RetrogeneDB ID: retro_tbel_4008

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_53546:256..812(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: AIMP1
• Ensembl ID: ENSTBEG00000004412
• Aliases: None
• Description: aminoacyl tRNA synthetase complex-interacting multifunctional protein 1 [Source:HGNC Symbol;Acc:10648]

Sequence

>retro_tbel_4008
GTGGAAAAGAAAGGAGAGATGCAGGGAAGAAAAATCAGACCATCTGTAGCACCAAGTGCTTAAGCCAGTAGCAGTTTAAC
GGAGTAGAGCTTCGAACGGATCGCATGGCAACTGTCAGAAAACAGCCTGATGCAGATTCTGGATATATGGAGGAAGTCGA
CGCTCGTGATACAGTCCCAAAACAGTTGTCAGTGGCGAGGGGAATCATGTTCCCCTCGAGCGGATGCAGAATCGGATGGT
GGTTTTACTGTGTAACCTGAAACAGCCGGAGATGAGGGGAGTACTGTCTCCAGCAAGGGTCATGTGTGGTAGCTCCCCCG
AGGAGGTCGAAATCTGGGCTCTTCCTGATGGGTCTGTTCCAGGAGACAAAATTACTTTCGATGCCTTCCCTGGAGAACCC
AACAAGGAGCTGAATCCGAAGAAGAAGATTTGGGAGCAGATCCAGCCCGATCTTCACACCAATGAGGACTGCGTGGCCAC
CTACAGAGGCGTGCCCTTCCAGGTGAAAGGGAAGGGCATGTGTAGGGCGCAGACCATGGCTAACAGCGGGATCAAA

Alignment

ORF - retro_tbel_4008 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.74 %
• Parental protein coverage: 60. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VEKKGEKKE-KKQPSVAASADSKPVDVSRLDLRIGCIVTARKHPDADSLYVEEVDVGEP-APRTVVSGLV
          VEKKGE....KK...................LR.....T.RK.PDADS.Y.EEVD......P.TVVSG..
Retrocopy VEKKGEMQG<KKNQTICSTKCLSQ*QFNGVELRTDRMATVRKQPDADSGYMEEVDARDT<SPKTVVSGEG

Parental  NHVPLEQMQNRMVVLLCNLKPAKMRGVVSQAMVMCASSPEKVEILAPPEGSVPGDKITFDAFPGEPDKEL
          NHVPLE.MQNRMVVLLCNLK...MRGV.S.A.VMC.SSPE.VEI.A.P.GSVPGDKITFDAFPGEP.KEL
Retrocopy NHVPLERMQNRMVVLLCNLKQPEMRGVLSPARVMCGSSPEEVEIWALPDGSVPGDKITFDAFPGEPNKEL

Parental  NPKKKIWEQIQPDLHTNEDCVATYRGVPFQVKGKGVCRAQTMANSGIK
          NPKKKIWEQIQPDLHTNEDCVATYRGVPFQVKGKG.CRAQTMANSGIK
Retrocopy NPKKKIWEQIQPDLHTNEDCVATYRGVPFQVKGKGMCRAQTMANSGIK

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_4008 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_4008 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 9 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000619	2 retrocopies	retro_chof_1176, retro_chof_2050,
Callithrix jacchus	ENSCJAG00000015885	1 retrocopy	retro_cjac_2504,
Dipodomys ordii	ENSDORG00000005018	1 retrocopy	retro_dord_540,
Mustela putorius furo	ENSMPUG00000008952	1 retrocopy	retro_mputfur_1606,
Mus musculus	ENSMUSG00000028029	2 retrocopies	retro_mmus_2271, retro_mmus_3334,
Pongo abelii	ENSPPYG00000014981	1 retrocopy	retro_pabe_1780,
Rattus norvegicus	ENSRNOG00000011384	1 retrocopy	retro_rnor_1704,
Ictidomys tridecemlineatus	ENSSTOG00000008178	1 retrocopy	retro_itri_1173,
Tupaia belangeri	ENSTBEG00000004412	1 retrocopy	retro_tbel_4008 ,