RetrogeneDB ID: retro_ogar_1814

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873567.1:12647722..12648572(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOGAG00000030656
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: DNAJA3
• Ensembl ID: ENSOGAG00000015227
• Aliases: None
• Description: DnaJ (Hsp40) homolog, subfamily A, member 3 [Source:HGNC Symbol;Acc:11808]

Sequence

>retro_ogar_1814
GGAACAAGAAGTTACCCTTTTAATTTGTACTGCCTTCATCCACATGAGCACCCCTTTGGCCAAAAAGATTATTACCAGGT
ATTAGGAATGTCCCAAAATGCCAGCCAGAAAGAAATCAAGAAAGCCTATTACCAACTTGCCAAGAAATATCACCCTGACA
CGAATAAGAAGGATCCCAAGGCTAAAGAGAAGTTCTCTCAGCTGGCAGAAGCTATGAGGTTTTGAGTGATGATGTAAGAG
GAAGCAGTGTGAAGCCTACAGCTCTTCTGGCTTTGATCCTGGGGCCAGCAGCTCTGGGCAGAGCTACTGGAAAGGAGGCC
CCGCTGCTGACCCTGAGGTTCAGGAAGATCTTTGGGGAGTTCTCATCATCTTCGTTTGGAGATTTTCAGGGTGTATTTGA
TCAGCCTCAGGAATACTTCATGGAGTTGACATTCAATCAAGCGGCTAAGGGGGTCAACAAGGAGTTCACTGTGAACATCA
TGGACACTGTGGGTGCTATGATGTCAAGGGGAATGAGCCTGGCACCAAAGTGCAGCATTGCTGCTACTGCAGCGGCTCTG
GCATGGAAACCATCATTAGGGGCCCTTTTGTGATGCGTTCCACAAGTTGGAGATGTGGCGGCCGTGGCTCCATCATTACA
GCTCTCTGTGTGATCTGCAGGGGAGTAGGACGAGCCAAACAGAAGAAATGAGTGGTGATCCCTAAGCCTGTAGGATTCAA
GGATGGCCAGACTATAGGAAAAAGAGAAATTTTCATCACATTCAGAGTACAGAAAAGCCTTGTATTCTGGAGGGACGGCA
CAGACATCCACTCTGATCTCTTTATTTCTATAGCTCAGGCTATTCTTGGG

Alignment

ORF - retro_ogar_1814 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.37 %
• Parental protein coverage: 60.5 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  GTKSYPF-ICTAFIHTSAPLAKE-DYYQVLGVPRNASQKEIKKAYYQEEKSSEHDDMNKTYPQLLAAYEN
          GT.SYPF.ICTAFIH.S.PLAK..DYYQVLG...NASQKEIKKAYYQ..K...H.D.NK..P........
Retrocopy GTRSYPF>ICTAFIHMSTPLAKK<DYYQVLGMSQNASQKEIKKAYYQLAKKY-HPDTNKKDPKAKEKFSQ

Parental  VIEKLK-VLSDEV-KRKQYDAYGSAGFDP-GASSSGQSYWRGGPTVDPEELFRKIFGEFSSSSFGDFQGV
          ..E....VLSD.V.KRKQ..AY.S.GFDP.G....G.......P.......FRKIFGEFSSSSFGDFQGV
Retrocopy LAEAMR<VLSDDV<KRKQCEAYSSSGFDP>GPAALGRATGKEAPLLTLR--FRKIFGEFSSSSFGDFQGV

Parental  FDQPQEYVMELTFNQAAKGVNKEFTVNIMDT-CERCDGKGNEPGTKVQHCHYCGGSGMETINTGPFVMRS
          FDQPQEY.MELTFNQAAKGVNKEFTVNIMDT.C...D.KGNEPGTKVQHC.YC.GSGMETI..GPFVMRS
Retrocopy FDQPQEYFMELTFNQAAKGVNKEFTVNIMDT<CGCYDVKGNEPGTKVQHCCYCSGSGMETIIRGPFVMRS

Parental  TCRRCGGRGSIIISPCVVCRGAGQAKQKKRVVIPVPAGVEDGQTVRMPVGKREIFITFRVQKSPVFRRDG
          T..RCGGRGSII...CV.CRG.G.AKQKK.VVIP.P.G..DGQT.....GKREIFITFRVQKS.VF.RDG
Retrocopy TSWRCGGRGSIITALCVICRGVGRAKQKK*VVIPKPVGFKDGQTI----GKREIFITFRVQKSLVFWRDG

Parental  ADIHSDLFISIAQAILG
          .DIHSDLFISIAQAILG
Retrocopy TDIHSDLFISIAQAILG

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_1814 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000010013	1 retrocopy	retro_btau_1376,
Otolemur garnettii	ENSOGAG00000015227	1 retrocopy	retro_ogar_1814 ,