RetrogeneDB ID: retro_tbel_525

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: GeneScaffold_2335:427077..427774(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NFU1
• Ensembl ID: ENSTBEG00000008616
• Aliases: None
• Description: NFU1 iron-sulfur cluster scaffold homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:16287]

Sequence

>retro_tbel_525
TGTCATACGATGATGAGTCATATACTATTAAGAAACAGACTCTGCATCAATTTGTGGTAAGAAGACCACTTTTCCCACTA
CCTGCAGCCTTGCTCAGCACAGTGAGATACATGATTATTCAAACACAAGATACTCCAAATCCCAACAGTTTAACGTTTAT
ACCAGGAAAACCTGTTCTTGAGACCAGGACCATGGATTTTCCTACAGGGGCTGCAGCATTCCACTCCCCTCTGGCTAGAC
AGTTATTTAGGATTGAAGGTGTACAAAGTGTCTTTTTTGGACCGGATTTCATCACTGTCACAAAAGAAAATGAAGAATTA
GATTGGAATTTACTGAAACCAGTTATTTATGCAACTATCATGGACTTCTTTGCATCTGGATTACTCCTATATACTGAGGA
AATGCCTTCAGGAGAAGCAGGATCTGAAGAAGATGATGAAGTTGTGGCAATGATTAAGGAATTGTTAGGCACTAGAATAC
GGCCAACTGTGCAGGAAGATGGCAGAGACATAATCTATAAAGGCTTTGAAGATGGCATTGTACAGTTGAAACTCCAAGGT
TCTTGTACTAGCTGTCCTAGTTCAAGCGTTACTCTGAAAAATGGAATTCAAAACAAGCTATAGTTTTATATTCCAGAAGT
AGAAGGCATAAAATAGTTATGGATGATGACTCAGATGAAAAAGAAGCAAAATCACCC

Alignment

ORF - retro_tbel_525 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.09 %
• Parental protein coverage: 91.34 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  CHMMMN-SYTIKKQTLHQFV-RRPLFPLPAALCNTVRYMFIQTQDTPNPNSLKFIPGKPVLETRTMDFPT
          CH.MM..SYTIKKQTLHQFV.RRPLFPLPAAL..TVRYM.IQTQDTPNPNSL.FIPGKPVLETRTMDFPT
Retrocopy CHTMMS<SYTIKKQTLHQFVVRRPLFPLPAALLSTVRYMIIQTQDTPNPNSLTFIPGKPVLETRTMDFPT

Parental  AAAAFRSPLARQLFRIEGVKSVFFGPDFITVTKENEELDWNLLKPDIYATIMDFFASGLPLVTEETSSGE
          .AAAF.SPLARQLFRIEGV.SVFFGPDFITVTKENEELDWNLLKP.IYATIMDFFASGL.L.TEE..SGE
Retrocopy GAAAFHSPLARQLFRIEGVQSVFFGPDFITVTKENEELDWNLLKPVIYATIMDFFASGLLLYTEEMPSGE

Parental  AGSEEDDEVVAMIKELLDTRIRPTVQEDGGDVIYKGFEDGIVQLKLQGSCTSCPSSIITLKNGIQNMLQF
          AGSEEDDEVVAMIKELL.TRIRPTVQEDG.D.IYKGFEDGIVQLKLQGSCTSCPSS..TLKNGIQN.L.F
Retrocopy AGSEEDDEVVAMIKELLGTRIRPTVQEDGRDIIYKGFEDGIVQLKLQGSCTSCPSSSVTLKNGIQNKL*F

Parental  YIPEVEGV-EQVMDDDSDEKEANSP
          YIPEVEG....VMDDDSDEKEA.SP
Retrocopy YIPEVEGI<KIVMDDDSDEKEAKSP

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_525 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_525 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 14 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000005978	1 retrocopy	retro_chof_456,
Callithrix jacchus	ENSCJAG00000019156	1 retrocopy	retro_cjac_1573,
Echinops telfairi	ENSETEG00000019002	1 retrocopy	retro_etel_1371,
Homo sapiens	ENSG00000169599	1 retrocopy	retro_hsap_2638,
Macaca mulatta	ENSMMUG00000000435	1 retrocopy	retro_mmul_1524,
Monodelphis domestica	ENSMODG00000011805	1 retrocopy	retro_mdom_1395,
Mustela putorius furo	ENSMPUG00000006663	1 retrocopy	retro_mputfur_67,
Mus musculus	ENSMUSG00000029993	1 retrocopy	retro_mmus_1401,
Nomascus leucogenys	ENSNLEG00000010101	1 retrocopy	retro_nleu_646,
Ochotona princeps	ENSOPRG00000016760	2 retrocopies	retro_opri_380, retro_opri_48,
Pongo abelii	ENSPPYG00000012339	1 retrocopy	retro_pabe_2329,
Pan troglodytes	ENSPTRG00000012016	1 retrocopy	retro_ptro_1778,
Tupaia belangeri	ENSTBEG00000008616	1 retrocopy	retro_tbel_525 ,
Tarsius syrichta	ENSTSYG00000013765	1 retrocopy	retro_tsyr_108,