RetrogeneDB ID: retro_shar_473

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL849613.1:47151..47583(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GBAS
• Ensembl ID: ENSSHAG00000009627
• Aliases: None
• Description: glioblastoma amplified sequence [Source:HGNC Symbol;Acc:4179]

Sequence

>retro_shar_473
AGTAAGTTCAGAGAAAATAAGGAATTTGTGGCCTTCCAGAAGGAAAGGGCAACATGCTGCTTTCTAGAAAAAAACAGCTG
CTGTTAGAGGGGAGTTTCTGGAATGAACCTGTCTCCAGACCAGGGCCTAACATATATGAACTCAGGCCTTACCCACTTAG
AACAGGAACAATGGTTGAATGGAGCAACTATTGGGCTCATGCAATTCATTTCAGACAGGACAATGAGGAAGCAGTTGGAG
GGATTTTCCTCTCAGATTGGGCAGTTATATATGGTACATCATCTTTAGGCTTACAAAGACCTGAAGTCCAGGGAAGACAC
CCTGAATGCAGCGTGGTATAGAAATGGCTGGGAAGAATGGGGCTATTATACAGTGCTTCTAATTCAGGAAATGGAGTCAA
GAATCATGATACCCCTGAAGATTTCACCCCTC

Alignment

ORF - retro_shar_473 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.56 %
• Parental protein coverage: 96.64 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SKLRENKEFVAFRKER-GNMLLSRKNQLLLEFSFWNEPVPRPGPNIYELRSYQLRPGTMIEWGNYWARAI
          SK.RENKEFVAF.KER.GNMLLSRK.QLLLE.SFWNEPV.RPGPNIYELR.Y.LR.GTM.EW.NYWA.AI
Retrocopy SKFRENKEFVAFQKER<GNMLLSRKKQLLLEGSFWNEPVSRPGPNIYELRPYPLRTGTMVEWSNYWAHAI

Parental  RFRQDNEEAVGGFF-SQIGQLYMVHHLWAYKDLQSREDTRNAAWHKHGWEELVYYTVPLIQEMESRIMIP
          .FRQDNEEAVGG.F.SQIGQLYMVHHL.AYKDL.SREDT.NAAW...GWEE..YYTV.LIQEMESRIMIP
Retrocopy HFRQDNEEAVGGIF>SQIGQLYMVHHL*AYKDLKSREDTLNAAWYRNGWEEWGYYTVLLIQEMESRIMIP

Parental  LKISPL
          LKISPL
Retrocopy LKISPL

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_473 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 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000031598	1 retrocopy	retro_btau_361,
Macropus eugenii	ENSMEUG00000005152	2 retrocopies	retro_meug_1273, retro_meug_469,
Myotis lucifugus	ENSMLUG00000015038	1 retrocopy	retro_mluc_762,
Oryctolagus cuniculus	ENSOCUG00000001768	1 retrocopy	retro_ocun_1396,
Sarcophilus harrisii	ENSSHAG00000009627	1 retrocopy	retro_shar_473 ,
Tursiops truncatus	ENSTTRG00000015145	1 retrocopy	retro_ttru_1885,