RetrogeneDB ID: retro_ogar_660

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873525.1:30629009..30629565(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOGAG00000028517
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CDO1
• Ensembl ID: ENSOGAG00000009306
• Aliases: None
• Description: cysteine dioxygenase type 1 [Source:HGNC Symbol;Acc:1795]

Sequence

>retro_ogar_660
GCTGATCTAATCCGCATCCTGCACCAGCTTTTCACCAGAGACAAAATCAATGTCGAGGAGGTGCCAGCCATCATGGAAGC
CTATGACTTGGCTGAGTGGGCAGTGTACGCCAAGTTCGATCAGTACAGGTATACAGAAAATCTTGTGGACCAAGGAAATG
GAAAATTTAATCTGATGATTTTATGTTGGGGTGAAGGACATGGCAGCAGTATTCGTGACCACACCAATTCCCACTGCTTT
CCGAAGATGCTACAGGGAAATCTAAAGGAGGCGCTATTTGCCTGGCCTGACAAAAAGTCCAATGAGATGGTCAAGAAGTC
TGAAAGAGACTTGAGGGACAACCGGCTGCCTGCGTCAGTGATTCCATTGGCTCACATCAAGTGGAGAACATCAGCCTCCA
GAACCTGCTGTGAGCCTTCACCTGTACAGTCCACTTTTTGATACATCCCATGCCTTTGATCAAAGAACGGGGCACAAAAA
TAACGTTACCATGACATTCCATAGCAAATTTGGAATCAGAACCCCATTTACAACTTCAGGTTCACTGGAGAACAAC

Alignment

ORF - retro_ogar_660 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.77 %
• Parental protein coverage: 94.06 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  ADLIRILHQLFAGDEVNVEEVQAVMEAYESDPAEWAVYAKFDQYRYTRNLVDQGNGKFNLMILCWGEGHG
          ADLIRILHQLF..D..NVEEV.A.MEAY..D.AEWAVYAKFDQYRYT.NLVDQGNGKFNLMILCWGEGHG
Retrocopy ADLIRILHQLFTRDKINVEEVPAIMEAY--DLAEWAVYAKFDQYRYTENLVDQGNGKFNLMILCWGEGHG

Parental  RYSSIHDHTDSHCFLKMLQGNLKETLFAWPDKKSNEMIKKSERVLRDNQ-CAYINDSIGLHRVENIS-HT
          ..SSI.DHT.SHCF.KMLQGNLKE.LFAWPDKKSNEM.KKSER.LRDN...A...DSIG.H.VENIS...
Retrocopy --SSIRDHTNSHCFPKMLQGNLKEALFAWPDKKSNEMVKKSERDLRDNR<AACVSDSIGSHQVENIS<PP

Parental  EPAVSLHLYSPPFDTCHALDQRTGHKNKVTMTFHSKFGVRTPYTTSGSLENN
          EPAVSLHLYSP.FDT.HA.DQRTGHKN.VTMTFHSKFG.RTP.TTSGSLENN
Retrocopy EPAVSLHLYSPLFDTSHAFDQRTGHKNNVTMTFHSKFGIRTPFTTSGSLENN

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_660 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
Dasypus novemcinctus	ENSDNOG00000009577	1 retrocopy	retro_dnov_2171,
Microcebus murinus	ENSMICG00000009005	1 retrocopy	retro_mmur_1405,
Otolemur garnettii	ENSOGAG00000009306	1 retrocopy	retro_ogar_660 ,
Tupaia belangeri	ENSTBEG00000003937	2 retrocopies	retro_tbel_3406, retro_tbel_4269,