RetrogeneDB ID: retro_tbel_3468

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_141588:59445..60035(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LDHC
• Ensembl ID: ENSTBEG00000011741
• Aliases: None
• Description: lactate dehydrogenase C [Source:HGNC Symbol;Acc:6544]

Sequence

>retro_tbel_3468
ATAGCATCTCTCAAGGATCAGCTGATTGTGACTCTTCTTAAGGAAGCCCAGGCCCCCAAAATAAGATTATGGTTGTTGGG
GTTGGTGCTATTGGCATGGCCTGGGCCATCAGTATCTTAGTGAAGGACTTGGCAGATGAACTTGGTCTTGTTGATGCCAT
GGAAGACAAATTGAAGGAAGAGATGATGGATTTCCAACATGGCAGCCTTTTCCTTAGAACACCAAAAATCGTCTCTGGTA
GAGACTCTAATGTGACTGAGAACGTCAAGCTGGTCATTATCACAGCTGGAGCTCATCAGCAAGAGGGAGAACGCTGTCTT
CACCTGGTCCAGCGCAACGTCAACCTCTTCAAATTCATCATTCCGAATGTTGTAAAATACGACCCAAACTGCAAATTGCT
TGTTGTTTCCAATCCAGTGTATATCTTGACCTATGTGGCTTGGAAGATAAGTGGCTTTCCCAAAAACCATGTTATTAAAA
GTGGTAGTAATCTGGATTCTGCCCAGTGCCATTACCTGATGGGAGAAAGGCTGGGAGTTCACCCATCAAGCTATCGTGGG
TGGGTCCTGGGGGAGCACAGAGACTCCAGT

Alignment

ORF - retro_tbel_3468 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.63 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSSVKEQLIENLTEEDKVS-HSKITIVGAGAVGMACAISILLKDLADELALVDVATDKLKGEMMDLQHGS
          ..S.K.QLI..L..E.......KI..VG.GA.GMA.AISIL.KDLADEL.LVD...DKLK.EMMD.QHGS
Retrocopy IASLKDQLIVTLLKEAQAP<QNKIMVVGVGAIGMAWAISILVKDLADELGLVDAMEDKLKEEMMDFQHGS

Parental  LFFSTSKITSGKDYSISANSKLVIVTAGARQQEGESRLALVQRNVNIMKSIIPTIVHYSPECKMLIVSNP
          LF..T.KI.SG.D.....N.KLVI.TAGA.QQEGE..L.LVQRNVN..K.IIP..V.Y.P.CK.L.VSNP
Retrocopy LFLRTPKIVSGRDSNVTENVKLVIITAGAHQQEGERCLHLVQRNVNLFKFIIPNVVKYDPNCKLLVVSNP

Parental  VDILTYVVWKLSGLPVTRVIGSGCNLDSARFRYLIGEKLGVHATSCHGWIIGEHGDSS
          V.ILTYV.WK.SG.P...VI.SG.NLDSA...YL.GE.LGVH..S..GW..GEH.DSS
Retrocopy VYILTYVAWKISGFPKNHVIKSGSNLDSAQCHYLMGERLGVHPSSYRGWVLGEHRDSS

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_3468 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_3468 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 3 parental genes, and 30 retrocopies.

Species	Parental gene accession	Retrocopies number
Rattus norvegicus	ENSRNOG00000013103	2 retrocopies	retro_rnor_2081, retro_rnor_499,
Tupaia belangeri	ENSTBEG00000011741	24 retrocopies	retro_tbel_1130, retro_tbel_1300, retro_tbel_1344, retro_tbel_1657, retro_tbel_2072, retro_tbel_2125, retro_tbel_2227, retro_tbel_2254, retro_tbel_2367, retro_tbel_2433, retro_tbel_2640, retro_tbel_2775, retro_tbel_2859, retro_tbel_2877, retro_tbel_2960, retro_tbel_3042, retro_tbel_3188, retro_tbel_3468 , retro_tbel_3683, retro_tbel_4189, retro_tbel_4323, retro_tbel_4557, retro_tbel_499, retro_tbel_676,
Tarsius syrichta	ENSTSYG00000008062	4 retrocopies	retro_tsyr_1811, retro_tsyr_2064, retro_tsyr_2071, retro_tsyr_731,