RetrogeneDB ID: retro_shar_250

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL835057.1:30150..30748(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TP53
• Ensembl ID: ENSSHAG00000015510
• Aliases: None
• Description: tumor protein p53 [Source:HGNC Symbol;Acc:11998]

Sequence

>retro_shar_250
CCCTGGCACCTGATCCAGGTAGAAGGATACCTATGCGCTGAATACCTCAGTGATGTCACCACGATGCAACAGAGTATGTC
TGTTCCTTACGAATCCCTAGAAGTCAGCTGTGATTGTAATATAGTAATGGACTACTATAATCAACTATATGTGCAACAGT
TCCTGGATGGGGGGCATGAACCTGCACCTGATCCTCATCATCCTAACCCTGGAAGTCTCCAGTGGTCAGTTACTTAGATG
TTGGAGCTTTGAAATACATGTATGTGTCTTCCTTGGAAGAGACCAGCAGACTGAGGAGGAAAATTTCTGTGAGAAAGGAG
GTTACAACCCACAGCCATTCTGAGAGCAGTAAGTATACATTGCCCACAATTCCTGGCAGGACCTCCAAAACTAAGAAACA
GCTAAGGGACAGAGAATATTCACCCTTTAGATTTGAGATTGCCATTGCACTGTAAGCTATTTGGGGAACTGATGAAGCCT
TGGAACTAAAAGAAGCTCACAATGGGAAAGAACCTGAAAGGAGCTGTCCCTACATAGCAAACTGAAGTCAAAGAGAGGAG
ATTCTATCCCATATCAAGGTAAAAGACTTTAGATGAAA

Alignment

ORF - retro_shar_250 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.05 %
• Parental protein coverage: 53.1 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  PQHLIRVEGNLRAEYLSDLTTKRQSVSVPYESPEVGCDYTTV--HYNYMCNSSCM-GGMNRRP-ILTIIT
          P.HLI.VEG.L.AEYLSD.TT..QS.SVPYES.EV.CD...V...YN.........GG....P.IL.I.T
Retrocopy PWHLIQVEGYLCAEYLSDVTTMQQSMSVPYESLEVSCDCNIVMDYYNQLYVQQFLDGGHEPAP>ILIILT

Parental  LEDSSGQLLGRRSFEVRVCACPGRDRRTEEENFRKKGGHNPQP-SSESNKRALPTTPSSTPKTKKKLMDG
          LE.SSGQLL...SFE..VC...GRD..TEEENF..KGG.NPQP.S..S.K..LPT.P..T.KTKK.L.D.
Retrocopy LEVSSGQLLRCWSFEIHVCVFLGRDQQTEEENFCEKGGYNPQP>SESS-KYTLPTIPGRTSKTKKQLRDR

Parental  EY-FTLQIRGRHRYELLREL-NEALELKEAHSGKDPEGNCPH-RSQLKSKRGDSTPCQGKRLLVK
          EY...L..R......L..EL..EALELKEAH.GK.PE..CP...S.LKSKRGDS.P.QGKRL..K
Retrocopy EY>HPLDLRLPLHCKLFGEL<DEALELKEAHNGKEPERSCPY<HSKLKSKRGDSIPYQGKRL*MK

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_250 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 5 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Macropus eugenii	ENSMEUG00000013135	2 retrocopies	retro_meug_1464, retro_meug_599,
Myotis lucifugus	ENSMLUG00000006411	3 retrocopies	retro_mluc_2049, retro_mluc_2050, retro_mluc_452,
Monodelphis domestica	ENSMODG00000007271	1 retrocopy	retro_mdom_372,
Rattus norvegicus	ENSRNOG00000010756	1 retrocopy	retro_rnor_1411,
Sarcophilus harrisii	ENSSHAG00000015510	1 retrocopy	retro_shar_250 ,