RetrogeneDB ID: retro_shar_420

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL841871.1:42156..42838(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SNX7
• Ensembl ID: ENSSHAG00000002487
• Aliases: None
• Description: sorting nexin 7 [Source:HGNC Symbol;Acc:14971]

Sequence

>retro_shar_420
GGAGCAGCAGTGCTGCAGCCTGAGGGGCTGGACCTAGATGAGGATCAGGATGACCTGGAGGTATCCACAAGGATGCCTCT
CTGATGGACATGAACTCTTTTAATCCTATGATGTCAACATTCCCCTTACCATGATAAACCAATATAAGTTAGAAGATAAG
TCATTCTCGAAGGACCTTTTCATTACAGTTGATGATCTGGAAAATCATATTACTACAACTGAAACTTTCATCACTTACAG
AGTTACAACTAAGACATCTTCTGGTGAATTTGATTCTAGTGAATTTGAAGTAAGAAGATGTTATCAAGATTTCCTATGGA
TAAAGGGAAAACTTGAAAAAACATATCCCAACCTCATTATTCCTCCTTTGCCAAAAAAATTCATAATGAAAGGCATGATG
GAACAGTTTAATGATGACTTCATTGAGACATGAAGAAAGGCACTGCAGAAATTCTTAAATCAAAGTGCTGATCATTCAAC
TTTAACTTTTAATGAAGACTTCAAAGTGTTTCTTATTGCAAGCCTGGGAGCTCTCTTTCATAAGAAAAAAGGTCCTGGAT
TGCTTAGCAGGATAGGACAGACAGTCACAGCTGTAGCATCTTCAGTGAGAGGAGTTAAAAACTGCCTAGATGAGTTCAGT
GAAATGAATGCCTGTGTGGGAACATTTAGCCAGGAAGTAAAC

Alignment

ORF - retro_shar_420 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.29 %
• Parental protein coverage: 50.55 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  GAVLLHPEVLDLDEDEDDLEVFS-KDASLMDMNSFSPLMPTSPL-SMINQYKFEDEPDSKDLFITVDDPE
          GA..L.PE.LDLDED.DDLEV...KDASLMDMNSF.P.M.T.PL..MINQYK.ED...SKDLFITVDD.E
Retrocopy GAAVLQPEGLDLDEDQDDLEVST<KDASLMDMNSFNPMMSTFPL<TMINQYKLEDKSFSKDLFITVDDLE

Parental  SHITTIETFITYRVTTKTSRGEFDSSEFEVRRRYQDFLWLKGKLEEAHPTLIIPPLPEKFIMKGMVERFN
          .HITT.ETFITYRVTTKT...........VRR.YQDFLW.KGKLE...P.LIIPPLP.KFIMKGM.E.FN
Retrocopy NHITTTETFITYRVTTKTXXXXXXXXXXXVRRCYQDFLWIKGKLEKTYPNLIIPPLPKKFIMKGMMEQFN

Parental  DDFIETRRKALHKFLNRIADHPTLTFNEDFKVFLTAQAWELSSHKKQGPGLLTRMGQTVRAVASSVRGVK
          DDFIET.RKAL.KFLN..ADH.TLTFNEDFKVFL.A....L..HKK.GPGLL.R.GQTV.AVASSVRGVK
Retrocopy DDFIET*RKALQKFLNQSADHSTLTFNEDFKVFLIASLGAL-FHKKKGPGLLSRIGQTVTAVASSVRGVK

Parental  NRPDEFNEMNDYMGTFSQEIN
          N..DEF.EMN...GTFSQE.N
Retrocopy NCLDEFSEMNACVGTFSQEVN

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_420 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 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000031461	1 retrocopy	retro_btau_453,
Choloepus hoffmanni	ENSCHOG00000008131	2 retrocopies	retro_chof_1097, retro_chof_1388,
Gorilla gorilla	ENSGGOG00000023577	1 retrocopy	retro_ggor_744,
Macropus eugenii	ENSMEUG00000011320	1 retrocopy	retro_meug_1016,
Sarcophilus harrisii	ENSSHAG00000000917	1 retrocopy	retro_shar_818,
Sarcophilus harrisii	ENSSHAG00000002487	1 retrocopy	retro_shar_420 ,
Tupaia belangeri	ENSTBEG00000000168	1 retrocopy	retro_tbel_2595,