RetrogeneDB ID: retro_ogar_1300

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873542.1:5346926..5347464(+)
• Located in intron of: ENSOGAG00000014459

Retrocopy information

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

Parental gene information

• Parental gene symbol: PITPNB
• Ensembl ID: ENSOGAG00000000391
• Aliases: None
• Description: phosphatidylinositol transfer protein, beta [Source:HGNC Symbol;Acc:9002]

Sequence

>retro_ogar_1300
CCCTACTGCAGAACAATTGTAACTAGTGAATATATGAAAGACAATTTCTTCATTAAAATTGAAACGTGGCACAAACCAGA
CTTGGGAACACTGGAAATGTATGTGGTTTAGATCCAAACATAAGGAAAACTGTTATAACTGTCTACGTAATATTGTAGAT
CGAAGTAAAGTTGCACCAGCAGACTACAAAGCTGATGAAGACCCAGCATTATTCTAGTCAGTCAAGACCAAGAGAGGCCC
TTTGGGACCCAACTGGAAGAAGGAGCTGGCCAACAACCCTGACTATCCTCAGATGTGTGCCTATAAGCTGGTGCCATCAA
ATGCAAGTGGTGGGGACTGCACAGCAAAATAGAAAACTTCATTCAGAAGCAGGAAAAAAGGATATTTACAAACTTTTTAT
CACTAGCTTTTTGTTGGATTGACAAGTGGATTGATCTGACAATGGGAGACATTAGGAGAATGGAAGGTGAGACTCAGAAA
GAATTAGAAACAATGTGTAGGAAGGGATCCCATTCAAGGCATGTTAACTGCTGATGTC

Alignment

ORF - retro_ogar_1300 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.89 %
• Parental protein coverage: 66.42 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  PYCRTIVTNEYMKDDFFIKIETWHKPDLGTLE-NVHGLDPNIWKTVEIVHI-DIADRSQVEPADYKADED
          PYCRTIVT.EYMKD.FFIKIETWHKPDLGTLE.NV.GLDPNI.KTV..V....I.DRS.V.PADYKADED
Retrocopy PYCRTIVTSEYMKDNFFIKIETWHKPDLGTLE<NVCGLDPNIRKTVITVYV<NIVDRSKVAPADYKADED

Parental  PALFQSVKTKRGPLGPNWKKELANSTDCPQMCAYKLV-TIKFKWWGLQSKVENFIQKQEKRIFTNFHRQL
          PALF.SVKTKRGPLGPNWKKELAN..D.PQMCAYKLV..IK.KWWGL.SK.ENFIQKQEKRIFTNF....
Retrocopy PALF*SVKTKRGPLGPNWKKELANNPDYPQMCAYKLV<AIKCKWWGLHSKIENFIQKQEKRIFTNFLSLA

Parental  FCWIDKWIDLTMEDIRRMEDETQKELETMRKKGS-VRGTSAADV
          FCWIDKWIDLTM.DIRRME.ETQKELETM..KGS...G...ADV
Retrocopy FCWIDKWIDLTMGDIRRMEGETQKELETMCRKGS>IQGMLTADV

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_1300 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 10 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000012309	2 retrocopies	retro_chof_2374, retro_chof_860,
Cavia porcellus	ENSCPOG00000012298	1 retrocopy	retro_cpor_957,
Macropus eugenii	ENSMEUG00000010442	3 retrocopies	retro_meug_392, retro_meug_689, retro_meug_786,
Oryctolagus cuniculus	ENSOCUG00000000511	1 retrocopy	retro_ocun_1620,
Otolemur garnettii	ENSOGAG00000000391	1 retrocopy	retro_ogar_1300 ,
Ochotona princeps	ENSOPRG00000002540	1 retrocopy	retro_opri_931,
Tupaia belangeri	ENSTBEG00000000293	1 retrocopy	retro_tbel_4285,
Takifugu rubripes	ENSTRUG00000018546	1 retrocopy	retro_trub_36,
Tarsius syrichta	ENSTSYG00000001148	1 retrocopy	retro_tsyr_503,
Tursiops truncatus	ENSTTRG00000001278	2 retrocopies	retro_ttru_1060, retro_ttru_1439,