RetrogeneDB ID: retro_ogar_1859

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873570.1:8972080..8973129(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GPBP1L1
• Ensembl ID: ENSOGAG00000004134
• Aliases: None
• Description: GC-rich promoter binding protein 1-like 1 [Source:HGNC Symbol;Acc:28843]

Sequence

>retro_ogar_1859
AATGGCAGCTTCCATTCTCAGAAAGGCTGCTCCTTTCAGGAAAGGGCACCTAAAGGGATTAGGGAAGAAGAGAAAGAAGA
CAAGGTAGAAAAGTTGCAGTTTGAAGAAGACGACTTTCCTTCTTTGAATCCAGAAGCTGGCAAACAGAATCAATCATGTA
GACCTTTTGGGACCCCCTTCAGGAGTATGAGAAAACCCACCTAGTGCCAAACAACCATCCAAAATGCTAGTTATCAAAAA
AGTTTCCAAAGAGGATCCTGTTGCTGCCTTCTCTGCTGCATTCACCTCACCAGGATCTTACCATGCAAATGGGAACAAAT
TATCCGTAGTTCCAAGTGCCTATAAGAACCTGTTTCCTGAGCCTGTACCACCTTCTTCTAAGCCCAGAAAATCTAACAGA
ATGGAAAACAAATCAGGATCCCTTTCCTCTAGCTGGAAGTGTGCTTTTACCAGTCCAATCTCTGTCACTAAACCAGTGCT
ACTGGCTGCTGGTGCAGCTCTGTGTTCTTCCAAAGAGTCCTTCCAACGCCACCCATCCAATTGAGATCAGCTCCTCTCGT
CTGACCAAGTTGACCCACTGAACCACTGACAGGAAGAGTGAATTCCTGCAGACTCTGAAAGTTGGCCGGAATGGAGATTT
CTCAGAGAACAGAGACTGTGATAAGCTGGAGGATTTAGAGGATGACAGCACAGCTGAACCAAAGAAAAATGGAAAGGAAG
GCTATCATCAGAATGGTCTTGTTCTCCCCAAACTGGAAAAAGGGGAGGTTCTCTCATACTCTCTGGAAGCAGAACACACG
TTTTTGAAAGCAATGGGATGGCAGAAATAGCCTGAAAATCATGAGACTTGCCTTCCCCTCAGAGTATGAGCTCAAAGAAT
TCCACATGAAACAGAGCAGCTGAGAAGAAATGGCTTTGGAAAGAATGGCTTCTTGCAAAGCCGTAGTTCCAGCCTGTTCT
CCCCTTGGAGAAGCACTTGTAAAGCAGAGTTTGAGGCTTCAGACACAAAAACCAGTAGCAGTGAAACATTAGATGACAAT
GCCTAGAAA

Alignment

ORF - retro_ogar_1859 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.93 %
• Parental protein coverage: 74.68 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  NGNVHSRKGCSFQERPPAEIREEKKEDKVEKLQFEEDDFPSLNPEAGKQNQPCRPFGTP-SGVWENPPSA
          NG..HS.KGCSFQER.P..IREE.KEDKVEKLQFEEDDFPSLNPEAGKQNQ.CRPFGTP.SGV.ENPPSA
Retrocopy NGSFHSQKGCSFQERAPKGIREEEKEDKVEKLQFEEDDFPSLNPEAGKQNQSCRPFGTP>SGV*ENPPSA

Parental  KQPSKMLVIKKVSKEDPAAAFAAAFTSPGSHPANGNKSSSIVPSVYKNLVPKPVPPPSKPSAWKANRMDH
          KQPSKMLVIKKVSKEDP.AAF.AAFTSPGS..ANGNK.S..VPS.YKNL.P.PVPP.SKP...K.NRM..
Retrocopy KQPSKMLVIKKVSKEDPVAAFSAAFTSPGSYHANGNKLS-VVPSAYKNLFPEPVPPSSKPR--KSNRMEN

Parental  KSGSLSSSRECAFTNPISVTKPVLLAAGAVLSS-PKESPSSITPPVEISSSRLTKLTRRTTDRKSEFLKT
          KSGSLSSS..CAFT.PISVTKPVLLAAGA.L.S.PK.SPS..T.P.EISSSRLTKLT..TTDRKSEFL.T
Retrocopy KSGSLSSSWKCAFTSPISVTKPVLLAAGAALCS>PK-SPSNATHPIEISSSRLTKLTH*TTDRKSEFLQT

Parental  LKDGRNGDFSDNRDCDKLEDLEDDSTPEPKQNGEEGCHQNGLALPILEEREILSHSLEAEHRLLKAMGWQ
          LK.GRNGDFS.NRDCDKLEDLEDDST.EPK.NG.EG.HQNGL.LP.LE..E.LS.SLEAEH..LKAMGWQ
Retrocopy LKVGRNGDFSENRDCDKLEDLEDDSTAEPKKNGKEGYHQNGLVLPKLEKGEVLSYSLEAEHTFLKAMGWQ

Parental  EYPENDENCLPLTEDELKEFHMKTEQLRRNGFGKNGFLQRRCSSLFSPWRSTCKAEFEASDTETSSSETS
          ..PEN.E.CLPL........H..TEQLRRNGFGKNGFLQ.R.SSLFSPWRSTCKAEFEASDT.TSSSET.
Retrocopy K*PENHETCLPLRV*AQRIPH-ETEQLRRNGFGKNGFLQSRSSSLFSPWRSTCKAEFEASDTKTSSSETL

Parental  DDDAWK
          DD.A.K
Retrocopy DDNA*K

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_1859 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 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000010454	1 retrocopy	retro_chof_53,
Microcebus murinus	ENSMICG00000008449	1 retrocopy	retro_mmur_164,
Myotis lucifugus	ENSMLUG00000012432	2 retrocopies	retro_mluc_211, retro_mluc_834,
Mus musculus	ENSMUSG00000034042	2 retrocopies	retro_mmus_1391, retro_mmus_405,
Oryctolagus cuniculus	ENSOCUG00000017939	1 retrocopy	retro_ocun_427,
Otolemur garnettii	ENSOGAG00000004134	1 retrocopy	retro_ogar_1859 ,
Otolemur garnettii	ENSOGAG00000013991	1 retrocopy	retro_ogar_1077,
Ochotona princeps	ENSOPRG00000001584	1 retrocopy	retro_opri_928,
Rattus norvegicus	ENSRNOG00000037595	1 retrocopy	retro_rnor_390,
Ictidomys tridecemlineatus	ENSSTOG00000013491	1 retrocopy	retro_itri_243,