RetrogeneDB ID: retro_tbel_1669

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: GeneScaffold_5420:229968..230493(-)
• Located in intron of: ENSTBEG00000008369

Retrocopy information

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

Parental gene information

• Parental gene symbol: PIR
• Ensembl ID: ENSTBEG00000008256
• Aliases: None
• Description: pirin (iron-binding nuclear protein) [Source:HGNC Symbol;Acc:30048]

Sequence

>retro_tbel_1669
ATGGGGTCCTCCAAGAAGGTTACTCTCTCAGTGCTCAGCAGGTAACAGTCGGAAGGGGTTGGCGCACGGGTCCGCAGGAT
CATTGGGAGACCTGAGTTAAAAAATCTGGATCCATTTTTACTGTTTGATGAATTTAAAGGAGGTAGACCAGGTGGATTTC
CTGACCACCCACATCAACGTTTTGAAACAGTGTCTTACCTCCTGGAAGGGGGCAACAGGGCTCATGAGGACTTCCGTGGA
CATGTTGGTAAACTGAACCCAGGAGACCTGCAGTGGATGACAGTGGGCCGGGGCATTCTGCATGCCCAGATGCCTTGTAC
AGAGGAACCAGCCCATGGCCTACAACTATGGGTTAATTTGAGGAGCTCAGAGAAGATGGTGGAACCTCAGTACCAGGAAC
TGAAAAGTGAAGAAATCCCTAAACCCAGTAAGGATGGTGTGACAGTTGCTGTCATTTCGGGAGAAGCCCTGGGAATAAAG
TCCAAGGTTTACACTCGTACACCAACCTTATATCTAGACTTCAAA

Alignment

ORF - retro_tbel_1669 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.43 %
• Parental protein coverage: 60.34 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGSSKKVTLSVLSREQSEGVGARVRRSIGRPELKNLVPFFLFEEFKGGRPGGFPGHPPRGFEPVSYLLEG
          MGSSKKVTLSVLSR.QSEGVGARVRR.IGRPELKNL.PF.LF.EFKGGRPGGFP.HP...FE.VSYLLEG
Retrocopy MGSSKKVTLSVLSR*QSEGVGARVRRIIGRPELKNLDPFLLFDEFKGGRPGGFPDHPHQRFETVSYLLEG

Parental  GSMAHEDFCGHVGKLNPGDLQWMTAGRGILHAEMPCTEEPAHGLQLWVNLRSSEKMVEPQYQELKSEEIP
          G..AHEDF.GHVGKLNPGDLQWMT.GRGILHA.MPCTEEPAHGLQLWVNLRSSEKMVEPQYQELKSEEIP
Retrocopy GNRAHEDFRGHVGKLNPGDLQWMTVGRGILHAQMPCTEEPAHGLQLWVNLRSSEKMVEPQYQELKSEEIP

Parental  KPSKDGVTVAVISGEALGIKSKVYTRTPTLYLDFK
          KPSKDGVTVAVISGEALGIKSKVYTRTPTLYLDFK
Retrocopy KPSKDGVTVAVISGEALGIKSKVYTRTPTLYLDFK

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_1669 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_1669 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 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000009477	1 retrocopy	retro_btau_298,
Felis catus	ENSFCAG00000010486	1 retrocopy	retro_fcat_779,
Otolemur garnettii	ENSOGAG00000003304	2 retrocopies	retro_ogar_1073, retro_ogar_1118,
Tupaia belangeri	ENSTBEG00000008256	1 retrocopy	retro_tbel_1669 ,
Tursiops truncatus	ENSTTRG00000006770	1 retrocopy	retro_ttru_448,