RetrogeneDB ID: retro_tbel_1048

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: GeneScaffold_3681:244481..244872(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PSMA7
• Ensembl ID: ENSTBEG00000012281
• Aliases: None
• Description: proteasome (prosome, macropain) subunit, alpha type, 7 [Source:HGNC Symbol;Acc:9536]

Sequence

>retro_tbel_1048
ATTGCAATTTGAGGTACCCAAATAGTTGTGCGTGGAGTAGGAAACAAGTCTGTTGTGAAGCTTCAAGATAAAAGAACTGT
GAGGAAAATGTGTACACTTGATGACCATGTCTGCATGGCTTTTGCGGGACTGACCACTGATGCTAGAGTTGTGATAAACA
GAGCCTGTGTGGAGTGCCAGGGTCACAAGCTCACGGTTGAGGACCCAGTCACTGTAGAATGTGTAACTCACTTTATAGCA
ACTTTAAAGCAGAAGTATACCCAGAGCAATGGACAAAGACCTTTGGCTATTTCTGCTTTAATCATAGGCTTTGATGATGA
TGGTATCCCAAGATTATCAGACAGATCTTTCTGGTACTTACCATGCTCAGAAAGCAAATGCAACAGTTAGA

Alignment

ORF - retro_tbel_1048 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.92 %
• Parental protein coverage: 60.65 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VGVRGRDIVVLGVEKKSVAKLQDERTVRKICALDDNVCMAFAGLTADARIVINRARVECQSHRLTVEDPV
          ....G..IVV.GV..KSV.KLQD.RTVRK.C.LDD.VCMAFAGLT.DAR.VINRA.VECQ.H.LTVEDPV
Retrocopy IAI*GTQIVVRGVGNKSVVKLQDKRTVRKMCTLDDHVCMAFAGLTTDARVVINRACVECQGHKLTVEDPV

Parental  TVEYITRYVASLKQRYTQSNGRRPFGISALIVGFDFDGT-PRL-YQTDPSGTYHAWKANAIGR
          TVE..T...A.LKQ.YTQSNG.RP..ISALI.GFD.DG..P...YQTD.SGTYHA.KANA..R
Retrocopy TVECVTHFIATLKQKYTQSNGQRPLAISALIIGFDDDGI<PKI<YQTDLSGTYHAQKANATVR

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_1048 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_1048 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
Bos taurus	ENSBTAG00000005127	1 retrocopy	retro_btau_1356,
Callithrix jacchus	ENSCJAG00000014419	1 retrocopy	retro_cjac_426,
Felis catus	ENSFCAG00000003249	1 retrocopy	retro_fcat_1621,
Mus musculus	ENSMUSG00000027566	1 retrocopy	retro_mmus_407,
Rattus norvegicus	ENSRNOG00000008630	1 retrocopy	retro_rnor_2693,
Ictidomys tridecemlineatus	ENSSTOG00000012489	1 retrocopy	retro_itri_279,
Tupaia belangeri	ENSTBEG00000012281	2 retrocopies	retro_tbel_1048 , retro_tbel_2392,
Drosophila melanogaster	FBgn0004066	1 retrocopy	retro_dmel_63,