RetrogeneDB ID: retro_ogar_3250

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873756.1:742561..743994(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ZC3H11A
• Ensembl ID: ENSOGAG00000000243
• Aliases: None
• Description: zinc finger CCCH-type containing 11A [Source:HGNC Symbol;Acc:29093]

Sequence

>retro_ogar_3250
AACTCTGTCAAAGGAGAAGAACCATTGGTTAGATTGAGTCTTACTGAGAGACTGGGGAAACAAAAATTTTCAGTTGGTGG
TGAGAGTGATCCTCCATTAAAGCGTAGCCTTATGCAGAGGCTAGGGAAGAAAGTTGAAGCTCTAGAAACTAATACTGACA
AAACACCAAAGAAGTTCAAGTTTCTAAGTCTCTGAAAGAGTGATTAGGCATGTCAGTTGGTCCAAATAATGACAAGGCAA
CTGAGAGAGTTAATAAAGTTGGTGAGATCCATGTGAAGACATTATAAGAAATTCTTCTTGAAAGAGCCAGTCAAAAACAT
GGAGAATTGCAAACTAAACTCAAGACAGAAGGACTTTCAAAAGCTGATGATTCTACTTCAGGAGCAAGAAGTTCTTCCAC
TATCCAAATCAAAACATTCTCTGAGGTACTGGCTGAACAAAAACATCAGCAGCAGGAAGCAGAGAAACAAAAATGCAAGA
AGATGCAACACGCATCAAACTAAAAACTGATAATGAAATTTAAAAAAAAGTTATTTTGCCACTCATAGTTGCCAGCAAAG
GACAATCAGAGGAACCTGCAGGTAGAACAAAGTCCATGCAGGAGGTACACATCAAGACGCTGGAGGAAATTAAACTAGAG
AAGGCACTGAGGGTGCAGCAGAGCTCTGAGAGCAGCACTAGCTCCCAGCCTCAACCTGAGGCCACCCAGGAGCAAGGCAG
GTGCTCTGAATCACCAAAAGAACAGGAATGAAGGAGAAGAAACTTCAGGAAGGAAGCGAAGCTGCTTTAAAGAGCAATGT
TACTAGAACAGAAGCTAAAGAGACTTCAGATGAGACCACAGGAGTTGACATCACTAAAATTCAAGTCAAGAGATGTGAGA
CTATGAAAGAGAAGCATATGTAGAAACAGCAGAAGAGGGGAGTGATACAGAAGGAAAAAATCACTCTTGATACCCCTTCA
CGGAGATGTAGGCTCTTGCAATACCCAAGTGGCAGAAAAACCAGTGCTCACTGCTGTGCCAGGCGTCATACGGCATCTGA
CCAAGCAGCTTCCCACAAAGTCATCCCAGAAGGTGGAAGTAGAAACTTCAGGGATTGGGGACTCAATATTAAATGTGAAA
TGTGCAGCACAGACCTTAGAGAAAAGAGATAAAGCTAAATCCAAAGTAAATGTAAAACCATCTGTGGTTAAAGTTGTTTC
ATCCCCCAAATTGGCTCCAAAACACAAGGCAGTGGAGGTGCACCACGCTGTCATTGCAGTGGTGAAGCCACTCAGTTCCA
GCAGTATCCTACAGGAAAGCCCAGCCAAAAAAGCAACTGTGGTTGTTGTCCTAGTCCTCTCTGAGGACAAATCAGTCAGT
TTCTACCTGAGGCAGAAACACATGCAGACAGCCTTGTGCGCCTCCAACCCAGTCTTCCTCAGATCCCTCACCC

Alignment

ORF - retro_ogar_3250 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.6 %
• Parental protein coverage: 58.7 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  SSKQGEEPLVRLSLTERLGKRKFSVGGESDPPLKRSLAQRLGKKVEAPETNTDKTPKK-VQVSKSLKERL
          .S..GEEPLVRLSLTERLGK.KFSVGGESDPPLKRSL.QRLGKKVEA.ETNTDKTPKK.VQVSKSLKE.L
Retrocopy NSVKGEEPLVRLSLTERLGKQKFSVGGESDPPLKRSLMQRLGKKVEALETNTDKTPKK<VQVSKSLKE*L

Parental  GMSAGPNNEEATERVNKVGEIHVKTLEEILLERASQKRGELQTKLKTEGPSKADDSTSGARSSSTIRIKT
          GMS.GPNN..ATERVNKVGEIHVKTL.EILLERASQK.GELQTKLKTEG.SKADDSTSGARSSSTI.IKT
Retrocopy GMSVGPNNDKATERVNKVGEIHVKTL*EILLERASQKHGELQTKLKTEGLSKADDSTSGARSSSTIQIKT

Parental  FSEVLAEKKHRQQEAEKQKCKK-DATCIKLKTDSEIKKAVVLPPIVASKGQSEEPAGKTKSMQEVHIKTL
          FSEVLAE.KH.QQEAEKQKCKK.DAT.IKLKTD.EI...V.LP.IVASKGQSEEPAG.TKSMQEVHIKTL
Retrocopy FSEVLAEQKHQQQEAEKQKCKK<DATRIKLKTDNEIXXXVILPLIVASKGQSEEPAGRTKSMQEVHIKTL

Parental  EEIKLEKALRVQQSSESSTSSQPQPEAT-PGARRLLRITKRTGMKEEKKLQEGSEVASQSNVARTEAKEA
          EEIKLEKALRVQQSSESSTSSQPQPEAT.PGAR..L.ITKRTGMKE.KKLQEGSE.A..SNV.RTEAKE.
Retrocopy EEIKLEKALRVQQSSESSTSSQPQPEAT<PGARQVL*ITKRTGMKE-KKLQEGSEAALKSNVTRTEAKET

Parental  SDETTGVDITKIQVKRCETMREKHLQKQQERGVIQKEK-SVLTPLQGDVGSCNTQVAEKPVLTAVPGVTR
          SDETTGVDITKIQVKRCETM.EKH..KQQ.RGVIQKEK.S.L.PL.GDVGSCNTQVAEKPVLTAVPGV.R
Retrocopy SDETTGVDITKIQVKRCETMKEKHM*KQQKRGVIQKEK>SLLIPLHGDVGSCNTQVAEKPVLTAVPGVIR

Parental  HLTKRLPTKSSQKVEVETSGIGDSILNVKCAAQTLEKRGKAKPKVNVKPSVVKVVSSPKLAPKRKAVEVH
          HLTK.LPTKSSQKVEVETSGIGDSILNVKCAAQTLEKR.KAK.KVNVKPSVVKVVSSPKLAPK.KAVEVH
Retrocopy HLTKQLPTKSSQKVEVETSGIGDSILNVKCAAQTLEKRDKAKSKVNVKPSVVKVVSSPKLAPKHKAVEVH

Parental  PAVIAAVKPLSSSSILQESPAKKAA-VVVVPVLSEDK-SVTVPEAEIPIDSLV-LPPTQSSSDPSP
          .AVIA.VKPLSSSSILQESPAKKA..VVV.........S...PEAE...DSLV..PPTQSSSDPSP
Retrocopy HAVIAVVKPLSSSSILQESPAKKATVVVVLVLSEDKS<SQFLPEAETHADSLV<APPTQSSSDPSP

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_3250 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 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000058673	2 retrocopies	retro_hsap_3481, retro_hsap_508,
Monodelphis domestica	ENSMODG00000001184	1 retrocopy	retro_mdom_1449,
Mus musculus	ENSMUSG00000026464	2 retrocopies	retro_mmus_3323, retro_mmus_564,
Otolemur garnettii	ENSOGAG00000000243	1 retrocopy	retro_ogar_3250 ,
Pan troglodytes	ENSPTRG00000001876	5 retrocopies	retro_ptro_2980, retro_ptro_2981, retro_ptro_2991, retro_ptro_380, retro_ptro_382,
Rattus norvegicus	ENSRNOG00000002993	3 retrocopies	retro_rnor_1570, retro_rnor_1673, retro_rnor_602,