RetrogeneDB ID: retro_tbel_4715

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_98601:5775..6244(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CALB1
• Ensembl ID: ENSTBEG00000005714
• Aliases: None
• Description: calbindin 1, 28kDa [Source:HGNC Symbol;Acc:1434]

Sequence

>retro_tbel_4715
TTGGCTCATGTATTACCCACAGAAGAGAATTTCCTCTGCTATTCCGATGCCAGCAGCTGAAGCCTGTGAGGAGTTCATGA
AGACATGGAGAAAATATGACTCTGATCTCAGTGGCTTCACAGATATTGAGGGACTTAAGAACGTTTTAAAAGACCTGCTA
GAAAAGGCAAACAAGACTGTCAGTGACACACAATTAGCGGAGCACACAGACCTAATGCTGAAATTGATTGATTCGAATAA
TGATGGGAAGCTGGAATGAACTGAGATGGCCAGGCTACTGCCCATGCAGGAGAGTTTTCTTCTTAAACTTCAGGGATCAA
GATGTGTGGAAAGAGTTCAGTAAGGCGTTTGAGTATATGATCAGGATGGAAATGGATGCACAGATGACAATGAATTTGAT
GCTTCACAGAAGGAGCTGTGTGGGAAGAATAAACAGGTCCTGGGCACTAATAATATACCAACATACAAG

Alignment

ORF - retro_tbel_4715 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.14 %
• Parental protein coverage: 60.77 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  LAHVLPTEENFL-LLFRCQQLK-SCEEFMKTWRKYDTDHSGFIETEELKNFLKDLLEKANKTVDDTKLAE
          LAHVLPTEENFL.LLFRCQQLK..CEEFMKTWRKYD.D.SGF...E.LKN.LKDLLEKANKTV.DT.LAE
Retrocopy LAHVLPTEENFL<LLFRCQQLK<ACEEFMKTWRKYDSDLSGFTDIEGLKNVLKDLLEKANKTVSDTQLAE

Parental  YTDLMLKLFDSNNDGKLELTEMARLLPVQENFLLKFQ-GIKMCG-KEFNKAFE-LYDQDGNGYIDENELD
          .TDLMLKL.DSNNDGKLE.TEMARLLP.QE.FLLK.Q.GIKMCG.KEF.KAFE..YDQDGNG..D.NE.D
Retrocopy HTDLMLKLIDSNNDGKLE*TEMARLLPMQESFLLKLQ<GIKMCG<KEFSKAFE<VYDQDGNGCTDDNEFD

Parental  ALLKDLCEKNKQDLDINNIPTYK
          A..K.LC.KNKQ.L..NNIPTYK
Retrocopy ASQKELCGKNKQVLGTNNIPTYK

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_4715 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_4715 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryctolagus cuniculus	ENSOCUG00000006341	1 retrocopy	retro_ocun_1552,
Tupaia belangeri	ENSTBEG00000005714	1 retrocopy	retro_tbel_4715 ,