RetrogeneDB ID: retro_tbel_2160

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_102892:6859..7389(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMEM97
• Ensembl ID: ENSTBEG00000005125
• Aliases: None
• Description: transmembrane protein 97 [Source:HGNC Symbol;Acc:28106]

Sequence

>retro_tbel_2160
ATGGGGACTCTGAGCACCAGGCTCTGCGTGGAGTGACTGCTGGGCCTCTACTTTCTGTGCCACATCCCCATCACCCTGTT
CTTGGACATGCAATTGGCGCTGCTGACTGAACTCCACCTGGTAGCGTTTAGAAACCTGCTGTAGTGGTATGCTGAGGAGT
TCAGAGAACCTCTGCTCTAGGATCAACAGGTGTGGTTTAAGTCCTTTCTGTTCTGCAGCTTTTGTTTTAGCTGTCCTTCT
TTCCCTTTGCAACATATGCCTTCCTCTAAGGAAGCTGCAGGTAGATCCACGCCCCTGCAGTCATCTACACAGTTCACACC
ACGACCACTTTAGTTCCAATTCTCTCCACCATTCTAGTTGAGGAATTTTCCAAGGCCAGTTGTTTCAAAGGACAAAGACC
TGAGACTTTTGGCCAATGACTAGCTAGCCCTCCTATCAGTCTATGCCCCTACTTACTCATCCCTTTTATACTCCTGCTTT
TCATGTTGTGGAATACCTACTTCAAGTATGTGGAGAAAAGAAAGAAAAAA

Alignment

ORF - retro_tbel_2160 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.79 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 7
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MGVLSSRRCVEWLLGLYFLCHIPITLFLDMQLVLPAELYPVEFRNLLKWYAKEFRDPLLQDPPAWFKSFL
          MG.LS.R.CVE.LLGLYFLCHIPITLFLDMQL.L..EL..V.FRNLL.WYA.EFR.PLL.D...WFKSFL
Retrocopy MGTLSTRLCVE*LLGLYFLCHIPITLFLDMQLALLTELHLVAFRNLL*WYAEEFREPLL*DQQVWFKSFL

Parental  LC-ELVFQLPFFPFATYAFFKGCCRWIRIPAIIYAVHTITALIPILSTILVEDFSKASGFKGQRPETLRE
          .C..L.F.L.FFPFATYAF..G.CR.I..PA.IY.VHT.T.L.PILSTILVE.FSKAS.FKGQRPET...
Retrocopy FC<QLLF*LSFFPFATYAFL*GSCR*IHAPAVIYTVHTTTTLVPILSTILVEEFSKASCFKGQRPETFGQ

Parental  RLALVSV-YAPYLLIPFVLLLFMLRNPYYKYEEKRKKK
          .LA.......PYLLIPF.LLLFML.N.Y.KY.EKRKKK
Retrocopy *LASPPISLCPYLLIPFILLLFMLWNTYFKYVEKRKKK

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_2160 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_2160 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 11 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000011105	1 retrocopy	retro_chof_566,
Homo sapiens	ENSG00000109084	1 retrocopy	retro_hsap_4027,
Gorilla gorilla	ENSGGOG00000004565	1 retrocopy	retro_ggor_2703,
Macaca mulatta	ENSMMUG00000019142	1 retrocopy	retro_mmul_2323,
Mus musculus	ENSMUSG00000037278	1 retrocopy	retro_mmus_1451,
Nomascus leucogenys	ENSNLEG00000001868	1 retrocopy	retro_nleu_1574,
Otolemur garnettii	ENSOGAG00000003329	1 retrocopy	retro_ogar_1913,
Pongo abelii	ENSPPYG00000008086	1 retrocopy	retro_pabe_3307,
Pan troglodytes	ENSPTRG00000008909	1 retrocopy	retro_ptro_2731,
Ictidomys tridecemlineatus	ENSSTOG00000007542	2 retrocopies	retro_itri_341, retro_itri_758,
Tupaia belangeri	ENSTBEG00000005125	2 retrocopies	retro_tbel_2160 , retro_tbel_2221,