RetrogeneDB ID: retro_tbel_1115

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: GeneScaffold_3895:82901..83352(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CENPQ
• Ensembl ID: ENSTBEG00000004322
• Aliases: None
• Description: centromere protein Q [Source:HGNC Symbol;Acc:21347]

Sequence

>retro_tbel_1115
TTGCTACAACTGTGTGGAATCCTGAAAGTCCCTCCAAAAAAGCAGGAAGATTTAGCTAATGGGCCAGGTCTACTGAAAAT
GGAAACAGTACAGAACAGTGCTAATGAAGAAGGTCAGGCATTATCGCAGGAAGAAATAGAAAAATAGTAGAGGCCGTGGA
GGCAGTAACTGGAAATATTCAGATGCTAAAGAACAAAATTCAAATCTGACGGGTGAGGTGGAAGAAGAGGAAAAGGAAAA
ATAGACACTTCAAATGGATAGCAGTAGAGTAGTACAGTCTCTTCCAGAATTTCCTCAGAACAGTCTGGAAGCACCCACAC
TTCAGAAAGAAACTTTGATGCTAATTCCAAACCACGACGCTCTTCTAAAGGACTAGGATGTTCATAATTCATCACAGATG
AAGAACTTACTAACATTCATCGAAGAAGCCTCTAAGAAATTGGATGCCTCT

Alignment

ORF - retro_tbel_1115 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.48 %
• Parental protein coverage: 57.14 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LLQRCETLKVPPKKLKDLTNVSSLLKMETVQNRANEEGLALLQEETDK-IVETVESVTGNIQRLKNKIQI
          LLQ.C..LKVPPKK..DL.N...LLKMETVQN.ANEEG.AL.QEE..K.IVE.VE.VTGNIQ.LKNKIQI
Retrocopy LLQLCGILKVPPKKQEDLANGPGLLKMETVQNSANEEGQALSQEEIEK<IVEAVEAVTGNIQMLKNKIQI

Parental  -LTSEVEEEEEKVKQMFHMDSTRVL-SLPELPQNSLKAPTLQEEILTLIPNHNALLKDLDVLHNSSQMKN
          .LT.EVEEEE.K.K....MDS.RV..SLPE.PQNSL.APTLQ.E.L.LIPNH.ALLKD.DV.HNSSQMKN
Retrocopy <LTGEVEEEE-KEK*TLQMDSSRVVQSLPEFPQNSLEAPTLQKETLMLIPNHDALLKD*DV-HNSSQMKN

Parental  LLTFIEEAYKKLDAS
          LLTFIEEA.KKLDAS
Retrocopy LLTFIEEASKKLDAS

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_1115 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_1115 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000345	1 retrocopy	retro_chof_1088,
Oryctolagus cuniculus	ENSOCUG00000006103	1 retrocopy	retro_ocun_32,
Ictidomys tridecemlineatus	ENSSTOG00000001426	1 retrocopy	retro_itri_1111,
Tupaia belangeri	ENSTBEG00000004322	1 retrocopy	retro_tbel_1115 ,