RetrogeneDB ID: retro_tbel_2538

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_112733:148726..149722(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FAM149A
• Ensembl ID: ENSTBEG00000003592
• Aliases: None
• Description: family with sequence similarity 149, member A [Source:HGNC Symbol;Acc:24527]

Sequence

>retro_tbel_2538
CACCATGGCCACCGCAGAGGGCTGTGTGCCTCTGGCTCTCAGGTAGTCCCAGCAGCCCTCCCTGCCTCCGCCCTGCCAGG
CCCCGATGGCACAGGGATCGCGGACCTCAGACCACGTTCATTCCTGGAAGAAGAGGTTTACAACATGGATAGAAAGATTG
AAGAATATTTTGCTTTGGACAGAAAAGAAGATGATGAGGCGTGTCCTGAACAGAAGCCACCTTATCGCCGTGGAAAGTGG
CAGAAACATGGACTTCCTCCCATTTCCCCTCATGATTGCATCAAAGATGCGGTGGTGTCGGAAGTGTTTGATCACGTCTG
GAAAAATTCGGTAGAAATATTGGAGGAACTGATTAGAAAAAAGTGGGAAACTACACTCACAGAAAATAAACAGAAAGAAA
TGTTGAAAGTAGCTGAAAATAAACCTTCAAATACACTCCTTTCCCGTATTAATGCTGACGTCTTAAGTGTTCCCCCGTCC
AGAAGTTCTGAAACTCGCAGCATATCTCTGGCTTCTCATCTTAATCCACCCCAGATTCCTCGCTTCTCCAGCAATTTTTA
TAGTGATTTGAAGGGCGTGATGACAATTCAAGCATAATCACTTCAGCAGAGACCTACCTATTTAGCAGACAGAACACAGA
ATGAGCAAGAAGACAAATCATTGGGCATTGGGGGCAACGCTCTTTTCTCTGCACGGCACCGACTGGGACGAATCTTAGAT
ACTCGAGGATTACAGACTTCTGCAAAGAAACACTGGTGCATAGGAACTTGCCATCTCTTGCTTCAGAGACACAGAGAATA
AAATCCCTAATGTGTATAGTGATGAAGTTCTTAGGAGAACAAAACTGCAAACCGGCACAACCACACATCTTCCCCTGTAG
CTCAAACCACTTGGAGCAGGTTTCCTCCCACAGGCTCAGAGACCGGGGAGCAACACCCAACAATTCCCAGATCCTGCGCT
GTTTCTTACAGAGGAAGATATTCACAAAACCGTGTT

Alignment

ORF - retro_tbel_2538 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.29 %
• Parental protein coverage: 59.96 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  HHGHRRGLCVSGSQVVPAALPASALPGPDGTGIADLTPRTSLEEEVYDMDGKIEEYFAFDRKEDDEACPE
          HHGHRRGLC.SGSQVVPAALPASALPGPDGTGIADL.PR..LEEEVY.MD.KIEEYFA.DRKEDDEACPE
Retrocopy HHGHRRGLCASGSQVVPAALPASALPGPDGTGIADLRPRSFLEEEVYNMDRKIEEYFALDRKEDDEACPE

Parental  QTPAHRRGKWRKHGLPPVSPHDCIKDAVVSEVFDHVWKNAVEILEELIRKKWETTLTEIKKQKEKLKVAE
          Q.P..RRGKW.KHGLPP.SPHDCIKDAVVSEVFDHVWKN.VEILEELIRKKWETTLTE..KQKE.LKVAE
Retrocopy QKPPYRRGKWQKHGLPPISPHDCIKDAVVSEVFDHVWKNSVEILEELIRKKWETTLTE-NKQKEMLKVAE

Parental  NKPANTLLSRINADVLSVPPSRSSETRSVSLASHLNPPQCYIPRFSSNFYSDLNGVMTIQAKPLQQRPTY
          NKP.NTLLSRINADVLSVPPSRSSETRS.SLASHLNPPQ..IPRFSSNFYSDL.GVMTIQA..LQQRPTY
Retrocopy NKPSNTLLSRINADVLSVPPSRSSETRSISLASHLNPPQ--IPRFSSNFYSDLKGVMTIQA*SLQQRPTY

Parental  FADRTQNEQEDKSLGTGGNALFSARHRLGRILDTRGSQTSAKK-TPVHRRLPSLASETQRIKT-PNVYSD
          .ADRTQNEQEDKSLG.GGNALFSARHRLGRILDTRG.QTSAKK.T.VHR.LPSLASETQRIK..PNVYSD
Retrocopy LADRTQNEQEDKSLGIGGNALFSARHRLGRILDTRGLQTSAKK<TLVHRNLPSLASETQRIKS<PNVYSD

Parental  EVLRGTKLQTGT-DHASSPAAPTTRSRFPPIGPETGXXHPAIPGSCPCFLYRGRYPQSRV
          EVLR.TKLQTGT..H.SSP.A.TT.SRFPP.G.ETG..HP.IP.SC....YRGRY.Q.RV
Retrocopy EVLRRTKLQTGT<NHTSSPVAQTTWSRFPPTGSETGEQHPTIPRSC-AVSYRGRYSQNRV

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_2538 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_2538 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 1 parental gene, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Tupaia belangeri	ENSTBEG00000003592	2 retrocopies	retro_tbel_2538 , retro_tbel_2863,