RetrogeneDB ID: retro_ogar_1347

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873543.1:5896757..5897812(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PDGFRL
• Ensembl ID: ENSOGAG00000004228
• Aliases: None
• Description: platelet-derived growth factor receptor-like [Source:HGNC Symbol;Acc:8805]

Sequence

>retro_ogar_1347
CCTCCCAAGAACAAGCGTGCAAAAGAGCCAGGAGAAAATAGAACCAAACCTACCAACAAAAAGGTGAAGCCCAAAATTCC
CCAAATAAAGGACAGGGACTCAGCTGACTCAACACCAAAAACACCATGTATAATAATGCAAGTGATGGATAAAGGTCGCT
TTCAGAAACCTGCTGCTGCCCTGAGCCTGTCGGCCAGGCAAACTGTAGAGCTCTGATGTAAAGGGAATAAAATTGGATGG
AGCTATCCTGCCTATCTTGACACCTTTAAGGACTCTCACCTCAGTGTCAAATAGCCTGAGCGCTATGGCCAGTTGACTCT
GGTCAATTCCACAGCCGCTGACACAGGCAAATTCAGCTGTTGGGGGCAGCTCTGCAACGCTACATCTGCAGGAAGGATGA
GGCCAAAATGGGCTCTACCTACATCTTTTTCACAGAGAAAGGAGAGCTGTTCGTGCTATCTCTCAGCTACTTCGATGTTG
TCTCCTTGAACCTGGACAGACAGGCGGTGGTTCCCTGTTGGGTAACAGTGCTGTCTGCCAAAGTCACCCTGCACAGGTAG
TTTCCAGCCAAGGAGATCCCAGCCAATGGGACAGATGTGGCCTATGATGTGAAGCGTGGCTTCATGTACCTGCAGTTGCG
GGCCACACAGCAGGGTGTCGTCTACTGCAGGGCTGAGGCTGGGGGTAGGTCACAGGTCTCGGTCAAGTACCAGCTGCTCT
ACGTGGAAGTTCCCAGTGGTCCTCCATCAACCACCATCATGGCCTCCTCAAACAAGGTGAAGGGCACGGATGACATCAGC
ATGGTCTGTACCATCCTGGGGGAGCCAGAAGTTGAGGTAGAGTTCAGGTGGATCTTTCCAGGGCAGAAGGATGACAGGCC
CACGACAATTCAAGACTCTTGGAGGCTGATCCACAGAGGGCGCGGTCACACCACAAGAATCTCCCAGAGCATCATCACAG
TGGAGGACTTTGAGACCATTGACGCAGGGTATTACATTTGCACTGCACAGAATCCTCAAGGACAGATGACAGTAGCTGCC
ACCATTGAGTTTTCC

Alignment

ORF - retro_ogar_1347 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.52 %
• Parental protein coverage: 93.87 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PPKNKRAKEPGENRIKPANKKVKPKVPKIKDRDAADSTPKTPSIMMQVMDKGRFQKPAATLSLSAGQTVE
          PPKNKRAKEPGENR.KP.NKKVKPK.P.IKDRD.ADSTPKTP.I.MQVMDKGRFQKPAA.LSLSA.QTVE
Retrocopy PPKNKRAKEPGENRTKPTNKKVKPKIPQIKDRDSADSTPKTPCIIMQVMDKGRFQKPAAALSLSARQTVE

Parental  LRCKGSKIGWSYPAYLDTFKDSRLSVKQHERYGQLTLVNSTAADTGEFSCWGQLCNG-YICRKDEAKMGS
          L.CKG.KIGWSYPAYLDTFKDS.LSVK..ERYGQLTLVNSTAADTG.FSCWGQLCN..YICRKDEAKMGS
Retrocopy L*CKGNKIGWSYPAYLDTFKDSHLSVK*PERYGQLTLVNSTAADTGKFSCWGQLCNA<YICRKDEAKMGS

Parental  TYIFFTEKGELFVPSPSYFDVVYLNPDRQAVVPCRVTVLSAKVTLHREFPAKEIPANGTDVAYDVKRGFV
          TYIFFTEKGELFV.S.SYFDVV.LN.DRQAVVPC.VTVLSAKVTLHR.FPAKEIPANGTDVAYDVKRGF.
Retrocopy TYIFFTEKGELFVLSLSYFDVVSLNLDRQAVVPCWVTVLSAKVTLHR*FPAKEIPANGTDVAYDVKRGFM

Parental  YLRPRATQQGVVYCRAEAGGRSQVSVKYQLLYVEVPSGPPSTTIVASSNKVKGGDDISVACTVLGEPDVE
          YL..RATQQGVVYCRAEAGGRSQVSVKYQLLYVEVPSGPPSTTI.ASSNKVKG.DDIS..CT.LGEP.VE
Retrocopy YLQLRATQQGVVYCRAEAGGRSQVSVKYQLLYVEVPSGPPSTTIMASSNKVKGTDDISMVCTILGEPEVE

Parental  VEFRWIFPGQKDDRPVTIQDSWRLIHRGRGHTTRISQSVITVEDFETIDAGYYICTAQNPQGQTTVATTV
          VEFRWIFPGQKDDRP.TIQDSWRLIHRGRGHTTRISQS.ITVEDFETIDAGYYICTAQNPQGQ.TVA.T.
Retrocopy VEFRWIFPGQKDDRPTTIQDSWRLIHRGRGHTTRISQSIITVEDFETIDAGYYICTAQNPQGQMTVAATI

Parental  EFS
          EFS
Retrocopy EFS

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_1347 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Otolemur garnettii	ENSOGAG00000004228	1 retrocopy	retro_ogar_1347 ,