RetrogeneDB ID: retro_ogar_2100

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873591.1:546662..547851(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOGAG00000026400
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: TFDP2
• Ensembl ID: ENSOGAG00000000168
• Aliases: None
• Description: transcription factor Dp-2 (E2F dimerization partner 2) [Source:HGNC Symbol;Acc:11751]

Sequence

>retro_ogar_2100
TTAGAAGCAATGAATGTAAATTTTGGATCCCAAATGATCATGAGCACACCACAGGGACTAACAAGTACAGGAGGTGTTCT
GATTGGGAGTCCATACATCCTTGCACCAGCAGTGATTAAGCAGACACACATAGTAGAAGCTGCTGGCTTGGTCCCTAGTG
ATGATAGCAAACAGGCTAGAGAATTTACAAAGTCTGGTTTTTCAGGAAGTAAACGAAGCAAAAAAGATAGAAATGGAAAA
GGCTTGAGGCATTTTTCAATGAAAGTGTGTGAGAAACTACAGCAAAAAGGCACAACATCATATAATGAAGTAGCAGATGA
GCTGGTGTCAGAGCTCACCAATCCAAATAACCGTTCGGCAGCTGATCCGCAGGCTTACGATGAGAAGAACATTAGGCGAA
GAGTTTATGATGCTTTAAATGTGCTGATGGCAATGAACATAATTTCAAAGGATAGAAAAGAAATCAAGTGGATTGGCCTA
CCTATCACCTGTGTTCAGGAATATCAAAACCTGGAGATAGAGAAGCAGAAGCTGATAGAACGGATCAAGGAGAAGCGGGC
CGAGCTGCAAGAGCTTCTTCTATACCAAATTTCTTTCAAAAACCTGGTACAGAGAAATCGTCAAAAAGAACAGCAGAATA
AGAGACCTCCACCTCTGAACACCACTGTCCAGCTGCCTTTTAAACTCATCACTGCAAACAAAAAGACAGTCATAGATTGC
AGCATCTCCAGTGATAAGTATAAATATATCTTCAATTTCGACAACACCTTTCAGATCCATGATGACACAGAATTACTGAA
GCGTATGGGAATGTCCTTGGGCCTGGAGTCAGGCAACTGCTCTCCAGAAAACCTGAAACGTGCTAAGTCCCTGGTGCCAA
GGGCTTTGCAAAGTTATATCACAGCCATCTCCACCGGACCATCTTGGCTAAATCAGGGACTACTTCCAAAACCTACTCAA
TCAGGTTCAAATTTCAAGTGGACCACTGATGCCACCCTACCCCAATCAAGTTTAAAGCGAGGGTTCTGCTTGGATACTGA
AGTAGCCTTAGCAACCGGGCAGTTCCGGGCCCCAAAGCGTCACCAGTTCAGCAGTGCCACCTCTCACTGCTCTGAGTCCC
GAGATGAAACCTCCCTGTTGTTTCAACGACAAAGACAAGGAAAATGATGAGGAGGATTCCTCTTCCCCA

Alignment

ORF - retro_ogar_2100 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.13 %
• Parental protein coverage: 92.96 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LGPINVNVGPQMIISTPQRLTSSGSVLIGSPYTPAPAMVTQTHITEAAGWVPGD-RKRAREFIDSDFSES
          L...NVN.G.QMI.STPQ.LTS.G.VLIGSPY..APA...QTHI.EAAG.VP.D..K.AREF..S.FS.S
Retrocopy LEAMNVNFGSQMIMSTPQGLTSTGGVLIGSPYILAPAVIKQTHIVEAAGLVPSDDSKQAREFTKSGFSGS

Parental  KRSKKGDKNGKGLRHFSMKVCEKVQRKGTTSYNEVADELVSEFTNSNNHLAADSQAYDQKNIRRRVYDAL
          KRSKK.D.NGKGLRHFSMKVCEK.Q.KGTTSYNEVADELVSE.TN.NN..AAD.QAYD.KNIRRRVYDAL
Retrocopy KRSKK-DRNGKGLRHFSMKVCEKLQQKGTTSYNEVADELVSELTNPNNRSAADPQAYDEKNIRRRVYDAL

Parental  NVLMAMNIISKEKKEIKWIGLPTNSAQECQNLEIEKQRRIERIKQKRAQLQELLLQQIAFKNLVQRNRQN
          NVLMAMNIISK..KEIKWIGLP....QE.QNLEIEKQ..IERIK.KRA.LQELLL.QI.FKNLVQRNRQ.
Retrocopy NVLMAMNIISKDRKEIKWIGLPITCVQEYQNLEIEKQKLIERIKEKRAELQELLLYQISFKNLVQRNRQK

Parental  EQQNQGPPALNSTIQLPFIIINTSRKTVIDCSISSDKFEYLFNFDNTFEIHDDIEVLKRMGMSFGLESGK
          EQQN..PP.LN.T.QLPF..I....KTVIDCSISSDK..Y.FNFDNTF.IHDD.E.LKRMGMS.GLESG.
Retrocopy EQQNKRPPPLNTTVQLPFKLITANKKTVIDCSISSDKYKYIFNFDNTFQIHDDTELLKRMGMSLGLESGN

Parental  CSLEDLKLAKSLVPKALEGYITDISTGPSWLNQGLLLNSTQSVSNLDLTTGATLPQSSVNQGLCLDAEVA
          CS.E.LK.AKSLVP.AL..YIT.ISTGPSWLNQGLL...TQS.SN...TT.ATLPQSS...G.CLD.EVA
Retrocopy CSPENLKRAKSLVPRALQSYITAISTGPSWLNQGLLPKPTQSGSNFKWTTDATLPQSSLKRGFCLDTEVA

Parental  LATGQFLAPNSHQSSSAASHCSESRGET-PCSFNDEDEEDDDEDSSSP
          LATGQF.AP..HQ.SSA.SHCSESR.ET.PC.FND.D.E.D.EDSSSP
Retrocopy LATGQFRAPKRHQFSSATSHCSESRDET>PCCFNDKDKENDEEDSSSP

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_2100 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000001950	1 retrocopy	retro_cjac_3164,
Otolemur garnettii	ENSOGAG00000000168	1 retrocopy	retro_ogar_2100 ,
Otolemur garnettii	ENSOGAG00000003532	1 retrocopy	retro_ogar_3334,