RetrogeneDB ID: retro_ogar_3495

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873943.1:67797..68498(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PBK
• Ensembl ID: ENSOGAG00000009887
• Aliases: None
• Description: PDZ binding kinase [Source:HGNC Symbol;Acc:18282]

Sequence

>retro_ogar_3495
TCTGTATTATGTTCAACTCCATGTATAAACATCTCTGCCTCTCCATTTATGCAGAAGCTTGGCTTTGGTACTGGGCTAAA
TGTTTAACTGATGAAAAGATCTCCAAAGGGTTTGTCTCATTCTCCTTGGGCAGTGAAAAAGATTAATCCTATATGTAACG
ATCATTATCGAAGAGTGTACCAAAGTAGATTAATCGATGAAGCTAAGATTTTGAAAAGCTTTCACCATCCAAACATTATA
GGCTATCGTGCTCTTTTTCTTACTGAAGCTAATGATGGAAGCCTATATCTTGCTATGGAATATGGAGGTGAAAAGTCTCT
ACATGGCTTAATAGAAGAACAAAATAAAGACAGTGGAGATCCTTTCCAGCAGCCATAATTTTAACAGTTGTTTTGAACAT
GGCAAGAGGGTTAAAGTACCTGCACCATGAAAAGAAACTGCTTCATGGAGATATAAAGTCTTCAAATGTTGTAATTGAAG
GTGATTTTGAAACAATTAAAATTTGTGATGTGGGGGTTTCTCTAACATTGGATGAAAATATGACTGTGACTGACCCTGAG
GCTTGTTACATTGGCACAGAGCCATGGACACTCAAGAAAGCTTTGGAAGAGAATGGTATTATTACTGACAAGGCAGACAC
ATTTGCCTTTGGCCTTACTCTGTGGGCAATGATGACTTTGTGTATTCCACATATCAGTCTT

Alignment

ORF - retro_ogar_3495 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.36 %
• Parental protein coverage: 71.6 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SVLCSTPCINIPASPFMQKLGFGTGVNVYLMKRSPKGLSHSPWAVKKINPVCNDHYRSVYQKRLIDEAKI
          SVLCSTPCINI.ASPFMQKLGFGTG.NV.LMKRSPKGLSHSPWAVKKINP.CNDHYR.VYQ.RLIDEAKI
Retrocopy SVLCSTPCINISASPFMQKLGFGTGLNV*LMKRSPKGLSHSPWAVKKINPICNDHYRRVYQSRLIDEAKI

Parental  LKSLHHPNIIGYRAF--TEANDGSLCLAMEYGGEKSLNDLIEERNKDSGDPF-PAAIILKVALNMARGLK
          LKS.HHPNIIGYRA...TEANDGSL.LAMEYGGEKSL..LIEE.NKDSGDPF.PAAIIL.V.LNMARGLK
Retrocopy LKSFHHPNIIGYRALFLTEANDGSLYLAMEYGGEKSLHGLIEEQNKDSGDPF<PAAIILTVVLNMARGLK

Parental  YLHQEKKLLHGDIKSSNVVIKGDFETIKICDVGVSLTLDENMTVTDPEACYIGTEPWKPKEALEENGIIT
          YLH.EKKLLHGDIKSSNVVI.GDFETIKICDVGVSLTLDENMTVTDPEACYIGTEPW..K.ALEENGIIT
Retrocopy YLHHEKKLLHGDIKSSNVVIEGDFETIKICDVGVSLTLDENMTVTDPEACYIGTEPWTLKKALEENGIIT

Parental  DKADIFAFGLTLWEMMTLCIPHINL
          DKAD.FAFGLTLW.MMTLCIPHI.L
Retrocopy DKADTFAFGLTLWAMMTLCIPHISL

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_3495 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 8 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000021069	1 retrocopy	retro_btau_150,
Canis familiaris	ENSCAFG00000008369	1 retrocopy	retro_cfam_1694,
Dipodomys ordii	ENSDORG00000014896	1 retrocopy	retro_dord_697,
Myotis lucifugus	ENSMLUG00000009596	1 retrocopy	retro_mluc_713,
Monodelphis domestica	ENSMODG00000015986	1 retrocopy	retro_mdom_245,
Mus musculus	ENSMUSG00000022033	1 retrocopy	retro_mmus_2452,
Otolemur garnettii	ENSOGAG00000009887	1 retrocopy	retro_ogar_3495 ,
Tupaia belangeri	ENSTBEG00000002239	1 retrocopy	retro_tbel_3290,