RetrogeneDB ID: retro_ogar_2343

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873613.1:5645750..5646901(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOGAG00000032437
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: IFT52
• Ensembl ID: ENSOGAG00000007699
• Aliases: None
• Description: intraflagellar transport 52 homolog (Chlamydomonas) [Source:HGNC Symbol;Acc:15901]

Sequence

>retro_ogar_2343
ATGGAGAAAGAACTCTGGTGCACCATTCTATTTAATGCATACAAAAAGGAGCTATTTACCACCAACAATGGCTATAAATC
CATGCAGAAGAAACTTCAGAGTAACTGGAAAATTCAGAGCTTAAAAGATGAAATCACATCTGAGAAATTAATTGGGGCAA
AACTGTGGATTACAGCTGAGCCAAGGGAAAGATTTACTGCAACTGAGTTTGAAGTCCTGAAGAAATACCTTGACAGTGGT
GGCGATATCCTTGTGATGCTAGAAGAAGGTGGAGAATCCAGATTTGATACCAATATCAACTTTTTGCCAGAAGAATATGG
AATTGTGGTTAATAATGATGCTGTTGTTAGAAATGTATATCATCAATATTTCCATCCTAAAGAAGCTTTAGTTTCCAATG
GAGTTTTGAACAGGGAAATTAGTCGAGCTGTAGGAAAAGCTGTGCCTGGAATCATTGATGAAGAAAGCAGTGGCAACAAT
GCCCAGGCTCTCACCTTTGTCTATCCTTTTGGTGCCACATTGAGTGTCGTGAAACCAGCAGTGGCTGTTCTGTCTACAGG
CCCTGTCTGTTTTCCACTTAACAGACCCATCCTGGCTTTCTATTATTCAAAGAGTCAAGGTGGGAAGGTGGCAGTGTTTG
GCTCTGTGACCAATATTTGGATAAAGAAGAAAACAGAAAAATCACAGATGTTGTTTTCCAGTGGCTCACCACAGAAGACA
TCCAACTAAATCAGACTGATGCTGAGGACGCTGAGATTTCTGACTACATGATGCTGCCCGACACAGCCACCCTTTCAGAG
CGACTTGGAGTGTGTCTACAGGAGGGCGATGAGAACCCTTGGGACTTTACCACCCTCTTTGACCTGTCCATTTACCAACT
GGATGCCACCTCCCTCCCTAAGGTCATCAAGGCACATGAGCACCTAAACGTGAAACATGAACCACTCCAGCTTTTCCATC
CTCAGTTTGAGACGCCACTGCCAGCCCTTTGGCCTTTGGTTTTTCCTCCTCATTTCAGGGAATTACCACCTCCTCTTCTG
GAGCTGTTTGACTCAGATGAGACATTCTCCTCTGAGAAGACACACCTTGCTCAGATTACCAATAAGTGTACTGAAGAAGA
TCTGGAATTTTATGTCAGGAAGTGTGGTGAC

Alignment

ORF - retro_ogar_2343 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.58 %
• Parental protein coverage: 88.76 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MEKELRSTILFNAYKKELFTTNNGYKSMQKKLRSNWKIQSLKDEITSEKLIGAKLWITAGPREKFTAAEF
          MEKEL..TILFNAYKKELFTTNNGYKSMQKKL.SNWKIQSLKDEITSEKLIGAKLWITA.PRE.FTA.EF
Retrocopy MEKELWCTILFNAYKKELFTTNNGYKSMQKKLQSNWKIQSLKDEITSEKLIGAKLWITAEPRERFTATEF

Parental  EVLKKYLDSGGDILVMLGEGGESRFDTNINFLLEEYGIMVNNDAVVRNVYYKYFHPKEALVSNGVLNREI
          EVLKKYLDSGGDILVML.EGGESRFDTNINFL.EEYGI.VNNDAVVRNVY..YFHPKEALVSNGVLNREI
Retrocopy EVLKKYLDSGGDILVMLEEGGESRFDTNINFLPEEYGIVVNNDAVVRNVYHQYFHPKEALVSNGVLNREI

Parental  SRAAGKAVPGIIDEESSGNNAQALTFVYPFGATLSVMKPAVAVLSTGSVCFPLNRPILAFYHSKSQGGKL
          SRA.GKAVPGIIDEESSGNNAQALTFVYPFGATLSV.KPAVAVLSTG.VCFPLNRPILAFY.SKSQGGK.
Retrocopy SRAVGKAVPGIIDEESSGNNAQALTFVYPFGATLSVVKPAVAVLSTGPVCFPLNRPILAFYYSKSQGGKV

Parental  AVLGS-CHMFSDQYLDKEENSKIM-VSFSSALKKFMYIERENSCDFQISDYMMLPDTATLSERLRVCLQE
          AV.GS.C....D....KEEN.KI..V.F................D..ISDYMMLPDTATLSERL.VCLQE
Retrocopy AVFGS<CDQYLD----KEENRKITDVVFQWLTTEDIQLNQTDAEDAEISDYMMLPDTATLSERLGVCLQE

Parental  GDENPRDFTTLFDLSIYQLDTTSLPKVIKAHEQLNVKHEPLQLIQPQFETPLPALQPAVFPPSFRELPPP
          GDENP.DFTTLFDLSIYQLD.TSLPKVIKAHE.LNVKHEPLQL..PQFETPLPAL.P.VFPP.FRELPPP
Retrocopy GDENPWDFTTLFDLSIYQLDATSLPKVIKAHEHLNVKHEPLQLFHPQFETPLPALWPLVFPPHFRELPPP

Parental  PLELFDLDETFSSEKTRLAQITNKCTEEDLEFYVRKCGD
          .LELFD.DETFSSEKT.LAQITNKCTEEDLEFYVRKCGD
Retrocopy LLELFDSDETFSSEKTHLAQITNKCTEEDLEFYVRKCGD

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_2343 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 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000027175	1 retrocopy	retro_cpor_301,
Microcebus murinus	ENSMICG00000015182	1 retrocopy	retro_mmur_400,
Myotis lucifugus	ENSMLUG00000016664	1 retrocopy	retro_mluc_990,
Otolemur garnettii	ENSOGAG00000007699	1 retrocopy	retro_ogar_2343 ,
Takifugu rubripes	ENSTRUG00000014953	1 retrocopy	retro_trub_46,