RetrogeneDB ID: retro_shar_78

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL867624.1:14996..16064(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSHAG00000001657
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: ELAVL4
• Ensembl ID: ENSSHAG00000013832
• Aliases: None
• Description: ELAV (embryonic lethal, abnormal vision, Drosophila)-like 4 [Source:HGNC Symbol;Acc:3315]

Sequence

>retro_shar_78
GCAGCTGCAACTGTTCCTCGGCCCCAGCCTGCACCATCCACCGCTGCTCCTCCTGCAGTGGCAGGTCCATCTTCATCCTC
AAGGGCTATGGAAGGAACATCATCTGATTCAAAGACCAATCTGATTATCAACTATCTGCCCCAGAGCATGACTGAAGAGG
AGTTGCGCAGCCTCTTTGCCCGTGTGGGTAAGATCCAATCTTGCAAATTAGTGCGGGACAGGGTGACAGGCCAAAGCCTT
GGCTATGGTTTTATTGACTATGTGCATCCCAGGGATGCAGAGAGGGCGGTGTGCTTGCTGAATGGACTTCAGTGCCCTCC
AAAAACCATTAAGGTGTCCTATGCTCGGCCTAACTCCTCCTCCATCAGAGATGCCAATCTTTATATCAATGGCCTGCCTA
AGAACATGACACAGAAGGAGCTAGAACACCTCTTCTCTCCTTACGGGCACATCATAACATCAAGAATCCTGACAGACAAG
GCTAGTGGAACCTCCCGGGGTGTGGGCTTTATTCGCTTTAACATGAAATCAGAGGCTGAAGAAGCCATCAAGGCTCTGAA
TGGCCAGAAGCCCTGTGGTATTCTGGAGCCCCTTGTTGTCAGGTTTGCTCATAATCAGACCCAGGTGACACCACAAAACC
CGTTGTGCCAGCTTCCCCACAGCTCCCACGGACCGCTGCCGCCTCAGCCCCGGAGGTCTGGCCTTAACAACACGCCCATC
CCGACCCGTGCAGCCCAGAATTTAACACCATCAACCACGGAGAACACGAGAGACCTAGTCGGAGTGACCTTCCCGGGGCA
GACGGTCACCGGTTGGTGTATTTTCATCTACAACCTCGCACCCGATTCCGATGAAAACATCTTGTGGCAATTATTTGGAC
CCTTTGGAGCAGTCAGTAATGTAAAGATCATCCGGGATTTCAACACCAACAAGTGCAAACGCTTTGGCTTTGTCACTATG
ACTAGCTACAATGAAGCAGCATTGGCCATCGCTAGCTTAAATGGGTATTGCCTTGGGGGTCGGGTTTTGCAGGTTTCATT
TAAGACCAACAAAGTTCATAAGGCTTGA

Alignment

ORF - retro_shar_78 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.96 %
• Parental protein coverage: 95.9 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PTSNTTNGPSSNSRNCPSPMQTGATTDDSKTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQ
          P...T...P........S....G.T..DSKTNLI.NYLPQ.MT.EE.RSLF...G.I.SCKLVRD..TGQ
Retrocopy PAPSTAAPPAVAGPSSSSRAMEG-TSSDSKTNLIINYLPQSMTEEELRSLFARVGKIQSCKLVRDRVTGQ

Parental  SLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARPSSASIRDANLYVSGLPKTMTQKELEQLFSQY
          SLGYGF..Y..P.DAE.A...LNGL....KTIKVSYARP.S.SIRDANLY..GLPK.MTQKELE.LFS.Y
Retrocopy SLGYGFIDYVHPRDAERAVCLLNGLQCPPKTIKVSYARPNSSSIRDANLYINGLPKNMTQKELEHLFSPY

Parental  GRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVKFANNPSQKTSQALLSQL
          G.IITSRIL.D...G.SRGVGFIRF....EAEEAIK.LNGQKP.G..EP..V.FA.N..Q.T.Q..L.QL
Retrocopy GHIITSRILTDKASGTSRGVGFIRFNMKSEAEEAIKALNGQKPCGILEPLVVRFAHNQTQVTPQNPLCQL

Parental  YQSPNRRYPGPLHHQAQRFRLDNLLNMAYGVKRFSPITIDGMTSLVGMNIPGHTGTGWCIFVYNLSPDSD
          ..S......GPL..Q..R..L.N............P.T......LVG...PG.T.TGWCIF.YNL.PDSD
Retrocopy PHSSH----GPLPPQPRRSGLNNTPIPTRAAQNLTPSTTENTRDLVGVTFPGQTVTGWCIFIYNLAPDSD

Parental  ESVLWQLFGPFGAVNNVKVIRDFNTNKCKGFGFVTMTNYDEAAMAIASLNGYRLGDRVLQVSFKTNKTHK
          E..LWQLFGPFGAV.NVK.IRDFNTNKCK.FGFVTMT.Y.EAA.AIASLNGY.LG.RVLQVSFKTNK.HK
Retrocopy ENILWQLFGPFGAVSNVKIIRDFNTNKCKRFGFVTMTSYNEAALAIASLNGYCLGGRVLQVSFKTNKVHK

Parental  S
          .
Retrocopy A

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_78 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 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000002464	1 retrocopy	retro_chof_1943,
Cavia porcellus	ENSCPOG00000002044	1 retrocopy	retro_cpor_1379,
Macropus eugenii	ENSMEUG00000007145	1 retrocopy	retro_meug_426,
Sarcophilus harrisii	ENSSHAG00000011267	1 retrocopy	retro_shar_24,
Sarcophilus harrisii	ENSSHAG00000013832	1 retrocopy	retro_shar_78 ,
Sarcophilus harrisii	ENSSHAG00000018139	1 retrocopy	retro_shar_823,