RetrogeneDB ID: retro_ogar_338

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873520.1:33856845..33857878(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GTF2H1
• Ensembl ID: ENSOGAG00000000710
• Aliases: None
• Description: general transcription factor IIH, polypeptide 1, 62kDa [Source:HGNC Symbol;Acc:4655]

Sequence

>retro_ogar_338
GGAGCTCTATACTTTTGTCAGAAATAATCTCTTGGGCACTGAAGGCATAGATAGATTTACAATCAACCATTTATATGCAG
ATATTCAATGCTAGAAAATCAGTCCTGAAGGAAAAGCTAAAATTCAGCTTCAGCTGGTCTTGCATGCAGGGGACACAACT
AACTCCCATTTTTTCAATGAAAGCACAACAGTGAAAGAGCAAAATGCAGTAAAAGACCTTCTTCAGCAGCTGCTGCCTAA
ATTCAAGAGGAAAGCAAATAAAGAACTGGAAGAAGAAAACAGAGTGCTGCAAGAAGAACCTGTCTTGTTTCAGCAAAAAG
ACCTTGTTGTGAGCCAAGTGATCAGCGCTGAGGAATTCTGGGCCAATCTTTTAAACGTGAACGCAACAGAGTTCTTCGAC
ATCCAATCTTAAGCAGGATGTTGGCATTTCTGCAGCATTTCTGGCTGATGTTCAGCCCCAAACTTACGGCTGCAATGGTC
TGAGATATAATTTAACCTCTGATATTACTGAGTCTATATTTAGGATCTATCCAAAGTAAAAATGAAATACACAGAAAATG
TTCCCCACAACATGATAGAGAAGGAATTCTGGACACGTTTTCTCCAGTTCCATTATTTTCAAAGGAACTTACTGAATACA
GGGTCAAAGGATCTCTTTGCAGAATGCACCAAAATAGGGTTAAAAACAATGGTTTCATTAGGAGTGAAAAATCCATTACT
CGATTTGACGGCTTTGGAAGATAAATCATTAGATGGGGGCTATGGCATTTCCTCTATGCCAACTACTTCCAATTCTAAAT
CCATAAAGGAAAATAGTAATGCTGCCATCATCAAGAGGTTTAACTATTGTAGTGACATGGTCCTGGCAGCAGGACTCAGG
AAACAAGAAGCACAAAACGAATAAAATGGTGAGCTCAGCAGCATGGATGGAAATTCTAGAGATGCAGATTGCTTTCAGCC
TGCAGGAAAAAGGGCGAAGTTACAAGAGTCTGTTAAATATGAAGACCTGGCAAAAAAAAATTCTGTAAATTCT

Alignment

ORF - retro_ogar_338 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.49 %
• Parental protein coverage: 63.87 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  GALY-LMAERIAWA-PEGKDRFTISHMYADIKCQKISPEGKAKIQLQLVLHAGDTTNFHFSNESTAVKER
          GALY.L..E.I.WA..EG.DRFTI.H.YADI.C.KISPEGKAKIQLQLVLHAGDTTN.HF.NEST.VKE.
Retrocopy GALY<LLSEIISWA<TEGIDRFTINHLYADIQC*KISPEGKAKIQLQLVLHAGDTTNSHFFNESTTVKEQ

Parental  DAVKDLLQQLLPKFKRKANKELEEKNRMLQEDPVLFQLYKDLVVSQVISAEEFWANRLNVNAAE-SSSTS
          .AVKDLLQQLLPKFKRKANKELEE.NR.LQE.PVLFQ..KDLVVSQVISAEEFWAN.LNVNA.E.SS.TS
Retrocopy NAVKDLLQQLLPKFKRKANKELEEENRVLQEEPVLFQ-QKDLVVSQVISAEEFWANLLNVNATE>SS-TS

Parental  NHKQDVGISAAFLADVRPQTDGCNGLRYNLTSDIIESIFRTYP-AVKMKYAENVPHNMTEKEFWTRFFQS
          N.KQDVGISAAFLADV.PQT.GCNGLRYNLTSDI.ESIFR.YP..VKMKY.ENVPHNM.EKEFWTRF.Q.
Retrocopy NLKQDVGISAAFLADVQPQTYGCNGLRYNLTSDITESIFRIYP<KVKMKYTENVPHNMIEKEFWTRFLQF

Parental  HYFHRDRLNTGSKDLFAECAKIDEKGLKTMVSLGVKNPLLDLTALEDKPLDEGYGISSVPTTSNSKSIKE
          HYF.R..LNTGSKDLFAEC.KI...GLKTMVSLGVKNPLLDLTALEDK.LD.GYGISS.PTTSNSKSIKE
Retrocopy HYFQRNLLNTGSKDLFAECTKI---GLKTMVSLGVKNPLLDLTALEDKSLDGGYGISSMPTTSNSKSIKE

Parental  NSNAAIIKRFNHHSAMVLAAGLRKQEAQNEQNGEPSSMDGNSGDADCFQPAVKRAKLQESIEYEDLAKNN
          NSNAAIIKRFN..S.MVLAAGLRKQEAQNE.NGE.SSMDGNS.DADCFQPA.KRAKLQES..YEDL....
Retrocopy NSNAAIIKRFNYCSDMVLAAGLRKQEAQNE*NGELSSMDGNSRDADCFQPAGKRAKLQESVKYEDLXXXX

Parental  SVKT
          SV..
Retrocopy SVNS

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_338 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 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000110768	1 retrocopy	retro_hsap_1892,
Gorilla gorilla	ENSGGOG00000008405	1 retrocopy	retro_ggor_1385,
Monodelphis domestica	ENSMODG00000006540	1 retrocopy	retro_mdom_1210,
Nomascus leucogenys	ENSNLEG00000017760	1 retrocopy	retro_nleu_1473,
Otolemur garnettii	ENSOGAG00000000710	1 retrocopy	retro_ogar_338 ,
Pan troglodytes	ENSPTRG00000003420	1 retrocopy	retro_ptro_1269,