RetrogeneDB ID: retro_shar_147

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL834466.1:570912..571249(-)
• Located in intron of: ENSSHAG00000009269

Retrocopy information

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

Parental gene information

• Parental gene symbol: SNRPD1
• Ensembl ID: ENSSHAG00000011791
• Aliases: None
• Description: small nuclear ribonucleoprotein D1 polypeptide 16kDa [Source:HGNC Symbol;Acc:11158]

Sequence

>retro_shar_147
AAACAGACTAATGAAACTGTAAATGTTGAATTCAAGAACTGCAGCCAGGTGCATAGAACAATTATAAGAGTGATGTCAGT
CTGATCACACATCTTAAAATTGTTAAAGGTACAGTGAAAAATAGAGAGCCAATATAGTTGTTAATACTGAGTATTCAAAG
GAATAACTTTTCATTCTTGTTTTTTTCCCAGATTGTTTACTTCTATATATACTACTTTTTGAAAATGAATCTAAAGTTAA
ATCTAAGAAGAGGGAAACAGTTGTAGGAGAAGATCAAGGAACAAGACAAGGAAGAGGTAGACCAGATAAAGGACATGGCA
GGGGAAGAACAAGTCCA

Alignment

ORF - retro_shar_147 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.78 %
• Parental protein coverage: 91.6 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KLSHETVTIELKNGTQVHGTITGV-DVSMNTHLKAVKMTLKNREPVQLETLSI-RGNNIRYFI-LPDSLP
          K...ETV..E.KN..QVH.TI..V.DVS..THLK.VK.T.KNREP..L..LSI.R.N....F...PD.L.
Retrocopy KQTNETVNVEFKNCSQVHRTIIRV<DVSLITHLKIVKGTVKNREPI*LLILSIQRNNFSFLFF<FPDCLL

Parental  LDTLLVDVEPKVKSKKREAVAGRGRGRGRGRGR---GRGRGRGGP
          L..LL...E.KVKSKKRE.V.G...G...GRGR...G.GRGR..P
Retrocopy LYILLFENESKVKSKKRETVVGEDQGTRQGRGRPDKGHGRGRTSP

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_147 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 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000006364	1 retrocopy	retro_acar_129,
Bos taurus	ENSBTAG00000008292	3 retrocopies	retro_btau_144, retro_btau_706, retro_btau_84,
Homo sapiens	ENSG00000167088	2 retrocopies	retro_hsap_1147, retro_hsap_372,
Mustela putorius furo	ENSMPUG00000005567	1 retrocopy	retro_mputfur_185,
Mus musculus	ENSMUSG00000002477	1 retrocopy	retro_mmus_1996,
Oryctolagus cuniculus	ENSOCUG00000023761	1 retrocopy	retro_ocun_224,
Sarcophilus harrisii	ENSSHAG00000011791	1 retrocopy	retro_shar_147 ,