RetrogeneDB ID: retro_ogar_2956

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873689.1:2788872..2789588(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TYMS
• Ensembl ID: ENSOGAG00000024349
• Aliases: None
• Description: thymidylate synthetase [Source:HGNC Symbol;Acc:12441]

Sequence

>retro_ogar_2956
GGGGCAGGACAGGTGCTGGGCGTGCAGAGTGCTGCAGCCCGAGAGGTGAATTTCCTCTGAGGACAAGCAAATGTGTGTCT
GGAAGGGTGTTTTGGAGAGTTGCTGTAGTTTATCAAGGGATCCACAAACGCTAAAGAACTGTCTTCCAAGGGAGTGAAAC
TCTGGAGTGCCAATGCATCCCAAGCCTTTTGGACAGACTGAGATTCTCCAACAGAGAGAAAGGGGACTTGGGCCCAGTCA
GTGGCTTTCCGTGGAGGCATTTTGGGGCACAATACAAAGATATGGATTCAGATCATTCAGGTCAAGGAGCTGACCGACTA
CAAAAACTGACTGAGACCATCAGAACCAACCCTGATGACAGAAGAATCATCACGTGTGCTTATAACTCAAAGATCCTCCT
CCCATGGCGCTGCCTCCATGCCAGGCCCTCTGCCAGTTTTTCGTGGTGACTGGTGAGCTGTGCTGCCAGCTGCACCAGTG
GTCAGGAGACATGGGCCTGGGTGTGCGGTTCAACATGGCCAGCCACTCCCTGGTCACCTGCATGATGGTGCACTCCGCGG
GTCCAAAGCCAGGTGACTTTGTACATACCTTGGGAGATGCACGTATTTCCTGAATCACATTGAGCTGCTGAACATTCAGC
TTTAGATTGAACCAAGGCCTTTCCTGAAGCTTGAAATACTTCTAAAAGTTGGGCAAATGATGATTTCAAAGCTAAG

Alignment

ORF - retro_ogar_2956 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.35 %
• Parental protein coverage: 77.0 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  GTLSVFGMQARY-SLRDEFPLLTTKRV-FWKGVLE-ELLWFIKGSTNAKELSSKGVKIWDANGSRDF-LD
          G...V.G.Q....S.R.EFPL.T.K.V..WKGVLE.ELL.FIKGSTNAKELSSKGVK.W.AN.S..F.LD
Retrocopy GAGQVLGVQSAA<SPRGEFPLRTSKCV<VWKGVLE<ELL*FIKGSTNAKELSSKGVKLWSANASQAF<LD

Parental  SLGFSKREEGDLGPVYGFQWRHFGAEYKDMDSDYSGQGVDQLQKVIDTIKTNPDDRRIIMCAWNP-KDLP
          .L.FS.RE.GDLGPV.GF.WRHFGA.YKDMDSD.SGQG.D.LQK...TI.TNPDDRRII.CA.N..KD.P
Retrocopy RLRFSNREKGDLGPVSGFPWRHFGAQYKDMDSDHSGQGADRLQKLTETIRTNPDDRRIITCAYNS<KDPP

Parental  LMALPPCHALCQFYVVNGELSCQLYQRSGDMGLGVPFNIASYSLLTYMIAHITGLKPGDFVHTLGDAHI-
          .MALPPC.ALCQF.VV.GEL.CQL.Q.SGDMGLGV.FN.AS.SL.T.M..H..G.KPGDFVHTLGDA.I.
Retrocopy PMALPPCQALCQFFVVTGELCCQLHQWSGDMGLGVRFNMASHSLVTCMMVHSAGPKPGDFVHTLGDARI<

Parental  YLNHVEPLKIQLQREPRPFPKLKILRKVETI-DDFKAE
          .LNH.E.L.IQL..EPRPF.KL.IL.KV....DDFKA.
Retrocopy FLNHIELLNIQL*IEPRPFLKLEILLKVGQM<DDFKAK

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_2956 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 9 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Felis catus	ENSFCAG00000009230	2 retrocopies	retro_fcat_1107, retro_fcat_339,
Loxodonta africana	ENSLAFG00000014910	2 retrocopies	retro_lafr_1030, retro_lafr_635,
Macropus eugenii	ENSMEUG00000009507	1 retrocopy	retro_meug_175,
Monodelphis domestica	ENSMODG00000021479	2 retrocopies	retro_mdom_1084, retro_mdom_1186,
Mustela putorius furo	ENSMPUG00000005419	2 retrocopies	retro_mputfur_1155, retro_mputfur_860,
Mus musculus	ENSMUSG00000025747	1 retrocopy	retro_mmus_584,
Otolemur garnettii	ENSOGAG00000024349	2 retrocopies	retro_ogar_2956 , retro_ogar_3211,
Sarcophilus harrisii	ENSSHAG00000003102	1 retrocopy	retro_shar_424,
Sus scrofa	ENSSSCG00000023869	2 retrocopies	retro_sscr_810, retro_sscr_841,