RetrogeneDB ID: retro_tbel_3042

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_127562:97818..98409(+)
• 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_3042
ATGACATCTCTCAAGGATCAGATGATTGTGAATCTTCTTAAGGAAGACCAGGTTCCCCAAAATAAGAGTACAGTTGTTGG
GTTTGGTGCTGTTGGCATGGCCTGTGACATCAGCATCTTAATGAAGGACTTGGCAGATGAACTTGCTCTTGTTGATGTCA
TGGAAGACAAATTGAAGGGAGAGATGATGGATCTCCAACACGGCAGCCTTTTCCACAGGACACCAAAAATCGTCTCTGGC
AAAGACTATAATGTAACCATGAACTCTAAGCTGGTCATTATCACAGCTGGAGCTCGTCAGTAAGAGGGAGAAAGCTGTCT
TAACCTGGTCCAGTGCAATGTCAATATATTCAAATTCATCATTCCTAATGTTGTAAAATACAGCCCAAACTGCAAGTTTC
TTATTGTTTCCAATCCAGTGGATATCTTGACCTATGTGGCTTGGAAGATAAGTGGCTTTCCCAAAAACCATGTTATTGAA
AGTGTTTGTAATCTGGATTCAGCCCGGTTCCATTACCTGATGGGGGAAAGGCTGAGAGTTCACCCATTAAGTTGTCATGG
GTGGGTCCTGGGAGAGCATGGAGACTCCAGC

Alignment

ORF - retro_tbel_3042 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.59 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSSVKEQLIENLTEEDKVSHSKITIVGAGAVGMACAISILLKDLADELALVDVATDKLKGEMMDLQHGSL
          M.S.K.Q.I.NL..ED.V...K.T.VG.GAVGMAC.ISIL.KDLADELALVDV..DKLKGEMMDLQHGSL
Retrocopy MTSLKDQMIVNLLKEDQVPQNKSTVVGFGAVGMACDISILMKDLADELALVDVMEDKLKGEMMDLQHGSL

Parental  FFSTSKITSGKDYSISANSKLVIVTAGARQQEGESRLALVQRNVNIMKSIIPTIVHYSPECKMLIVSNPV
          F..T.KI.SGKDY....NSKLVI.TAGARQ.EGES.L.LVQ.NVNI.K.IIP..V.YSP.CK.LIVSNPV
Retrocopy FHRTPKIVSGKDYNVTMNSKLVIITAGARQ*EGESCLNLVQCNVNIFKFIIPNVVKYSPNCKFLIVSNPV

Parental  DILTYVVWKLSGLPVTRVIGSGCNLDSARFRYLIGEKLGVHATSCHGWIIGEHGDSS
          DILTYV.WK.SG.P...VI.S.CNLDSARF.YL.GE.L.VH..SCHGW..GEHGDSS
Retrocopy DILTYVAWKISGFPKNHVIESVCNLDSARFHYLMGERLRVHPLSCHGWVLGEHGDSS

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_3042 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_3042 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,