RetrogeneDB ID: retro_tbel_3626

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_147223:33704..34507(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NAB1
• Ensembl ID: ENSTBEG00000011954
• Aliases: None
• Description: NGFI-A binding protein 1 (EGR1 binding protein 1) [Source:HGNC Symbol;Acc:7626]

Sequence

>retro_tbel_3626
TGGGTTACAAACTGTGGCCATTTTAATCAGCCACTGACTTTCCTTCCTATCAGTAGCATACCCACCTATAAATTGCCCGA
GGGATATCCAATGTGGGTGGGAATAACCTGCAGTAGTTATGAAAAGAATAGCAATGCCTGGGAATCTCATTTTAAAATCC
CCAAATGTGCAGACACCTCCTGTGTACAGAGCTTGGGACAGGGGGCGTCAGCTGTGGTGAAGAGCTTAGCACTGCAGAGT
GCTGGTGAGTCCAGACTCTGGCAAGGCCACCATGCCACTGAGAGTGAGCAGTCTCTCCCCAGCAGATCTTGGCCCCCCAG
CTTCCCCAGAGGAGAGCAGTGAAGGCTGGATGCTGCTGCTGCACTGTGGGTGGAGTGAATGGCCCCCATGCTGTCAAAAA
GTGACTTGAATGAAGTAAAGGAACTACTGAAATCCCAAAAGAAGTTGGCCAAAGTGATTGATCACATCTTTGAGATGAGT
GATGATGATCCACACAAAGAGGAGGAAATTAGAAAATATAGTGGAAAATATGGCAGATCTGACTCAAAGAGAAAGGGTGG
GAAACATCACACACTTCATGAGCTCACTATTAATGAAGCAGCTGCTTGATTCTGTGTGAAGGATAATGCCCTGCTGATAA
GAAGAGACAATTTTTTGCCCTGGCTAGGTAGATTTTTCATGAAGTGACATATCAATATATTTACAGAACCACCAAGACAA
AATGTGGAGAAAGAGATGAATTATCACTGAGGAGGATTAAAGTAGAGGATGGGTTTCCAGATTTCCAGGATTCTGTGCAC
ACT

Alignment

ORF - retro_tbel_3626 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.35 %
• Parental protein coverage: 56.06 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  WVTNPGLFNQPLTSLPVSSIPIYKLPEGSPTWLGITCSSYERNSNAREPHLKIPKCAATTCVQSLGQGKS
          WVTN.G.FNQPLT.LP.SSIP.YKLPEG.P.W.GITCSSYE.NSNA.E.H.KIPKCA.T.CVQSLGQG.S
Retrocopy WVTNCGHFNQPLTFLPISSIPTYKLPEGYPMWVGITCSSYEKNSNAWESHFKIPKCADTSCVQSLGQGAS

Parental  DVVGNLALQSAGESRLWQGHHATESEHSLSPA-DLGSPASPKESSEA-LDAAAALSVAECVERMAPTLPK
          .VV..LALQSAGESRLWQGHHATESE.SL.P..DLG.PASP.ESSE..LDAAAAL.V....E.MAP.L.K
Retrocopy AVVKSLALQSAGESRLWQGHHATESEQSL-PS>DLGPPASPEESSEG<LDAAAALWV----E*MAPMLSK

Parental  SDLNEVKELLKSNKKLAKMIGHIFEMSDDDPHKEEEIRKYSAIYGRFDSKRKDGKHLTLHELTVNEAAAQ
          SDLNEVKELLKS.KKLAK.I.HIFEMSDDDPHKEEEIRKYS..YGR.DSKRK.GKH.TLHELT.NEAAA.
Retrocopy SDLNEVKELLKSQKKLAKVIDHIFEMSDDDPHKEEEIRKYSGKYGRSDSKRKGGKHHTLHELTINEAAA*

Parental  LCVKDNALLTRRD-ELFALARQISREVTYKYTYRTTKSKCGERDELSPKRIKVEDGFPDFQDSVHT
          .CVKDNALL.RRD...FALAR.I..EVTY.Y.YRTTK.KCGERDELS..RIKVEDGFPDFQDSVHT
Retrocopy FCVKDNALLIRRD<QFFALAR*IFHEVTYQYIYRTTKTKCGERDELSLRRIKVEDGFPDFQDSVHT

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_3626 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_3626 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 8 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000010241	1 retrocopy	retro_chof_2490,
Callithrix jacchus	ENSCJAG00000005748	1 retrocopy	retro_cjac_4224,
Gorilla gorilla	ENSGGOG00000013842	1 retrocopy	retro_ggor_3068,
Microcebus murinus	ENSMICG00000007306	2 retrocopies	retro_mmur_1155, retro_mmur_1211,
Nomascus leucogenys	ENSNLEG00000006665	1 retrocopy	retro_nleu_2288,
Pongo abelii	ENSPPYG00000013025	1 retrocopy	retro_pabe_3822,
Ictidomys tridecemlineatus	ENSSTOG00000000098	1 retrocopy	retro_itri_1621,
Tupaia belangeri	ENSTBEG00000011954	1 retrocopy	retro_tbel_3626 ,