RetrogeneDB ID: retro_ogar_1719

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873562.1:11148262..11149713(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PES1
• Ensembl ID: ENSOGAG00000005804
• Aliases: None
• Description: pescadillo ribosomal biogenesis factor 1 [Source:HGNC Symbol;Acc:8848]

Sequence

>retro_ogar_1719
GAGTGGAACACTGTGGAACGTCTGAAGGACAATAAGCCTAACTATAAACTTGACCACATCATCACGGAGCAGTACCCCAC
TTTCATCGATGCTCTGTGGGACCTGGATGATGCCCTCTCCATGTGCTTTCTCTTTTCCACCTTCCCTTGGACTGGCAAGT
GTCACATGCAGACCATTCAACTGTGCCACCGGCTCACTGTAGAGTTCTTGCACTGCGTCCTTGCCACCCATGCCCTGCAC
AAGGTCTTCCTGTCCATCAAAGGCATCTACTAGCAGGCTGAAGTGCTAGGACAACCTATTATATGGATCACACCCTACGC
CTTCTCCCACAATCACCCAACATATGTTGACTACAGAATCATGGCCACCTTCACCGAGTTCTACACCACCTTGCTGGGCT
TTGTCAACTTCTGCCTCTAACAGTCATTCAACCTCCACTACTCACTCAAGCTTGAGGGTCAGGTTGAAGCAAAGGTGAAG
GACAGTGAGGGCACCTATACACTGGGCTCTGAAAGCTCTGTGGAGAAACTGGCAGCCCTCAGTGCCAGCCTGGCCCGCGT
GGTGGTGCCTGCCATTGAGGAGGCGGCCAAGGTGGATGAATTTCCTGCTGATGAGGAGATGGCTCTGTGGGAAGAGGACC
ACAGGAAGGAACTGGAGGCACAGAAAAAGCACAAGAAGCCCTTTAAGGGCCTGAAGTTCTTCCTGAATCGTGAGGTGCCC
CGTGAGGCCCTGGCCTTCATCACCATCAGTTCTGGGGGGGACGTATTCTGGGACAAGTCTGTGTGCATTCAAGCCACCTA
GGATGTCACATACTCCTGGGTCCCCACCAGACTGTCCACTGACCTGGGCAGCAGACCCCTGTCATTGGCAGGTACTATGT
GCAGTCTCAGTAAGTGTTTGACTCTGTGAATACCCGGTTCCTCCTCCCTGTGTCAGAGTACTTCCCTGGTGTGAAGCTGC
CCCACACCTTTCACCCTTTGTGTCTGAGAAGGAAGGAGATTACATCCCACCTGAGAAGCTGAAGCTGCTGGCTCTACAGC
GGGGAGAGGACCCAGGAAACTTGAATGAGTCTGAAGAAGAGGAGAAGGAGGAAGACAATGAAGGTGATGGCAATGAAGGG
GGAGAAAATGAAGAAGAGGAGGAAGATGTGGAAACTAGTTCAGAAAAGGAAGAAGCCTAACAGCTCTGGAGAAGCAGAGG
ATGGAGAGAAAGAAGCCCTGTGTGATAGAAGGCACCATGAAGCTGGAGGACAAGCAGCGGCTGGTCCAGGAGGAAGAGAG
CGAGACCAAATGCCTGGCTATTATGATGATGATGAAGAGAAATATCTGTACAACAAGATCATATTTGGCAAGAGGCGCAA
AATCTGTGAGGCCAACAAGCTGGCAGAGAAGCAGAAAGCCCATGATGAGGCCTTGAGGTCTGAGAAGAAGGCCAAGAAGG
CAAAGGTGGTG

Alignment

ORF - retro_ogar_1719 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.28 %
• Parental protein coverage: 83.11 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  EWNTVERLKDNKPNYKLDHIIKERYPTFIDALRDLDDALSMCFLFSTFPRTGKCHVQTIQLCRRLTVEFM
          EWNTVERLKDNKPNYKLDHII.E.YPTFIDAL.DLDDALSMCFLFSTFP.TGKCH.QTIQLC.RLTVEF.
Retrocopy EWNTVERLKDNKPNYKLDHIITEQYPTFIDALWDLDDALSMCFLFSTFPWTGKCHMQTIQLCHRLTVEFL

Parental  HYIIAARALRKVFLSIKGIYYQAEVLGQPIVWITPYAFSHDHPTDVDYRVMATFTEFYTTLLGFVNFRLY
          H...A..AL.KVFLSIKGIY.QAEVLGQPI.WITPYAFSH.HPT.VDYR.MATFTEFYTTLLGFVNF.L.
Retrocopy HCVLATHALHKVFLSIKGIY*QAEVLGQPIIWITPYAFSHNHPTYVDYRIMATFTEFYTTLLGFVNFCL*

Parental  QSLNLHYPPKLEDQVEAKVKDSEGTYALDSESSMEKLAALSASLARVVVPAIEEEAEVDEFPADEEIAVR
          QS.NLHY..KLE.QVEAKVKDSEGTY.L.SESS.EKLAALSASLARVVVPAIEE.A.VDEFPADEE.A..
Retrocopy QSFNLHYSLKLEGQVEAKVKDSEGTYTLGSESSVEKLAALSASLARVVVPAIEEAAKVDEFPADEEMALW

Parental  EEDHRKELEAQEKHKKLFEDLKFFLNREVPREALAFIIRSFGGDVSWDKSVCIGATYDVTNSCIT-HQIV
          EEDHRKELEAQ.KHKK.F..LKFFLNREVPREALAFI..S.GGDV.WDKSVCI.AT.DVT.S....HQ.V
Retrocopy EEDHRKELEAQKKHKKPFKGLKFFLNREVPREALAFITISSGGDVFWDKSVCIQAT*DVTYSWVP<HQTV

Parental  DRPGQQTSVIGSTLYQPQWVFDSVNARLLLPVSEYFPGVKLP-PHLSPFVSEKEGDYIPPEKLKLLALQR
          ..PGQQT.VIG....Q.Q.VFDSVN.R.LLPVSEYFPGVKLP.PHLSPFVSEKEGDYIPPEKLKLLALQR
Retrocopy H*PGQQTPVIGRYYVQSQ*VFDSVNTRFLLPVSEYFPGVKLP<PHLSPFVSEKEGDYIPPEKLKLLALQR

Parental  GEDPGNLNESEEEEKEEDNEGDGNEGGENEEEEDVETSSEKEEEAR-LTALEEQRMEKKKPQVMEGTMKL
          GEDPGNLNESEEEEKEEDNEGDGNEGGENEEEE........E.E...LTALE.QRME.KKP.V.EGTMKL
Retrocopy GEDPGNLNESEEEEKEEDNEGDGNEGGENEEEEE-DVETSSEKEEA<LTALEKQRMERKKPCVIEGTMKL

Parental  EDKQRLAQEEESEAKRLAIMMMKKR-EKYLYNKIMFGKRRKIREANKLAEKRKAHDEALRSEKKAKKAKV
          EDKQRL.QEEESE.K.LAI.MM....EKYLYNKI.FGKRRKI.EANKLAEK.KAHDEALRSEKKAKKAKV
Retrocopy EDKQRLVQEEESETKCLAI-MMMMK<EKYLYNKIIFGKRRKICEANKLAEKQKAHDEALRSEKKAKKAKV

Parental  V
          V
Retrocopy V

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_1719 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 8 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000010617	1 retrocopy	retro_cjac_3182,
Cavia porcellus	ENSCPOG00000003565	1 retrocopy	retro_cpor_986,
Homo sapiens	ENSG00000100029	1 retrocopy	retro_hsap_4133,
Otolemur garnettii	ENSOGAG00000005804	1 retrocopy	retro_ogar_1719 ,
Pongo abelii	ENSPPYG00000011716	1 retrocopy	retro_pabe_3471,
Pan troglodytes	ENSPTRG00000014251	2 retrocopies	retro_ptro_2018, retro_ptro_2809,
Rattus norvegicus	ENSRNOG00000004515	2 retrocopies	retro_rnor_2953, retro_rnor_824,
Tupaia belangeri	ENSTBEG00000009825	1 retrocopy	retro_tbel_1000,