RetrogeneDB ID: retro_tbel_4254

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_73351:974..1686(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: AADAT
• Ensembl ID: ENSTBEG00000015548
• Aliases: None
• Description: aminoadipate aminotransferase [Source:HGNC Symbol;Acc:17929]

Sequence

>retro_tbel_4254
GACATATTGAGCAGGTCATAAAAGCCACTCACCCCTTTGGGATCACTAAATCTGAACATGCTTCCCTTTAAGATGGCTGT
TCTCACTGTAGAAGATGGAGAGACCATCCAATGTGGAGAAGAGATGAAGAGAGCGCTTCAGTATTCTCCAAGTGCTGGAA
TGCCAGCACTTGTGTCTTGGCTCAAACAGCTACAAATAAAATTGCATAATCCTCCCATGCATTACTCACTCAGTCAAGGA
CAAATAGACTTATATGTCACATCTGGCAGCCAAGATGGCTTTGTAAGGTATTCGACATGATCGTTAATCCTGGAGATACT
ACCCTGCAAATGAACCTGTATTCAGGAACTCTTCAAACCCTTCGACCACTGGGCTGCAACGTTACTAATGTTGCCAGTGA
TGAGATGGGGTGATTCCAGACTCCCTTGAGGAAACTCTTTCCAAATGGAAACCAGAAGATTCAAAGAATTCTAAGAAAAA
CACCCCCAAACTTCTTTATACTGTTCCAGATGGCAATAACCCTATTCAGTACTCCTTGACAAGTGATGGCTAAAAAGAAA
TCTGATCGTGCAAGAAAATATGATTTTTTCATAATAGAAGATGATCCTTACTATTAATATTTTCTTCAGTTGATGAGTTT
TGGGCACTTATGTTTCTTTCCATGGGCGTTGATGGGCGTGTCATCAGAGTGGACTCTTTCAAAAATCCTCTC

Alignment

ORF - retro_tbel_4254 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.53 %
• Parental protein coverage: 60.35 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  DILVRSQKPLIPLGTGSPNPNMFPFKTAVITVENGKPIQFEEEMMKKALQYSPSTGIPELVSWLKKLQIK
          DIL.RS.KPL.PLG..S.N.NM.PFK.AV.TVE.G..IQ..EEM.K.ALQYSPS.G.P.LVSWLK.LQIK
Retrocopy DILSRS*KPLTPLG--SLNLNMLPFKMAVLTVEDGETIQCGEEM-KRALQYSPSAGMPALVSWLKQLQIK

Parental  LHNPPTIHSPSSEGQMDLCVTSGSQEG-LCKVFEMIINPGDNVLVNEPIYSGTLQVFRALGCNMINVASD
          LHNPP..H...S.GQ.DL.VTSGSQ.G.LCKVF.MI.NPGD..L.....YSGTLQ..R.LGCN..NVASD
Retrocopy LHNPP-MHYSLSQGQIDLYVTSGSQDG<LCKVFDMIVNPGDTTLQMN-LYSGTLQTLRPLGCNVTNVASD

Parental  E-NGMIPDSLEEILSKWKPEDSKNPKKNTPKLLYTVPNGNNPTGYSLTSD-RKNKIYKLARKYDFLIVED
          E..G.IPDSLEE.LSKWKPEDSKN.KKNTPKLLYTVP.GNNP..YSLTSD..K.K.........F.I.ED
Retrocopy E<DGVIPDSLEETLSKWKPEDSKNSKKNTPKLLYTVPDGNNPIQYSLTSD>AKKKSDRARKYDFFII-ED

Parental  DPY--YFLQF-NEPWEPTFLSMDIDGRVIRADSLSKIL
          DPY..YFLQ...E.W...FLSM..DGRVIR.DS....L
Retrocopy DPYY*YFLQL<DEFWALMFLSMGVDGRVIRVDSFKNPL

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_4254 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_4254 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 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Otolemur garnettii	ENSOGAG00000008331	2 retrocopies	retro_ogar_1395, retro_ogar_90,
Tupaia belangeri	ENSTBEG00000015548	1 retrocopy	retro_tbel_4254 ,