RetrogeneDB ID: retro_ogar_3398

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873818.1:561089..562027(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CDC25A
• Ensembl ID: ENSOGAG00000002994
• Aliases: None
• Description: cell division cycle 25A [Source:HGNC Symbol;Acc:1725]

Sequence

>retro_ogar_3398
GATGAAGATGATGGCTTCCTGGACCTTCTTGATGGAGAGAATGTAAAGAATGATGAGGAGACCCCATCATGCATGGCAAA
CGGCTGGACAACTTCCCTTGTCATGAGAAGAACTACAAACCTGGGCAACTGAAGCAAGCTGTTTGACTCCCTTTCCTTTG
TAGCTCCAGCACTGGGTTATCATTGAAGAGACCAGAGCTATCTCAAGATGAGTCACCACCAGGAAATAGGAAGCAGAGAA
AAAGCGTAGGTGGGGACAGCCCCAAAGAAGCAGTTAATCCAGAGAAGGCCCGGGAGATTCCACTTCAGTCTTTATCTCTC
GTATCTTCGCCCAAAGGGACCATTGAGAACATTTTGGATAATGACCCAAGGGACCTTCTAGGAGATTTCTCCAAGGGTTG
TCTCTTTTATACAGTCACAGGGAAACATCAGGATTTGAAATACACATCTCCAGAAATTATAGGGTCTGTTCTGAGTGCCA
AGTTTGCCAACCTTATAAAAGAATTTGTTATCATTGACTGCTGATACCCATATGAACATGAGGGAGGCCACGTCGAGAGT
GCGGTAAATTTGCACATGGAAGAAGAGGTTGAAGACTTCTTACTCAAAAAGCCTATTGTTCCTACTGATGGCAAGCGTGT
CATTGTTGTGTTCCACTGCTAGTTTTCTTCTGAGAGAGGTCTCTGCATGTGCTAGTATGTGAAAAAAGGGAGATCAACTT
GGTAATGAATATCCCAAACTCCACTATGAGCTGTATGTCCTGAAGGGGGTTGGGTACAAGGAATTCTTCCTGAAATGCCA
ATTTCACTGTGAGCCTCCCAGCTATGGACTCAGGCACAGTGAGGACTTTAAAGAAGACCTAAGGAAGTCCTGCACCAAGA
GCTGGACCTAGGCAGGGGAAAGAGGAAAAGGGAGATGTACAGTCATTTGAAGAAGCTC

Alignment

ORF - retro_ogar_3398 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.44 %
• Parental protein coverage: 59.62 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  DEDDGFMDLLDGENLKNDEETSSCMASLWTAPLVMRRTTNVGNRSKLFD-FPSLCSASTRSSLKRPERSQ
          DEDDGF.DLLDGEN.KNDEET.SCMA..WT..LVMRRTTN.GN.SKLFD..P.LCS.ST..SLKRPE.SQ
Retrocopy DEDDGFLDLLDGENVKNDEETPSCMANGWTTSLVMRRTTNLGN*SKLFD<LPFLCSSSTGLSLKRPELSQ

Parental  DESPPGNTKRRKSISGDSPKEAASPEKAQEIPHQSLSLVSSPKGTIENILDNDPRDLIGDFSKGYLFHTV
          DESPPGN.K.RKS..GDSPKEA..PEKA.EIP.QSLSLVSSPKGTIENILDNDPRDL.GDFSKG.LF.TV
Retrocopy DESPPGNRKQRKSVGGDSPKEAVNPEKAREIPLQSLSLVSSPKGTIENILDNDPRDLLGDFSKGCLFYTV

Parental  AGKHQDLKYISPEIMASVLNGKFANLIKEFVIIDCRYPYEYEGGHIKGAVNLHMEEEVEDFLLKKPIVPT
          .GKHQDLKY.SPEI..SVL..KFANLIKEFVIIDC.YPYE.EGGH...AVNLHMEEEVEDFLLKKPIVPT
Retrocopy TGKHQDLKYTSPEIIGSVLSAKFANLIKEFVIIDC*YPYEHEGGHVESAVNLHMEEEVEDFLLKKPIVPT

Parental  DGKRVIVVFHCEFSSERGPRMCRYV-RERDRLGNEYPKLHYPELYVLKG-GYKEFFLKCQSHCEPPSYRP
          DGKRVIVVFHC.FSSERG..MC.YV....D.LGNEYPKLHY.ELYVLKG.GYKEFFLKCQ.HCEPPSY..
Retrocopy DGKRVIVVFHC*FSSERGLCMC*YV>KKGDQLGNEYPKLHY-ELYVLKGVGYKEFFLKCQFHCEPPSYGL

Parental  MHHEDFKEDLKKFRTKSRTWAGE-KSKREMYSRLKKL
          .H.EDFKEDL.K..TKS.T.AGE.K.KREMYS.LKKL
Retrocopy RHSEDFKEDLRKSCTKSWT*AGE<KRKREMYSHLKKL

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_3398 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 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000011077	2 retrocopies	retro_dord_336, retro_dord_783,
Nomascus leucogenys	ENSNLEG00000006390	1 retrocopy	retro_nleu_2333,
Otolemur garnettii	ENSOGAG00000002994	1 retrocopy	retro_ogar_3398 ,