RetrogeneDB ID: retro_tbel_2390

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_109842:39810..40308(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MAPRE3
• Ensembl ID: ENSTBEG00000013617
• Aliases: None
• Description: microtubule-associated protein, RP/EB family, member 3 [Source:HGNC Symbol;Acc:6892]

Sequence

>retro_tbel_2390
ATAGCAGTGAATGTGTACTCGACTTCAGTCACCAGTGATAACCTAAGTCGACATGACATGTTGGCCTGGATCAATGAATC
TCTGCAGTTGAATCTGACAAAAATCGAACAGTTGTGCCCAGGGGCAGCTTATTGTCAGTTTATGGACATGCTGCTCCCTG
GCTCCATTGCCCTGTGAAGAAAACAAAATTCTAAGCAAAGTTAGAACACGAATACATCCAGAACTTCAAAATATTACAGG
CAGATTTTAAGAGGATGGGTGTTGACAAAATAATTCCTGTGGACAAATTAGTAAAAGGAAAAGTTTCAGGATTTGTTCAG
TGGGTCAAGAAGTTTTTTGATGCAAACTATGATGGAAAAGACTATGACCCTGTAGCTGTCAGACAAGATCAGGAGATTAT
AGTAGCTCCTTTCCTTGTTGCTCCAGCTCTGAATAAACTGAAGAAACCTCTCAGCTCTAGCAGTACAGCTCCACAGAGGC
CCTTTCAACCCAGAGAAC

Alignment

ORF - retro_tbel_2390 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.16 %
• Parental protein coverage: 59.79 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAVNVYSTSVTSENLSRHDMLAWVNDSLHLNYTKIEQLCSGAAYCQFMDMLFPGCVHL-RK-VKFQAKLE
          .AVNVYSTSVTS.NLSRHDMLAW.N.SL.LN.TKIEQLC.GAAYCQFMDML.PG...L.RK..KF.AKLE
Retrocopy IAVNVYSTSVTSDNLSRHDMLAWINESLQLNLTKIEQLCPGAAYCQFMDMLLPGSIAL*RK<TKF*AKLE

Parental  HEYIHNFKVLQAAFKKMGVDKIIPVEKLVKGKFQDNFEFIQWFKKFFDANYDGKDYNPLLARQGQDVAPP
          HEYI.NFK.LQA.FK.MGVDKIIPV.KLVKGK..........F...FDANYDGKDY.P...RQ.Q.....
Retrocopy HEYIQNFKILQADFKRMGVDKIIPVDKLVKGKVSGFVQWVKKF---FDANYDGKDYDPVAVRQDQEIIVA

Parental  PNPGDQIFNKSKK-LIGTAVPQRTSPTGPKN
          P.......NK.KK.L...AV.....P..P.N
Retrocopy PFLVAPALNKLKK>LSALAVQLHRGPFNPEN

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_2390 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_2390 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000016515	1 retrocopy	retro_ecab_40,
Ictidomys tridecemlineatus	ENSSTOG00000015500	1 retrocopy	retro_itri_147,
Tupaia belangeri	ENSTBEG00000013617	1 retrocopy	retro_tbel_2390 ,
Drosophila melanogaster	FBgn0027066	1 retrocopy	retro_dmel_83,