RetrogeneDB ID: retro_ogar_1077

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873535.1:19646913..19647867(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GPBP1
• Ensembl ID: ENSOGAG00000013991
• Aliases: None
• Description: GC-rich promoter binding protein 1 [Source:HGNC Symbol;Acc:29520]

Sequence

>retro_ogar_1077
GCTCCTCTCTTAGAATATCCTCTGAATCCTAAATCTAGAGCTCCAAGGATGCTGGTCATTAAGAAAGGTAATACAAAAGA
CTTACAGCTATCTGGATTCCCAGTAGTAGGAAATCTTCAGTCACAGCCAGTTAAGAACGGAACTGGTCCCAGTGTTTATA
AAGGTTTAGTCCCCAAACCTGCTGCTCCACCTATAACACCTATACCATGGAAAAGCCAAACTAAAGAAAATAAAGTTGGG
ACTTCTTTCCCCAATGAGTCTACATATGGTGTTGGCAACTTTCATGCTTTTAAATCAACTGCCAAGAATTTTAGTCCATC
AGCTAATTCAGTGAAAGAGTGTAATTGCTCAAATTCCTCTTCACCTGTTGACAAACTTAATCAGCAGCCTCCTCTAACCA
AACTGACATGAATGTGCACTGATAAGAAGAGTGAATTTTTGAAAGCATTGAAAAGGGACAGAGTAGAAGAGGAACATGAA
GATGAAAGCCATGCTGGCTCAGAGAAGGATGAAGACTCATTTAATTTACATAACAGCAATAGCACTCACCAAGAAAGGGA
TATAAACTGGAACTTGGATGAAAATGAAATTCCGCAAGAGAATGGCAATGTCTCAGTGATTTCCCAACAAGTCATTCATT
CTTCAACCTTCCTGCAAACTGACGTTCTTTCAAGTTCACTTGAGGCAGAACACAGACTGTTGAAGGAGATGGGCTGGCAG
GAAGGCAGTGAAAATGATGAAACATGTGCTCCTTTAACTGAGGATGAAATGAGAGAATTCCAAGTTATCAGTGAACAGTT
ACAGAAGAATGGTCTGAGAAAAAACGGCATTTTGAAAAATGGCCTGACCTGTGACTTCAAGTTTGGACCTTGGAAAAACA
GCACTTTCAAACCCACAATTGAGAATGATGACACAGAGACAAGTAGCAGTGACACACTGGATGACGACGATGTG

Alignment

ORF - retro_ogar_1077 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.45 %
• Parental protein coverage: 69.74 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AGVWEYPPNPKSRAPRMLVIKKGNTKDLQLSGFPVVGNLQSQPVKNGTGPSVYKGLVPKPAAPPTKPTQW
          A...EYP.NPKSRAPRMLVIKKGNTKDLQLSGFPVVGNLQSQPVKNGTGPSVYKGLVPKPAAPP..P..W
Retrocopy APLLEYPLNPKSRAPRMLVIKKGNTKDLQLSGFPVVGNLQSQPVKNGTGPSVYKGLVPKPAAPPITPIPW

Parental  KSQTKENKVGTSFPHESTYGVGNFNAFKSTAKNFSPSANSVKECNRSNSSSPVDKLNQQPRLTKLTRMRT
          KSQTKENKVGTSFP.ESTYGVGNF.AFKSTAKNFSPSANSVKECN.SNSSSPVDKLNQQP.LTKLT.M.T
Retrocopy KSQTKENKVGTSFPNESTYGVGNFHAFKSTAKNFSPSANSVKECNCSNSSSPVDKLNQQPPLTKLT*MCT

Parental  DKKSEFLKALKRDRVEEEHEDESHAGSEKDDDSFNLHNSNSTHQERDINRNFDENEIPQENGNASVISQQ
          DKKSEFLKALKRDRVEEEHEDESHAGSEKD.DSFNLHNSNSTHQERDIN.N.DENEIPQENGN.SVISQQ
Retrocopy DKKSEFLKALKRDRVEEEHEDESHAGSEKDEDSFNLHNSNSTHQERDINWNLDENEIPQENGNVSVISQQ

Parental  IIRSSTFPQTDVLSSSLEAEHRLLKEMGWQEDSENDETCAPLTEDEMREFQVISEQLQKNGLRKNGILKN
          .I.SSTF.QTDVLSSSLEAEHRLLKEMGWQE.SENDETCAPLTEDEMREFQVISEQLQKNGLRKNGILKN
Retrocopy VIHSSTFLQTDVLSSSLEAEHRLLKEMGWQEGSENDETCAPLTEDEMREFQVISEQLQKNGLRKNGILKN

Parental  GLICDFKFGPWKNSTFKPTIENDDTETSSSDTSDDDDV
          GL.CDFKFGPWKNSTFKPTIENDDTETSSSDT.DDDDV
Retrocopy GLTCDFKFGPWKNSTFKPTIENDDTETSSSDTLDDDDV

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_1077 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 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000015104	1 retrocopy	retro_cjac_3961,
Microcebus murinus	ENSMICG00000014678	1 retrocopy	retro_mmur_1198,
Myotis lucifugus	ENSMLUG00000007462	1 retrocopy	retro_mluc_155,
Monodelphis domestica	ENSMODG00000019540	1 retrocopy	retro_mdom_283,
Otolemur garnettii	ENSOGAG00000004134	1 retrocopy	retro_ogar_1859,
Otolemur garnettii	ENSOGAG00000013991	1 retrocopy	retro_ogar_1077 ,
Ictidomys tridecemlineatus	ENSSTOG00000003057	1 retrocopy	retro_itri_1678,