGAAGAGAAATAAGAATCACGACAATGAAAGA
ACGACAGAGAAAGAGATGGAAGTGCCTGCAGAGAAGAGGAAATGGAAGCACTCACAAAAAGAAGCTGATTCT

Alignment

ORF - retro_shar_821 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.28 %
• Parental protein coverage: 74.74 %
• Number of stop codons detected: 7
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  FTCNACGESVKKGQVEKHVNICKNCQYLSCIDCGKDFWGDEYK-KHVKCITEDQKYGGKGYEVKTSKGDV
          FTCN.CGESVKKGQV.KHV.....CQY.S...CGKDFW.DE.K.K..K.I...QKY..K.YE.K..K...
Retrocopy FTCNECGESVKKGQVKKHVEMFNKCQYIS---CGKDFWNDEFK<KPEKFISDNQKYYHKSYEIKNNK-EL

Parental  KQQEWIQKIHEVMKKPSVSPKLREILEKVSGFDNIPRKKAKFQNWMKNSLKIYNDSLQEQV----WDI-F
          KQQ.WIQK.HE.MKK.S.S.KL.EILEK.S.FD.I..KKAKFQNWMKNSLK.YN..LQEQV....WDI.F
Retrocopy KQQKWIQKVHELMKKTSISFKLQEILEKGSSFDSITEKKAKFQNWMKNSLKNYN-CLQEQVWNILWDIFF

Parental  SEATRNGPNTKEQEKHPLNQVENQHSENKVKAAPPEGGE-KPAGQPEVKKNKRERKEERQKSRKKEKK-E
          .....N..N.KEQ...PLNQV.NQHSENKVK...PE..E.KP.GQ...K.N.....E..QK..KK.K...
Retrocopy *NE*MNESNKKEQ*T*PLNQVGNQHSENKVKTTHPEVSE<KPVGQ*KGKENNSKCREGQQKNTKKQKN*S

Parental  LKLENHQENSSDPKSKKRKRAQAEGDAGREEKP-EISNAEKRKNKKK-KAKKECAPDAEVNGDGSQDGER
          .K...H.......K.K...RAQ.E.D..R..KP..I.NA.KR.N..K..AKKE.....E.......D.ER
Retrocopy *KSQEHSGDPKSKKDK---RAQEEIDVKRKGKP<KIINAGKRGNFFK<NAKKEYSVESERKRNKNHDNER

Parental  MAEEAPRAP-EKRKRKHSEEEADS
          ..E.....P.EKRK.KHS..EADS
Retrocopy TTEKEMEVPAEKRKWKHSQKEADS

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_821 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	ENSSHAG00000008286	1 retrocopy	retro_shar_821 ,