RetrogeneDB ID: retro_ogar_3272

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873762.1:14972..15877(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GALNT13
• Ensembl ID: ENSOGAG00000016208
• Aliases: None
• Description: UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 13 (GalNAc-T13) [Source:HGNC Symbol;Acc:23242]

Sequence

>retro_ogar_3272
GACATGACCTATGGTGGATTCAACTGAGAGCTCAGTTTTCACTCATATCCTGTTCCCTAAAGAAAAATGGACAGAAGGAA
AGGTGATTGAACTCTTCCTGTCAGAACACCTACCATAATAGCAGGAGGCCTTTTCTCTATAGACAGAGATTACTTCAGGA
AATTGGAACATATGATGCTGGAATGGATATTTGGGGAGGAGAACCTAGAAATTTCCTTTAAAATCTGGCAGTGTGGAGGG
ACTTTGGCAATTGTCACATGCTCACATGTGGGACATGTGTTTTGGAAAGCTACACCTTACACATTTCCAGGAAGCACAGG
GCAGACTATCAATAAAAATAATAGATGACTTCCTGAAGTGTGGATGGGTGAACTCAAGAATTTTTTCTATATAATTTCTC
CAAGTGTTACAAAGGTAAATTATGGAGCTATATCATCCAGACTCAATCTAAGACACAAACTACAATACAGATCTTTCTTT
TGGTACCTAGAGAATATTTATACTGATTCTCAAATTCCACATTACTATTTCTCATTGGGAGAGATACAAAATGTGGAAAC
AAATCAACATCTAGTAACATGGCTAGAAAAGAGAATGAAAATGGAATTTTTAATTGTCACAGTATGGGAAGTAATCAGGT
TTTCTCTTGTATTGCCAGCTAAGAAATTAGAACAGATGACCTTTGCTTGGATGTTTCCAAACTTAATGGCCCAGTCACAA
TTCTCAAATGTCACCACCTAAAAGGCAACCAACTTTGGGAGTATGACTCAGTGAAATTAGCCCTGCGACATGTGAACAGT
AATCAGTGCCTGGATAAAACCACAGAAGAGGATAGCTAGGTGACCAACATTAGAGGCTGCAATGGAAGCCCGTCCCAGCA
GTGGCTTCTTTAAAATGTTACCCTT

Alignment

ORF - retro_ogar_3272 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.96 %
• Parental protein coverage: 64.33 %
• Number of stop codons detected: 8
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  DMTYGGFNWKLNFRWYPVPQREMDRRKGDRTLPVRTPT-MAGGLFSIDRNYF-EEIGTYDAGMDIWGGE-
          DMTYGGFN..L.F..YPVP.R.MDRRKGD.TLPVRTPT..AGGLFSIDR.YF..EIGTYDAGMDIWGGE.
Retrocopy DMTYGGFN*ELSFHSYPVP*RKMDRRKGD*TLPVRTPTIIAGGLFSIDRDYF<QEIGTYDAGMDIWGGEP

Parental  -NLEMSFRIWQCGGSLEIVTC-SHVGHVFRKATPYTFPGGTGHVINKNNRRLAEVWMDEFKDFFYIISPG
          .N.......W...G.....TC..HV...F.KATPYTFPG.TG..INKNNR.L.EVWM.E.K.FFYIISP.
Retrocopy RNFL*NLAVWRDFGNCHMLTC>GHV---FWKATPYTFPGSTGQTINKNNR*LPEVWMGELKNFFYIISPS

Parental  VVKVDYGDVSVRKTLRENLKCKPFSWYLENIYPDSQIPRRYYSLGEIRNVETNQCL-DNMGRKENEKVGI
          V.KV.YG..S.R..LR..L....F.WYLENIY.DSQIP..Y.SLGEI.NVETNQ.L..NM.RKENE..GI
Retrocopy VTKVNYGAISSRLNLRHKLQYRSFFWYLENIYTDSQIPHYYFSLGEIQNVETNQHL<SNMARKENEN-GI

Parental  FNCHGMGGNQVFSYTADKEIRTDDLCLDVSRLNGPVIMLKCHHMRGNQLWDYDSERLTLRHVNSNQCLDE
          FNCH.MG.NQVFS..A..EIRTDDLCLDVS.LNGPV..LKCHH..GNQLW.YDS..L.LRHVNSNQCLD.
Retrocopy FNCHSMGSNQVFSCIAS*EIRTDDLCLDVSKLNGPVTILKCHHLKGNQLWEYDSVKLALRHVNSNQCLDK

Parental  PSEEDKMVPTMQDCSGSRSQQWLLRNMTL
          ..EED..V.....C.GS.SQQWLL.N.TL
Retrocopy TTEEDS*VTNIRGCNGSPSQQWLL*NVTL

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_3272 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 6 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Microcebus murinus	ENSMICG00000013917	1 retrocopy	retro_mmur_228,
Oryctolagus cuniculus	ENSOCUG00000017645	1 retrocopy	retro_ocun_274,
Otolemur garnettii	ENSOGAG00000001408	2 retrocopies	retro_ogar_3253, retro_ogar_717,
Otolemur garnettii	ENSOGAG00000016208	2 retrocopies	retro_ogar_2525, retro_ogar_3272 ,
Tupaia belangeri	ENSTBEG00000000869	1 retrocopy	retro_tbel_1671,
Tursiops truncatus	ENSTTRG00000002506	2 retrocopies	retro_ttru_793, retro_ttru_854,