RetrogeneDB ID: retro_tbel_2889

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_122381:50078..50836(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PSMB7
• Ensembl ID: ENSTBEG00000009196
• Aliases: None
• Description: proteasome (prosome, macropain) subunit, beta type, 7 [Source:HGNC Symbol;Acc:9544]

Sequence

>retro_tbel_2889
ATGGTGGCTGTGTCGGCCTTTGTGCCACCAGTTGGAGGTTTCTCTTTTGATAACTGCTGTAGGAATGCTGTCTTGGAAGC
CAGTTTTGCAAAGAAGGGGTACAAACTTCTAAAGACCCAGATAACTGACATGACAATTGCGGGGGTGGTCTATAAGGATG
GCATAGTTCTTGGAGGAGATACAAGAGCAACTGAAGGGATGGTTGTTGCTGACAAGAACTGTTCAAAAATACACTTCATA
TCTCCTAATATTTATTGCTGTGGTGCTGGGACAGCTGCAGACACAGACATGACAACCCAGCTCATTTCTTCCAACCTGGA
GCTCCACTCCCTCTCCGCTGGCTGCCTTCCCAGAGTTGTGACAGCCAATTGGATGCTAAAGCAGATGCTTTTCAGGTGTC
AAGGTTACATTGGTGCGGCCCTAGTTTCAGGGGGAGTAGATGTTACTGGACCTCACCTCTACAACAACTATTCCCACAGA
TCAACTGATAAGTTGCCATATGTCACCATGGGTTCTGGCTCTTTGGCTGCAATGGCTATGTTTGAAGATAAGATTAGGCC
AGATATGGAGGAGGAAGAAGCCAAGAAGCTGGTGAATGAAGCCATTGCAGCTGGCATTTCAACGACTTGGGGTCTGGAAG
CAACATGGACCTCTGCGTCATCAGCAAGAGCAAGCTGAATTTCCTCCATCCCTACTCGGTGCCCAAGAAGGGGACCAGGT
TTGGTCGGTACAGGTGTGAGAAAGGGACTACTGCGGTC

Alignment

ORF - retro_tbel_2889 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.63 %
• Parental protein coverage: 91.7 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAAVSVFAPPVGGFSFDNCRRNAVLEADFAKKGYKLPKARKTGTTIAGVVYKDGIVLGADTRATEGMVVA
          M.AVS.F.PPVGGFSFDNC.RNAVLEA.FAKKGYKL.K...T..TIAGVVYKDGIVLG.DTRATEGMVVA
Retrocopy MVAVSAFVPPVGGFSFDNCCRNAVLEASFAKKGYKLLKTQITDMTIAGVVYKDGIVLGGDTRATEGMVVA

Parental  DKNCSKIHFISPNIYCCGAGTAADTDMTTQLISSNLELHSLSTGRLPRVVTANRMLKQMLFRYQGYIGAA
          DKNCSKIHFISPNIYCCGAGTAADTDMTTQLISSNLELHSLS.G.LPRVVTAN.MLKQMLFR.QGYIGAA
Retrocopy DKNCSKIHFISPNIYCCGAGTAADTDMTTQLISSNLELHSLSAGCLPRVVTANWMLKQMLFRCQGYIGAA

Parental  LVLGGVDVTGPHLYSIYPHGSTDKLPYVTMGSGSLAAMAVFEDKFRPDMEEEEAKKLVSEAIAAGI-FND
          LV.GGVDVTGPHLY..Y.H.STDKLPYVTMGSGSLAAMA.FEDK.RPDMEEEEAKKLV.EAIAAGI.FND
Retrocopy LVSGGVDVTGPHLYNNYSHRSTDKLPYVTMGSGSLAAMAMFEDKIRPDMEEEEAKKLVNEAIAAGI<FND

Parental  LGSGSNIDLCVISKSKLDFLRPYSVPNKKGTRFGRYRCEKGTTAV
          LGSGSN.DLCVISKSKL.FL.PYSVP.KKGTRFGRYRCEKGTTAV
Retrocopy LGSGSNMDLCVISKSKLNFLHPYSVP-KKGTRFGRYRCEKGTTAV

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_2889 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_2889 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 13 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000003067	2 retrocopies	retro_btau_1722, retro_btau_983,
Echinops telfairi	ENSETEG00000005432	2 retrocopies	retro_etel_2093, retro_etel_231,
Homo sapiens	ENSG00000136930	1 retrocopy	retro_hsap_1303,
Gorilla gorilla	ENSGGOG00000012164	1 retrocopy	retro_ggor_1019,
Nomascus leucogenys	ENSNLEG00000017268	1 retrocopy	retro_nleu_2947,
Otolemur garnettii	ENSOGAG00000003513	1 retrocopy	retro_ogar_2828,
Pongo abelii	ENSPPYG00000019596	1 retrocopy	retro_pabe_1092,
Pan troglodytes	ENSPTRG00000021354	1 retrocopy	retro_ptro_893,
Pteropus vampyrus	ENSPVAG00000000204	2 retrocopies	retro_pvam_1271, retro_pvam_866,
Rattus norvegicus	ENSRNOG00000011732	3 retrocopies	retro_rnor_1581, retro_rnor_1582, retro_rnor_2469,
Sorex araneus	ENSSARG00000009395	1 retrocopy	retro_sara_532,
Tupaia belangeri	ENSTBEG00000003501	1 retrocopy	retro_tbel_3171,
Tupaia belangeri	ENSTBEG00000009196	2 retrocopies	retro_tbel_2889 , retro_tbel_751,