RetrogeneDB ID: retro_tbel_4634

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_94884:466..863(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RAB11B
• Ensembl ID: ENSTBEG00000000667
• Aliases: None
• Description: RAB11B, member RAS oncogene family [Source:HGNC Symbol;Acc:9761]

Sequence

>retro_tbel_4634
TACTGTGGAGGCGCTGTAGGTGTCTTACTGGGTTATGACATTGCTAAACATCTCACCTACGAAAATGTGGAGCATGACTG
AAAGCACTGAGAGATCAAGCCGACAGTAACATTGTTATCATGCTCCTGGGCAACAAGAGTGATTTACCTCATCGCAGGGC
AGTTCCTACAGATGAAGCAAGAGCTTTTGCAGAAAAGAGTGGTTTGAGACATCTGCTCTGGACTCTACAAATGTAGAAGC
TGCTTTTCAGACAACTCTAACAGAGACATATCGCAGTGTTTCTCGGAAGCAAATGTCAGACAGACGTGAAAACGACACAT
CTCCAAGCAACATGATTCCTATTCATGTCCCACCAACCACTGAATACAAGCCAATTGTGCAGGGCTGTCAGAACATC

Alignment

ORF - retro_tbel_4634 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.25 %
• Parental protein coverage: 63.76 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  YYRGAVGALLVYDIAKHLTYENVERW-LKELRDHADSNIVIMLVGNKSDLRHLRAVPTDEAR-AFAEKNN
          Y..GAVG.LL.YDIAKHLTYENVE...LK.LRD.ADSNIVIML.GNKSDL.H.RAVPTDEAR..F..K..
Retrocopy YCGGAVGVLLGYDIAKHLTYENVEHD<LKALRDQADSNIVIMLLGNKSDLPHRRAVPTDEAR<SFCRKE-

Parental  LSFIETSALDSTNVEEAFKNILTEIYRIVSQKQIADRAAHDESPGNNVVDISVPPTTDGQKPNKLQCCQN
          ....ETSALDSTNVE.AF...LTE.YR.VS.KQ..DR...D.SP..N...I.VPPTT...KP...Q.CQN
Retrocopy --WFETSALDSTNVEAAFQTTLTETYRSVSRKQMSDRRENDTSP-SNMIPIHVPPTTE-YKP-IVQGCQN

Parental  L
          .
Retrocopy I

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_4634 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_4634 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 9 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000013525	1 retrocopy	retro_chof_1582,
Callithrix jacchus	ENSCJAG00000010778	2 retrocopies	retro_cjac_3866, retro_cjac_3917,
Erinaceus europaeus	ENSEEUG00000009165	2 retrocopies	retro_eeur_284, retro_eeur_565,
Mus musculus	ENSMUSG00000077450	1 retrocopy	retro_mmus_1846,
Otolemur garnettii	ENSOGAG00000003227	1 retrocopy	retro_ogar_2405,
Petromyzon marinus	ENSPMAG00000009335	1 retrocopy	retro_pmar_25,
Pteropus vampyrus	ENSPVAG00000009645	1 retrocopy	retro_pvam_64,
Sarcophilus harrisii	ENSSHAG00000006816	1 retrocopy	retro_shar_189,
Tupaia belangeri	ENSTBEG00000000667	1 retrocopy	retro_tbel_4634 ,