RetrogeneDB ID: retro_tbel_339

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: GeneScaffold_1805:190981..191295(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HESX1
• Ensembl ID: ENSTBEG00000017505
• Aliases: None
• Description: HESX homeobox 1 [Source:HGNC Symbol;Acc:4877]

Sequence

>retro_tbel_339
TTGCCAAAAGACAGAGTTTTGAAATATGAAAATTACTTTACAGCCACAGAAAGACTGTTTTCGAAAAGAGTTGAGTTCGA
TAGCGGGTGAAGACCAGAAATGGCTTTTATTCAAAACCAGATTGAAGTATTAAAAATGTCTTTAGAGTAAATTGCTATTC
TGGCATTGATATCAGAGAAGGCTTAGTTCAAGAATTGAATCTAGAGGAAGAAAGAATCCAGATTGTTCCAGAATTGATTG
CAAAGCTGAAAAGTTCCCATAGAGAATCACAGTTTGTAATAGTGAAAAAAAAAATCAACACAAGTCTCATGGAA

Alignment

ORF - retro_tbel_339 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.33 %
• Parental protein coverage: 57.84 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VPEDRALQYEHCFSASERLSLKRELSWYRGRRPRTAFTQNQIEVLE-TVFRVNCYPGIDIREDLAKKLNL
          .P.DR.L.YE..F.A.ERL..KR......G.RP..AF.QNQIEVL...VFRVNCY.GIDIRE.L...LNL
Retrocopy LPKDRVLKYENYFTATERLFSKR-VEFDSG*RPEMAFIQNQIEVLK<NVFRVNCYSGIDIREGLVQELNL

Parental  EEDRIQIWFQNRRAKLKRSHRESQFLMAKKNFNTNLLE
          EE.RIQI......AKLK.SHRESQF.......NT.L.E
Retrocopy EEERIQI-VPELIAKLKSSHRESQFVIVXXXXNTSLME

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_339 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_339 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 6 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000007995	2 retrocopies	retro_cfam_1907, retro_cfam_954,
Choloepus hoffmanni	ENSCHOG00000013897	1 retrocopy	retro_chof_123,
Cavia porcellus	ENSCPOG00000012741	1 retrocopy	retro_cpor_1067,
Mustela putorius furo	ENSMPUG00000016854	2 retrocopies	retro_mputfur_112, retro_mputfur_174,
Tupaia belangeri	ENSTBEG00000002729	1 retrocopy	retro_tbel_3738,
Tupaia belangeri	ENSTBEG00000017505	1 retrocopy	retro_tbel_339 ,