RetrogeneDB ID: retro_tbel_1671

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: GeneScaffold_5424:98922..99804(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GALNT13
• Ensembl ID: ENSTBEG00000000869
• Aliases: None
• Description: UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 13 (GalNAc-T13) [Source:HGNC Symbol;Acc:23242]

Sequence

>retro_tbel_1671
GTAGATGATGCCAGTGAAACAGACTCTTTGAAAAGACCCTATAGAGTTATATGAAAAAACTAAAAGTACTAGTTATGTCA
TTCAAATGGAACAATGCTCTGGGTTGATCAGAGCTAGATTAAAAGGAGCTGCTGTGTCTAAAGGCCAAATGATCACCTTC
TTGGATGCTCATCATGAGTGCACAGTGGGTGACTGGAGCGTCTGTTAGCCAGGATCAAACATGACAGGAAAACAGTAGTA
TGCCCTATCACTGATGTGATCAGTGATGTCACTTTTGAGTACATGGCAGGCTCAGATATGACTTATAGTGGATTCAACTG
GAAGCTACATTTTCACTGGTATCCTGTTCCCCAACAAGAATGAACAGAAGGAGATTAGACTCTTCCCGTCAGAACACCTA
TAACAGTAGGAGGCCTTTTTTCAATAGACAGAGATTACTTTCAGGAAACTGGAACATACGATGCTAGAGTAGGTATTTGG
GGAGGAGAAAACCTAGAAATTTCTTTTAGAATTTGGCAGTGTGAGGAACCTGGGAAATTGTTATGTGCTCACATGTTGGA
CATGCATTTCAGAAAGTGACACTTTACACGTTTCCAGAAGGCACAGAACAGATTATCAGTAAAAATTAAAGACAATTTGC
AGAAGTATGGGAAGATGAATTCAAGAATTTCTTCTATTTAATTTTCCCAGGTGTTACAATGGTAGATCATGGGGATATAT
CATCAAGACTCAGTCTTAGACACAAACAACAATGCAAATCTTTTTCTTGGTTTCCAGAAAATATTTATCTTAATTCTCAA
ATTCCATGTCACTATTTCTCACTGGGAGAGAAATTAACACATGGAAACAAATCAGTGTCTACATAATAGGGTTAGAAAAG
AG

Alignment

ORF - retro_tbel_1671 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.54 %
• Parental protein coverage: 58.46 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  VDDASERDFLKL-TLENYVKNLEVPVK-IIRMEERSGLIRARLRGAAASKGQVITFLDAHCECTLGW-LE
          VDDASE.D.LK..TL..Y.K.L.V.V...I.ME..SGLIRARL.GAA.SKGQ.ITFLDAH.ECT.G..LE
Retrocopy VDDASETDSLKR<TL*SYMKKLKVLVM<VIQMEQCSGLIRARLKGAAVSKGQMITFLDAHHECTVGD<LE

Parental  PLLARIKEDRKTVVCPIIDVISDDTFEYMAGSDMTYGGFNWKLNFRWYPVPQREMDRRKGDRTLPVRTPT
          .LLARIK.DRKTVVCPI.DVISD.TFEYMAGSDMTY.GFNWKL.F.WYPVPQ.E.....GD.TLPVRTP.
Retrocopy RLLARIKHDRKTVVCPITDVISDVTFEYMAGSDMTYSGFNWKLHFHWYPVPQQE*T--EGD*TLPVRTPI

Parental  MAGGLFSIDRNYFEEIGTYDAGMDIWGGENLEMSFRIWQCG-GSLEIVTCSHVGHVFRKATPYTFPGGTG
          ..GGLFSIDR.YF.E.GTYDA...IWGGENLE.SFRIWQC..G..EIV.CSHVGH.F.K.T.YTFP.GT.
Retrocopy TVGGLFSIDRDYFQETGTYDARVGIWGGENLEISFRIWQCE<GTWEIVMCSHVGHAFQKVTLYTFPEGTE

Parental  HVINKNNRRLAEVWMDEFKDFFYIISPGVVKVDYGDVSVRKTLRENLKCKPFSWYLENIYPDSQIPRRYY
          ..I.KN.R..AEVW.DEFK.FFY.I.PGV..VD.GD.S.R..LR....CK.FSW..ENIY..SQIP..Y.
Retrocopy QIISKN*RQFAEVWEDEFKNFFYLIFPGVTMVDHGDISSRLSLRHKQQCKSFSWFPENIYLNSQIPCHYF

Parental  SLGEIR-NVETNQCLDNMGRKE
          SLGE.....ETNQCL.N..RKE
Retrocopy SLGEKL>HMETNQCLHNRVRKE

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Tupaia belangeri was not studied using RNA-Seq expression data.

ChIP-Seq

Tupaia belangeri was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_tbel_1671 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_1671 was not experimentally validated.

Homology

Retrocopy orthology:

Tupaia belangeri 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 7 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	ENSOGAG00000016208	2 retrocopies	retro_ogar_2525, retro_ogar_3272,
Tupaia belangeri	ENSTBEG00000000869	1 retrocopy	retro_tbel_1671 ,
Tupaia belangeri	ENSTBEG00000003627	1 retrocopy	retro_tbel_2065,
Tupaia belangeri	ENSTBEG00000012122	1 retrocopy	retro_tbel_2374,
Tursiops truncatus	ENSTTRG00000002506	2 retrocopies	retro_ttru_793, retro_ttru_854,