RetrogeneDB ID: retro_ogar_1455

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873547.1:17736051..17736849(-)
• Located in intron of: ENSOGAG00000033298

Retrocopy information

• Ensembl ID: ENSOGAG00000001783
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CAB39
• Ensembl ID: ENSOGAG00000002000
• Aliases: None
• Description: calcium binding protein 39 [Source:HGNC Symbol;Acc:20292]

Sequence

>retro_ogar_1455
TATATAACAGCGGCCTCCGGCACCCTGGTAGCTGATTTGCAGCTCATTGACTTTGAGGGCAAAAAAGACGTGGCTCAAAT
TTTCAACAATATTCTCAGAAGACAAATTGGTACAAGAACTCCTACTGTTGAATACATCTGCACCCAACAGAATATTTTGT
TCATGTTATTGAAAGGGTATGAATCTCCAGAAATAGCTCTAAATTGTGGAATAATGTTAGGAGACTGCATCAGACATGAA
CCACTTGCAAAAATCATTTTGTGGTCGGAACAGTTTTATGATTTCTTCAGCTATGTGGAAATGTCAACATTTGACATAGC
TTCAGATGCATTTGCCACATTCAAGGATTTACTTACAAGACATAAATTGCTCAGTGCAGAATTTTTGGAGCAGCATTATG
ATAGATTTTTCAGTGAGTATGAGAAGTTACTTCATTCAGAAAATTATGTGACAAAAAGGCAGTCACTCAAGCTTCTTGGT
GAACTACTATTAGATAGACACAACTTCACAATTATGACAAAATACATCAGTAAACCTGAGACCCTCAAATTAATGATGAA
CCTTCTACGAGACAAAAGCTGTAACATCCAGTTTGAGGCCTTCCACGTTTTTAAGGTGTTTGTAGCCAATCCTAACAAGA
CACAGCCCATCCTGGACATCCTCAAGAACCAGACCAAACTCCTAGAGTTCCTCAGCAAGTTTCAGAATGACAGGACCAAG
GACGAGCAGTTTAACGATGAGAAGACCTATTTAGTTAAACAGATCAGGGATTTGAAGAGACCAGCTCAGCAAGAAGCT

Alignment

ORF - retro_ogar_1455 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.76 %
• Parental protein coverage: 78.3 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  YNSGLLSTLVADLQLIDFEGKKDVAQIFNNILRRQIGTRTPTVEYICTQQNILFMLLKGYESPEIALNCG
          Y......TLVADLQLIDFEGKKDVAQIFNNILRRQIGTRTPTVEYICTQQNILFMLLKGYESPEIALNCG
Retrocopy YITAASGTLVADLQLIDFEGKKDVAQIFNNILRRQIGTRTPTVEYICTQQNILFMLLKGYESPEIALNCG

Parental  IMLRECIRHEPLAKIILWSEQFYDFFRYVEMSTFDIASDAFATFKDLLTRHKLLSAEFLEQHYDRFFSEY
          IML..CIRHEPLAKIILWSEQFYDFF.YVEMSTFDIASDAFATFKDLLTRHKLLSAEFLEQHYDRFFSEY
Retrocopy IMLGDCIRHEPLAKIILWSEQFYDFFSYVEMSTFDIASDAFATFKDLLTRHKLLSAEFLEQHYDRFFSEY

Parental  EKLLHSENYVTKRQSLKLLGELLLDRHNFTIMTKYISKPENLKLMMNLLRDKSRNIQFEAFHVFKVFVAN
          EKLLHSENYVTKRQSLKLLGELLLDRHNFTIMTKYISKPE.LKLMMNLLRDKS.NIQFEAFHVFKVFVAN
Retrocopy EKLLHSENYVTKRQSLKLLGELLLDRHNFTIMTKYISKPETLKLMMNLLRDKSCNIQFEAFHVFKVFVAN

Parental  PNKTQPILDILLKNQTKLIEFLSKFQNDRTEDEQFNDEKTYLVKQIRDLKRPAQQEA
          PNKTQPILDI.LKNQTKL.EFLSKFQNDRT.DEQFNDEKTYLVKQIRDLKRPAQQEA
Retrocopy PNKTQPILDI-LKNQTKLLEFLSKFQNDRTKDEQFNDEKTYLVKQIRDLKRPAQQEA

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_1455 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 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000013349	1 retrocopy	retro_cjac_4227,
Equus caballus	ENSECAG00000015288	1 retrocopy	retro_ecab_288,
Otolemur garnettii	ENSOGAG00000002000	1 retrocopy	retro_ogar_1455 ,
Otolemur garnettii	ENSOGAG00000016755	2 retrocopies	retro_ogar_2297, retro_ogar_3157,