RetrogeneDB ID: retro_tbel_3220

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_134109:1125..2009(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ATL2
• Ensembl ID: ENSTBEG00000002649
• Aliases: None
• Description: atlastin GTPase 2 [Source:HGNC Symbol;Acc:24047]

Sequence

>retro_tbel_3220
ACTTTAATGTTTTTGATTCAAGATTGGAGTTATTATAAACATTCTTATGGTTTGGAAGGTGGAAAACAATTCCTTGAAAG
AGATTGCAGATAAAACAAAATCAACATGAAGAGCTACAGAATGTAAGGAAGCACATTAATAATTATTTCTCAAATCTTGA
CTGCATCCTTTTGCCATATCCTATTCTTAAAGTTGCAACTAATCCTAGTTTTGATGGGAGAATGAAAGATATTGCTGAAG
ACTTTAAATGAGAGCTTCAAATTCTAGTTCCATTGCTGCTTGCCCCTGAGAATTTGGTAGAAAAAGAATTAAGTGATCTG
AAGTCACTTATAGAGATCTTGTAGAATATTTTAAGGCTTACATTAAAGTTTATCAAAGAGAGGAGCTTCCACGTCCAAAG
TCCTCGCTTCAGGCAATAGCTGAAGCTAATACTCTTACTGTAGTAGTGTGAGCAAGAGATACCCATTGCAAAAGTATGGA
ACAGATACGTGGTGGGGACAAGGTTTATATTGCACCTTCAGATCTGGAGCAAAAACACCTTGATCTCAAGGAAGTGGCTA
TCAAACAGTTTTGTTCTGTAAAAAAAAAAAGGGGCAGAGATCAGTTCTGCCATTTATAGCAGGACTAGCTTGAAGCTGAA
ATTGAGGAAACCTATGCAAATTTTACAAAGCACAATTGCAAAAATATCTTCTATGTTGTTAGTACTCCTGCTACCCTGTC
CGCGGTCTGTTTACTATGTATATAATCTCAAAACTGACTGGCTTCATTGGCCTAAATCTATTGCTGTCTTGTGTAACCTT
GTCATGGGGTTAGCACTGATGTCTCTTTGTAGATGGGCATATTTTAAATACTCTGGGGAGTTCAGATAAATTGGAACAAT
GATT

Alignment

ORF - retro_tbel_3220 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.15 %
• Parental protein coverage: 54.7 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  TLMFLIRDWSYPYEHSYGLEGGKQFLE-KRLQVKQNQHEELQNVRKHIHNCFSNLGCFLLPHPGLKVATN
          TLMFLI.DWSY.Y.HSYGLEGGKQFLE.KRLQ.KQNQHEELQNVRKHI.N.FSNL.C.LLP.P.LKVATN
Retrocopy TLMFLIQDWSY-YKHSYGLEGGKQFLE<KRLQIKQNQHEELQNVRKHINNYFSNLDCILLPYPILKVATN

Parental  PSFDGRLKDIDEDFKRELRNLVPLLLAPENLVEKEISG-SKVTCRDLVEYFKAYIKIYQGEELPHPKSML
          PSFDGR.KDI.EDFK.EL..LVPLLLAPENLVEKE.S..S.VT.RDLVEYFKAYIK.YQ.EELP.PKS.L
Retrocopy PSFDGRMKDIAEDFK*ELQILVPLLLAPENLVEKELSD<SEVTYRDLVEYFKAYIKVYQREELPRPKSSL

Parental  QATAEANNLAAVAGARDIYCKSMEQVCGGDKPYIAPSDLERKHLDLKEVAIKTFRSVKKMGG-DEFCRRY
          QA.AEAN.L..V..ARD..CKSMEQ..GGDK.YIAPSDLE.KHLDLKEVAIK.F.S.....G.D.FC...
Retrocopy QAIAEANTLTVVV*ARDTHCKSMEQIRGGDKVYIAPSDLEQKHLDLKEVAIKQFCSXXXXXGRDQFCHL*

Parental  QDQLEAEIEETYANFIKHNDGKNIFYAARTPATLFAV-MFAMYIISGLTGFIGLN-SIAVLCNLVMGLAL
          QD.LEAEIEETYANF.KHN..KNIFY...TPATL.AV..F.MYIIS.LTGFIGLN.SIAVLCNLVMGLAL
Retrocopy QD*LEAEIEETYANFTKHN-CKNIFYVVSTPATLSAV<LFTMYIISKLTGFIGLN<SIAVLCNLVMGLAL

Parental  TSLCTWAYVKYSGEFREIGTMI
          .SLC.WAY.KYSGEFR.IGTMI
Retrocopy MSLCRWAYFKYSGEFR*IGTMI

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_3220 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_3220 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
Cavia porcellus	ENSCPOG00000013597	1 retrocopy	retro_cpor_1282,
Tupaia belangeri	ENSTBEG00000002649	1 retrocopy	retro_tbel_3220 ,