RetrogeneDB ID: retro_ogar_2612

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873638.1:6603631..6605617(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TPX2
• Ensembl ID: ENSOGAG00000012423
• Aliases: None
• Description: TPX2, microtubule-associated, homolog (Xenopus laevis) [Source:HGNC Symbol;Acc:1249]

Sequence

>retro_ogar_2612
GAAAAAGAAAATTTTGTGGGACAATCAATTTCATCAAATACTTGTTCTTCCTTGGAAGTTGAGGGACCTGTATCAAGAAA
AACTCCAGCCCAACCACAGAGAAGATCTATTAGACTCTCTGCTCAGAGAGATTTGGAACAGAAAGGAACAGATCATGAGA
AAATGAAAGCCAAGAGATGTGCCACTCCTGTGGTCTTAGACGAAATTCCACCCCCTGAAAAAATGAAAGTTTCTAACAAG
AAAAAGAAGCCAGAGGAAGAAGATAGTGCTCATCAAGATACTTCTGAAAAGAATGAGTCTTCCCCAGAGAAAGAAAAGGG
CAGACGTACTGTGCCCTTTATACTACCCGTAAGGCAGAAGATTCTGAAAAGTACTGAGGAACAAGACTTGGAGAAGAGAA
TGAAGATGCAGCAGGTGGTGATGGAGAAGCAGAGAAAGAATGAAGAATTCAAGAAATTTGCTCTTGCAGGAGCAGGGCAA
CCTGTGAAGAAATCAGTGAGCCAGGTAACCAAATCAATTGACTTCCACTTCCACACAGATGAGCGCATTAAGCAACATCC
TAAGAACCAAGAGGAGTATAAGGAAGTGGACTTTACTTCTGAACTTCAAAAGCATCCTTCATCTCCTGCCCAAGTGACTA
AGGGATGTACCATTTTTAAGCCTTTCAACTTGTCCCAGGGAAAGAAAAGAGCATTTGATGAAGCAGCTTCTACATATCTG
CCCCTTGCGCAGCAGGTTGAAGCCTTCCATAAACAAACCCCTAACAGATATCATTTGAGAAGCAAGAAGGGTGATATTAG
TCTGTTACCTTCCAAATCTTCTGTGGCCCAGATCTCCAGAGATCCACAGACTCCTGTACTGCAAACCAAACAGCACACAA
GGCCTGTGACCTACAAAAGTGCTGCAGATCAGGAGGCTGAGGAGCTTGAGAAACTGCAACAATACAAATTCAAAGCACGT
GAACTTGATCCCAGAATTCTTAAAGGTGGGCATATCTTAACCAAGAAACCACCCATGAAACCACCCACTCAGCCTATTGG
CTTTGATTTAGAAATTGAGAAAAGAATCTAAGAGCAAGAGTCAAAGAAGAAATCAGATGATAAACACTTTGAATTTCATT
CCAGACCTTGCCCTACTAAGATTTTGGAAGATGTTGTGGGTGTTCCTGAAAAGAAGGTACTTCCAATCACTGTCCCCAAG
TCACCAGCTTTTGCACTGAAGAACAGAATTCGGATACCCACCAAAGGAGATGAGGAAGAAGATGAACCAGTAGTGGTAAG
AGCTTAACCTGTGCCACATTATGGGGTGCCTTTTAAGCCCCAAATCCCAGAGGCAAGAACTGTGGAGTTATGCCCTTTCT
CCTTTGATTCTCAGGACAAAGAACATCAGTTAAAGAAAGAGATGAAAATAAGAGAACTGCAGAAAGAGGAGGTACCCGTG
TTCAAGGCACTTCCCTTGCCTCATTTTGACACTATTAACCTGCCAGAGAAGAAGGTAAAGAATGTGACCCAGGTTGAGCC
TTTCTGCTTGGAGACTGACAAAAGAGGTGCTCTGAAGGCGCAGATTTGAAAGAACCAGCTGGAGGAAGAACTGAAACAAC
AGAAGGAAGCAGCTTGTTTCAAGGCTCGTCCAAACACCGTCATCTCCCAGGAGCCCTTTGTTCCCAAGAAAGAAAAAAAA
ACAGTTACTGAAGGCCTTTCTGGTTCTCTAGTTCAGGAACCTTTTCAGCTAGCTACTGAGAAGAGAGCCAAGGAGCAGCA
GGAGTTAGAGTAGAGAATGGTTGAGATTGAAGCCCAGAGAGGCCAGCAGTTGGAGGAAGCCAGGCAACAGGAGGAAGAAC
GGCAGAAGGAAGAGCTAGCCAGGCTACAGAAAGAACTGGTGCATAAGGCAAATCCAATATGCAAGTACCAGGGTGTGGAG
GTAAACTCAAGTGACCAGCCTTTGACTGTGCCTGTATTTCCCAAGTTCTCTACCCAATTCCACTGC

Alignment

ORF - retro_ogar_2612 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.96 %
• Parental protein coverage: 88.62 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EKENFVGQSISSNTCSSLEVEGPVSRKTPAQPQRRSIRLSAQRDLEQKGTDHVKMKAKRCATPVVLDEIP
          EKENFVGQSISSNTCSSLEVEGPVSRKTPAQPQRRSIRLSAQRDLEQKGTDH.KMKAKRCATPVVLDEIP
Retrocopy EKENFVGQSISSNTCSSLEVEGPVSRKTPAQPQRRSIRLSAQRDLEQKGTDHEKMKAKRCATPVVLDEIP

Parental  PPKKMKVSNKKKKPEEGDSARQDTSEKNESSPEKEKGRRTVPFIRPVRQKILKSTEEQDLEKRMKMQQAV
          PP.KMKVSNKKKKPEE.DSA.QDTSEKNESSPEKEKGRRTVPFI.PVRQKILKSTEEQDLEKRMKMQQ.V
Retrocopy PPEKMKVSNKKKKPEEEDSAHQDTSEKNESSPEKEKGRRTVPFILPVRQKILKSTEEQDLEKRMKMQQVV

Parental  MEMRRKNEEFKKFALAGAGQPVKKSVSQVTKSIDFHFHTDERIKQHPINQEEYKEVDFTSELRKHPSSPA
          ME..RKNEEFKKFALAGAGQPVKKSVSQVTKSIDFHFHTDERIKQHP.NQEEYKEVDFTSEL.KHPSSPA
Retrocopy MEKQRKNEEFKKFALAGAGQPVKKSVSQVTKSIDFHFHTDERIKQHPKNQEEYKEVDFTSELQKHPSSPA

Parental  RVTKGCTIIKPFNLSQGKKRAFDEAASTYVPLAQQVEAFHKQTPNRYHLRSKKDDISLLPSKSSVAQISR
          .VTKGCTI.KPFNLSQGKKRAFDEAASTY.PLAQQVEAFHKQTPNRYHLRSKK.DISLLPSKSSVAQISR
Retrocopy QVTKGCTIFKPFNLSQGKKRAFDEAASTYLPLAQQVEAFHKQTPNRYHLRSKKGDISLLPSKSSVAQISR

Parental  DPQTPVLQTKQRTRPVTYKSAADQEAEELEKLQQYKFKARELDPRILKGGPILPKKPPVKPPTQPIGFDL
          DPQTPVLQTKQ.TRPVTYKSAADQEAEELEKLQQYKFKARELDPRILKGG.IL.KKPP.KPPTQPIGFDL
Retrocopy DPQTPVLQTKQHTRPVTYKSAADQEAEELEKLQQYKFKARELDPRILKGGHILTKKPPMKPPTQPIGFDL

Parental  EIEKRIQERESKKKSDDEHFEFHSRPCPTKILEDVVGVPEKKVLPITVPKSPAFALKNRIRIPTKGDEEE
          EIEKRI.E.ESKKKSDD.HFEFHSRPCPTKILEDVVGVPEKKVLPITVPKSPAFALKNRIRIPTKGDEEE
Retrocopy EIEKRI*EQESKKKSDDKHFEFHSRPCPTKILEDVVGVPEKKVLPITVPKSPAFALKNRIRIPTKGDEEE

Parental  DEPVVVRAQPVPHYGVPFKPQIPEARTVELCPFSFDSRDKERQLKKEMKIRELQKGEVPVFKALPLPHFD
          DEPVVVRA.PVPHYGVPFKPQIPEARTVELCPFSFDS.DKE.QLKKEMKIRELQK.EVPVFKALPLPHFD
Retrocopy DEPVVVRA*PVPHYGVPFKPQIPEARTVELCPFSFDSQDKEHQLKKEMKIRELQKEEVPVFKALPLPHFD

Parental  TINLPEKKVKNVTQVEPFCLETDKRGALKAQIWKHQLEEELKQQKEAACFKARPNTVISQEPFVPKKEKK
          TINLPEKKVKNVTQVEPFCLETDKRGALKAQI.K.QLEEELKQQKEAACFKARPNTVISQEPFVPKK...
Retrocopy TINLPEKKVKNVTQVEPFCLETDKRGALKAQI*KNQLEEELKQQKEAACFKARPNTVISQEPFVPKKXXX

Parental  SVTEGLSGSLVQEPFQLATEKRAKERQELEKRMVEIEAQRAQQLEEARQQEEEQQKEELARLRKELVHKA
          .VTEGLSGSLVQEPFQLATEKRAKE.QELE.RMVEIEAQR.QQLEEARQQEEE.QKEELARL.KELVHKA
Retrocopy XVTEGLSGSLVQEPFQLATEKRAKEQQELE*RMVEIEAQRGQQLEEARQQEEERQKEELARLQKELVHKA

Parental  NPIRKYQGVEVKSSDQPLTVPVSPKFSTRFHC
          NPI.KYQGVEV.SSDQPLTVPV.PKFST.FHC
Retrocopy NPICKYQGVEVNSSDQPLTVPVFPKFSTQFHC

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_2612 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Myotis lucifugus	ENSMLUG00000007248	1 retrocopy	retro_mluc_724,
Otolemur garnettii	ENSOGAG00000012423	1 retrocopy	retro_ogar_2612 ,