RetrogeneDB ID: retro_ogar_3421

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873825.1:501231..501553(-)
• Located in intron of: ENSOGAG00000016081

Retrocopy information

• Ensembl ID: ENSOGAG00000026032
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: TUSC2
• Ensembl ID: ENSOGAG00000008080
• Aliases: None
• Description: tumor suppressor candidate 2 [Source:HGNC Symbol;Acc:17034]

Sequence

>retro_ogar_3421
ATGGGCGCCAGTGATTCCAAAGGTCGGGGCCTGTGGCCCTTTGCCGTGGGGGGAGCAGCAGCCCAGAGGTGCAGGCACTG
AGCAAGCTTTGGTGTGGCCTAGTGGCTGAGCCATGCCCCCCTTTGTATTCATGTGCGGCAACTCCATGTTCTATGCCGAG
GATGGAGATCTGGCCCAGTTCTATGAGGAGACAATTGTCACCAAGAACCGGCAGAAGTGGGCCAAGCTGAGGTGGGTGCA
TAAGAATCTGATTGCTCAGGGCATTGTGAAGCTGGATACCACCTGCATCTATGTGGATTTCCCTGTGATCTTCCATGAGG
TA

Alignment

ORF - retro_ogar_3421 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.32 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MGASGSKARGLWPFASAAGA-SSPE-AAAAEQALVRPRGRAVPPFVFTRRGSMFYDEDGDLAHEFYEETI
          MGAS.SK.RGLWPFA...GA.SSPE..A..EQALV.P.G.A.PPFVF....SMFY.EDGDLA..FYEETI
Retrocopy MGASDSKGRGLWPFA-VGGA<SSPE<GAGTEQALVWPSG*AMPPFVFMCGNSMFYAEDGDLA-QFYEETI

Parental  VTKNGQKRAKLRRVHKNLIPQGIVKLDPPRIHVDFPVILYEV
          VTKN.QK.AKLR.VHKNLI.QGIVKLD...I.VDFPVI..EV
Retrocopy VTKNRQKWAKLRWVHKNLIAQGIVKLDTTCIYVDFPVIFHEV

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Otolemur garnettii was not studied using RNA-Seq expression data.

ChIP-Seq

Otolemur garnettii was not studied using ChIP-Seq data.

EST

Otolemur garnettii was not studied using EST data.

TSS

Otolemur garnettii was not studied using FANTOM5 data.

Lab

retro_ogar_3421 was not experimentally validated.

Homology

Retrocopy orthology:

Otolemur garnettii 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 6 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000007859	2 retrocopies	retro_dord_20, retro_dord_590,
Felis catus	ENSFCAG00000031595	1 retrocopy	retro_fcat_1831,
Myotis lucifugus	ENSMLUG00000002499	1 retrocopy	retro_mluc_874,
Otolemur garnettii	ENSOGAG00000008080	3 retrocopies	retro_ogar_2293, retro_ogar_2714, retro_ogar_3421 ,
Tarsius syrichta	ENSTSYG00000010483	2 retrocopies	retro_tsyr_1922, retro_tsyr_2132,
Vicugna pacos	ENSVPAG00000007903	1 retrocopy	retro_vpac_221,