RetrogeneDB ID: retro_tbel_4420

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_82033:13299..14119(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SRP54
• Ensembl ID: ENSTBEG00000011409
• Aliases: None
• Description: signal recognition particle 54kDa [Source:HGNC Symbol;Acc:11301]

Sequence

>retro_tbel_4420
TTGAACAAAAGAAAATAATTTAGCATGTTGTATTTAAAGAACTTGTGAAGACTGCAGACCCTGGAGTTAAAGCATGGACT
AAAGGAAAACAGAATGTGATCATGGTTGCTGGATTAGGAGTGGTAAAACAGCAACATGTTCAAAGTTAGCATATTATTAC
CAGAGAAGTGTTGGAAGACCTGTTTGATACGTGCAGACAATCAGAGCAGGGGCTTTTGATGAACTAAAATAGAATGCAAT
CAAAGTAAGGATTCCATTCTATGGAAGTGATACAGAAATGGATCCTGTTATCAATGCTTCTGAAAGCAATAGAGAAATTA
AAAATGAAAATTTTGAAATAATTATTGTGAATACAAGTGGCTGCCACAAACAAAAAGACTCTTTGAGGAGATGCTTCAAT
TGGCTAATGCTGTTCAACCTGATAACATTGTTTACGGGATTCATCTGGCAGGCTTGTGAAGCTCAGGCTAAGGCTTCTAA
AGATAAGGTAGATGTAGTAGCTTCAGTAATAGTGACAAAACCTGAAGGTCATGCAAAAGGAGGTGGTGCCCTCAGTGCGG
TTGCTGCCACAAAAAGTACAATTGTTTTCATTGGTACAGGGGAATACATAGATGCCTTTGAACCATTCAAAACACAGCCT
TTCCTCAACAAACTTCTTAGTATGGGTGACATTGAAGGACTGATAGATAAAGTAAACGAGTGGAAGTTGGATGACAATGA
AGCAGTTATAGAGAAGTTGAAGCATGGTCAGGTTACACTGTGAGACATGTATGAACAATTTTAAAATATTATGAAAACGG
GTCCCTTCAGTCAGATCTTG

Alignment

ORF - retro_tbel_4420 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.31 %
• Parental protein coverage: 62.86 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LNKRK-MIQHAVFKELVKLVDPGVKAWTPTKGKQNVIMFVGLQG-SGKTTTCSKLAYYYQRKGWKTCLIC
          LNKRK..I.H.VFKELVK..DPGVKAWT..KGKQN....V...G.SGKT.TCSKLAY.Y...........
Retrocopy LNKRK<II*HVVFKELVKTADPGVKAWT--KGKQN-VIMVAGLG<SGKTATCSKLAY-YYQRSVGRPV*Y

Parental  ADTFRAGAFDQLKQNATKARIPFYGSYTEMDPVIIASEGVEKFKNENFEIIIVDTSGRHKQEDSLFEEML
          ..T.RAGAFD.LK.NA.K.RIPFYGS.TEMDPVI.ASE.....KNENFEIIIV.TSG.HKQ.........
Retrocopy VQTIRAGAFDELK*NAIKVRIPFYGSDTEMDPVINASESNREIKNENFEIIIVNTSGCHKQK----DSLR

Parental  QVANAIQPDNIVYVMDASIGQACEAQAKAFKDKVDV-ASVIVTKLDGHAKGGGALSAXXATKSPIIFIGT
          ...N.....N........I.QACEAQAKA.KDKVDV.ASVIVTK..GHAKGGGALSA..ATKS.I.FIGT
Retrocopy RCFNWLMLFNLITLFTGFIWQACEAQAKASKDKVDVVASVIVTKPEGHAKGGGALSAVAATKSTIVFIGT

Parental  GEHIDDFEPFKTQPFISKLLGMGDIEGLIDKVNELKLDDNEALIEKLKHGQFTLRDMYEQFQNIMKMGPF
          GE.ID.FEPFKTQPF..KLL.MGDIEGLIDKVNE.KLDDNEA.IEKLKHGQ.TL.DMYEQF.NIMK.GPF
Retrocopy GEYIDAFEPFKTQPFLNKLLSMGDIEGLIDKVNEWKLDDNEAVIEKLKHGQVTL*DMYEQF*NIMKTGPF

Parental  SQIL
          SQIL
Retrocopy SQIL

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Tupaia belangeri was not studied using RNA-Seq expression data.

ChIP-Seq

Tupaia belangeri was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_tbel_4420 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_4420 was not experimentally validated.

Homology

Retrocopy orthology:

Tupaia belangeri 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000012925	1 retrocopy	retro_mdom_82,
Tupaia belangeri	ENSTBEG00000011409	1 retrocopy	retro_tbel_4420 ,