RetrogeneDB ID: retro_tbel_1764

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: GeneScaffold_5664:11331..12509(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSTBEG00000005111
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSTBEG00000011602
• Aliases: None
• Description: None

Sequence

>retro_tbel_1764
CATGTCCTGATCTTTGATCTGGGCGGAGGCACTTTTGACGTGTCCATCTTGACCATAGACGATGGGATTTTTGAGGTGAA
GTGCCTATCGGCCGGGGACACGCACCTGGGTGGGGAGGACTTCGACAACAGGCTGGTGAACCACTTCGTGGAGGAGTTCA
AGAGGAAGCACAAGAAGGACATCAGCCAGAACAAGCGCGCCGTGAGGCGGCTGCGCACGGCCTGCGAGCGCGCCAAGAGG
ACCCTGTCGTCCAGCACGCAGGCCAACCTGGAGATCGACTCGCTGTTCGAGGGCATCGACTTCTACACGTCCATCACCAG
AGCCCGGTTTGAAGAGTTGTGTGCAGACTTGTTTAGGGGCACCTTGGAACCTGTGGAAAAAGCTCTTCGGGATGCCAAGA
TGGACAAGGCTAAAATCCATGACATTGTTTTAGTAGGGGGCTCCACCCGCATCCCTAAGGTGCAGAGGCTGCTTCAAGAT
TACTTTAATGGACGTGATCTCAATAAGAGCATCAACCCTGACGAGGCGGTGGCCTACGGGGCGGCGGTGCAGGCCGCCAT
CCTGATGGGGGACAAGTCTGAAAAGGTGCAGGACCTGCTGCTGCTGGACGTGGCGCCCCTGTCGCTGGGGCTGGAGACTG
CGGGCGGTGTGATGACTGTCCTGATCAAGCGCAACTCCACCATCCCCACCAAGCAGACGCAGATCTTCACCACGTACTCG
GACAACCAGCCCGGGGTGCTGATCCAGGTGTACGAGGGTGAGAGGGCCATGACGAAGGACACAACCTGCTGGGGCGCTTT
GACCTGACTGGAATCCCTCCCGCACCCAGAGGAGTTCCTCAGATTGAGGTGACCTTTGACATCGACGCCAATGGCATCCT
GAACGTCACGGCCATGGACAAGAGCACCGGCAAGGCCAACAAGATCACCATCACCAACGACAAGGGCCGCCTGAGCAAGG
AGGAGATCGAGCGCATGGTGCAGGAGGCCGAGAAGTACAAAGCCGAGGACGAGGTCCAGAGGGAGAAAATTGCTGCCAAA
AATGCCTTAGAATCCTATGCTTTTAATATGAAGAGTGCTGTGAGTGATGATGGTTTAAAGGGCAAGATCAGCGAGTCTGA
TAAGAAGAAAATACTGGATAAATGCAACGAGGTCCTTTCATGGCTCGAGGCCAATCAA

Alignment

ORF - retro_tbel_1764 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.53 %
• Parental protein coverage: 67.01 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  NVLIFDLGGGTFDVSILTIEDGIFEVKS-TAGDTHLGGEDFDNRMVNHFIAEFKRKHKKDISENKRAVRR
          .VLIFDLGGGTFDVSILTI.DGIFEVK...AGDTHLGGEDFDNR.VNHF..EFKRKHKKDIS.NKRAVRR
Retrocopy HVLIFDLGGGTFDVSILTIDDGIFEVKCLSAGDTHLGGEDFDNRLVNHFVEEFKRKHKKDISQNKRAVRR

Parental  LRTACERAKRTLSSSTQASIEIDSLYEGIDFYTSITRARFEELNADLFRGTLDPVEKALRDAKLDKSQIH
          LRTACERAKRTLSSSTQA..EIDSL.EGIDFYTSITRARFEEL.ADLFRGTL.PVEKALRDAK.DK..IH
Retrocopy LRTACERAKRTLSSSTQANLEIDSLFEGIDFYTSITRARFEELCADLFRGTLEPVEKALRDAKMDKAKIH

Parental  DIVLVGGSTRIPKIQKLLQDFFNGKELNKSINPDEAVAYGAAVQAAILSGDKSENVQDLLLLDVTPLSLG
          DIVLVGGSTRIPK.Q.LLQD.FNG..LNKSINPDEAVAYGAAVQAAIL.GDKSE.VQDLLLLDV.PLSLG
Retrocopy DIVLVGGSTRIPKVQRLLQDYFNGRDLNKSINPDEAVAYGAAVQAAILMGDKSEKVQDLLLLDVAPLSLG

Parental  IETAGGVMTVLIKRNTTIPTKQTQTFTTYSDNQPGVLIQVYEGERAMTKD-NNLLGKFELTGIPPAPRGV
          .ETAGGVMTVLIKRN.TIPTKQTQ.FTTYSDNQPGVLIQVYEGERAMTKD..NLLG.F.LTGIPPAPRGV
Retrocopy LETAGGVMTVLIKRNSTIPTKQTQIFTTYSDNQPGVLIQVYEGERAMTKD<HNLLGRFDLTGIPPAPRGV

Parental  PQIEVTFDIDANGILNVSAVDKSTGKENKITITNDKGRLSKEDIERMVQEAEKYKAEDEKQRDKVSSKNS
          PQIEVTFDIDANGILNV.A.DKSTGK.NKITITNDKGRLSKE.IERMVQEAEKYKAEDE.QR.K...KN.
Retrocopy PQIEVTFDIDANGILNVTAMDKSTGKANKITITNDKGRLSKEEIERMVQEAEKYKAEDEVQREKIAAKNA

Parental  LESYAFNMKATVEDEKLQGKINDEDKQKILDKCNEIINWLDKNQ
          LESYAFNMK..V.D..L.GKI...DK.KILDKCNE...WL..NQ
Retrocopy LESYAFNMKSAVSDDGLKGKISESDKKKILDKCNEVLSWLEANQ

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_1764 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_1764 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 4 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Erinaceus europaeus	ENSEEUG00000012704	1 retrocopy	retro_eeur_8,
Microcebus murinus	ENSMICG00000004702	1 retrocopy	retro_mmur_7,
Sorex araneus	ENSSARG00000000161	1 retrocopy	retro_sara_31,
Tupaia belangeri	ENSTBEG00000011602	8 retrocopies	retro_tbel_1764 , retro_tbel_344, retro_tbel_3488, retro_tbel_3524, retro_tbel_4348, retro_tbel_4412, retro_tbel_4490, retro_tbel_471,