RetrogeneDB ID: retro_tbel_2807

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_119614:62574..63005(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PFDN2
• Ensembl ID: ENSTBEG00000015982
• Aliases: None
• Description: prefoldin subunit 2 [Source:HGNC Symbol;Acc:8867]

Sequence

>retro_tbel_2807
GGAGAGCAGCAGCAGTAAGGCATGAGGAAGAGGGCGATGTGGATGAAGCAGGTAATTGCTGGCTTTAGCTGCATTCAGCA
GGAACAGCAGGGCCTGGCCTCGAAAGCAGCCAAGCTAGAGGTGGAGTTGAATGAGCACAGCCTGCTGACACACTGAAGGA
GGAGAATGAAAATCCACAATTGCTGCCGCATGGTTGGCTGGATACTGGTGGAGTAGATTGTCAAAGATGTGCTGCCCGCC
TTGGAGAACAGGAACAGATACAGAAGGTTATTGAGACACTGACACAGCAGCTTCAGGCAAAGGGGAAATAACTAAATGAA
TTCTGGGAAAAGCACAATGTCCATCTCATGGGGGAAGATGAGAAGCCAGTAGTCAAGGAAAACTCAGAAGGGACTGGGTC
TAAGGCCAGCTTAGCCAGAATGTTGGCCTCC

Alignment

ORF - retro_tbel_2807 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.18 %
• Parental protein coverage: 94.81 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GKSSGSGVGKGAVSAEQVIAGFNRLRQEQRGLASKAAELEMELNEHSLVIDTLKEVDETRKCYRMVGGVL
          G.....G..K.A....QVIAGF....QEQ.GLASKAA.LE.ELNEHSL.............C.RMVG..L
Retrocopy GEQQQ*GMRKRAMWMKQVIAGFSCIQQEQQGLASKAAKLEVELNEHSLLTH*RRRM-KIHNCCRMVGWIL

Parental  VERTVKEVLPALENNKEQIQKII-ETLTQQLQAKGKELNEFREKHNIRLMGEDEKPAAKENSEGAGAKAS
          VE..VK.VLPALE.N.........ETLTQQLQAKGK.LNEF.EKHN..LMGEDEKP..KENSEG.G.KAS
Retrocopy VE*IVKDVLPALE-NRNRYRRLL<ETLTQQLQAKGK*LNEFWEKHNVHLMGEDEKPVVKENSEGTGSKAS

Parental  SAGVLVS
          .A..L.S
Retrocopy LARMLAS

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_2807 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_2807 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 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000004588	1 retrocopy	retro_dord_362,
Myotis lucifugus	ENSMLUG00000004526	1 retrocopy	retro_mluc_1293,
Mus musculus	ENSMUSG00000006412	1 retrocopy	retro_mmus_307,
Tupaia belangeri	ENSTBEG00000015982	1 retrocopy	retro_tbel_2807 ,
Tursiops truncatus	ENSTTRG00000009181	1 retrocopy	retro_ttru_1756,