RetrogeneDB ID: retro_tbel_1231

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: GeneScaffold_4187:88175..88816(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EXOG
• Ensembl ID: ENSTBEG00000011185
• Aliases: None
• Description: endo/exonuclease (5'-3'), endonuclease G-like [Source:HGNC Symbol;Acc:3347]

Sequence

>retro_tbel_1231
AAAGCCATGGCTGAAACCTTTTATCTTTCTAATATTGTGCCTCAGAATTTTGATAATAAGTCTGGATACTGGAACAGAAT
GGAAATGTACTGTCGAGAACTGACAGAGAGGTTTGAAGAAGTTTGGGTAGTGTCTAGACCTTTGACTTTGCCAGAGACTA
AAAAGTGATGGAAAGAAAACAGTTATCAGGAGATCAGTGAGGACAACGTGGCAGTCCCCTCTCACCTTTACAAGGTGATC
CTGGCTCGCAGAAGCCCAGTCTCTACTGAACCCCTAGCACTCGGGGCCTTTGTGGTGCCCCATGAAGCCATTGGCTTCCA
ACCCCAGTTAACCGAATTCTAAGTGAGCCTCCAGGAACTGGAGAAGTGGTCAGGAAGTTGTCAGTTGTCTCATTTGGTTA
GAAATAGCAATATCACAAATATCTGCTCTGTGGACACATGCAAGTCCCTGGAGTTTCATGAGTTCACTCTGTACCTGAGT
ACAAGAAAGGTTTAGTGAGCCCAATCAGAGGGCAGGCTGGAGGAGGTCATGGAAAATTTGAAGAATGCAGAGGTCAAACC
AGATGACTATTTCCTGAGTCGCTATGAGAAGAAATTGGAAGAACTCAAAACCCAGAAGCAGTCAGGGACCCAGATGGAAA
A

Alignment

ORF - retro_tbel_1231 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.48 %
• Parental protein coverage: 58.74 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KAMAETFYLSNIVPQNFDNNSGYWNRMEMYCRELTERFEDVWVVSGPLTLPETKSDGKKTVSYQVIGEDN
          KAMAETFYLSNIVPQNFDN.SGYWNRMEMYCRELTERFE.VWVVS.PLTLPETK...K...SYQ.I.EDN
Retrocopy KAMAETFYLSNIVPQNFDNKSGYWNRMEMYCRELTERFEEVWVVSRPLTLPETKK*WKEN-SYQEISEDN

Parental  VAVPSHLYKVILARRSPDSTEPLALGAFVVPNEAIGFQPQLTEFQVSLQELEKLSGLVFFPHLDRNSNIT
          VAVPSHLYKVILARRSP.STEPLALGAFVVP.EAIGFQPQLTEF.VSLQELEK.SG.....HL.RNSNIT
Retrocopy VAVPSHLYKVILARRSPVSTEPLALGAFVVPHEAIGFQPQLTEF*VSLQELEKWSGSCQLSHLVRNSNIT

Parental  NICSVDTCRLLDFQEFTLYLSTRKIEGARSVGRLEKVMEHLKNAGIKPDDYFLSRYERKLQELKTQEQSG
          NICSVDTC..L.F.EFTLYLSTRK...A.S.GRLE.VME.LKNA..KPDDYFLSRYE.KL.ELKTQ.QSG
Retrocopy NICSVDTCKSLEFHEFTLYLSTRKV**AQSEGRLEEVMENLKNAEVKPDDYFLSRYEKKLEELKTQKQSG

Parental  S-PGGK
          ..P.GK
Retrocopy T<PDGK

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_1231 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_1231 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000005039	1 retrocopy	retro_cfam_1666,
Sorex araneus	ENSSARG00000009026	1 retrocopy	retro_sara_524,
Tupaia belangeri	ENSTBEG00000011185	1 retrocopy	retro_tbel_1231 ,