RetrogeneDB ID: retro_tbel_4326

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_7690:4051..4515(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SC5D
• Ensembl ID: ENSTBEG00000000490
• Aliases: None
• Description: sterol-C5-desaturase [Source:HGNC Symbol;Acc:10547]

Sequence

>retro_tbel_4326
TTTTTTACCCCATATGCATATCCAGCCTCCTGGCCAGTGGATGACATCTTCCAACAAACAATTAGTCTCCTGGTTGTAAC
AAACATTGGTGCTTATATCTTTCATTTCTTCTGTGCAACATTGAGCTATTATTTTGTCTTTGATCATGACTTAATAAAAC
ATCCACAATTTTTAAAGAATCAAGTCTATCAAGAGATTAAGTTTATTGTCCAGTCATTACCATGGCTAAGTATTCACACT
ATTTCATTGTTCCTGCTGGAGCTGAGAGGTTATAGCAAATTATATGATGACATAGGAGAGTTTCCAAATGGCTGGTTTCA
ACTCATCTTTAGTATAATATTCTTCCTCTTTTTAACTGGCATGCAGATCTAGTGGATTCACAGAGGACTTCATCAAGACT
CATGTATAAGTGCATACATAAGACTTATCATATTTGGAAGAGTCTGACTCCATTTGTAAGTCAT

Alignment

ORF - retro_tbel_4326 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.92 %
• Parental protein coverage: 52.01 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  FFTPYVYPATWPEDNIFRQTISLLIVTNIGAYILYFICATLSYYFVFDHDLMKHPQFLKNQVYREIKFTV
          FFTPY.YPA.WP.D.IF.QTISLL.VTNIGAYI..F.CATLSYYFVFDHDL.KHPQFLKNQVY.EIKF.V
Retrocopy FFTPYAYPASWPVDDIFQQTISLLVVTNIGAYIFHFFCATLSYYFVFDHDLIKHPQFLKNQVYQEIKFIV

Parental  QSLPWISIPTVLLFLLELRGYSKLYDDVGEFPNGWFHLVLSVGSFLFFTDMLIYWIHRGLHH-RLVYKRI
          QSLPW.SI.T..LFLLELRGYSKLYDD.GEFPNGWF.L..S...FLF.T.M.I.WIHRGLH..RL.YK.I
Retrocopy QSLPWLSIHTISLFLLELRGYSKLYDDIGEFPNGWFQLIFSIIFFLFLTGMQI*WIHRGLHQ<RLMYKCI

Parental  HKPHHIWKIPTPFASH
          HK..HIWK..TPF.SH
Retrocopy HKTYHIWKSLTPFVSH

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_4326 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_4326 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 10 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000019246	1 retrocopy	retro_btau_813,
Canis familiaris	ENSCAFG00000011805	1 retrocopy	retro_cfam_291,
Callithrix jacchus	ENSCJAG00000007436	1 retrocopy	retro_cjac_1911,
Monodelphis domestica	ENSMODG00000013028	1 retrocopy	retro_mdom_1086,
Mustela putorius furo	ENSMPUG00000005754	1 retrocopy	retro_mputfur_484,
Ochotona princeps	ENSOPRG00000003219	1 retrocopy	retro_opri_1143,
Ictidomys tridecemlineatus	ENSSTOG00000008946	1 retrocopy	retro_itri_964,
Tupaia belangeri	ENSTBEG00000000490	1 retrocopy	retro_tbel_4326 ,
Tarsius syrichta	ENSTSYG00000011139	1 retrocopy	retro_tsyr_1097,
Tursiops truncatus	ENSTTRG00000006908	1 retrocopy	retro_ttru_777,