RetrogeneDB ID: retro_tbel_3228

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_134381:93220..93727(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSTBEG00000015277
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: DAZAP2
• Ensembl ID: ENSTBEG00000013232
• Aliases: None
• Description: DAZ associated protein 2 [Source:HGNC Symbol;Acc:2684]

Sequence

>retro_tbel_3228
ATGAACAGCAAAGGTCAGTATCCAACACAGCCAACCTATCCCGTGCAGCCTCCTGGGAATCCAGTGTACCCCCAGACCTT
GCATCTTCCTCAGGCTCCACCCTATACTGATGCTCCACCTGCCTATTCAGAGCTCTATCGCCCAAGCTTTGTGCATCCAG
GGGCTGCTGCAGTACCTACCATGTCAGCTGCATTTCCTGGCACCTCCCTGTATCTTCCTATGGCCCAGTCTGTGGCTGTT
GGGCCTTTAGGTTCCACAATCCCCATGGCATATTATCCAGTTGGTCCCATCTATCCCCCTGGTTCAGCAGTGCTGGTGGA
AGGAGGATATGATGCAGGTGCCAGATTTGGGAGCTGGGGCTACTGCTGGCAACATTCCTCCTCCACCTCCTGGATGTCCT
CCCAATGCTGCTCAGCTTGCAAGTCATGCAGGGGAGCCACGTCCTCGTAACTCAGCGGAAGGGAAACTTCTTCATGGGGT
GGCTCAATGGGGGGCTACACCATCTGG

Alignment

ORF - retro_tbel_3228 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.91 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MNSKGQYPTQPTYPVQPPGNPVYPQTLHLPQAPPYTDAPPAYSELYRPSFVHPGAATVPTMSAAFPGTSL
          MNSKGQYPTQPTYPVQPPGNPVYPQTLHLPQAPPYTDAPPAYSELYRPSFVHPGAA.VPTMSAAFPGTSL
Retrocopy MNSKGQYPTQPTYPVQPPGNPVYPQTLHLPQAPPYTDAPPAYSELYRPSFVHPGAAAVPTMSAAFPGTSL

Parental  YLPMAQSVAVGPLGSTIPMAYYPVGPIYPPGSAVLVEGGYDAGARFG-AGATAGNIPPPPPGCPPNAAQL
          YLPMAQSVAVGPLGSTIPMAYYPVGPIYPPGSAVLVEGGYDAGARFG.AGATAGNIPPPPPGCPPNAAQL
Retrocopy YLPMAQSVAVGPLGSTIPMAYYPVGPIYPPGSAVLVEGGYDAGARFG>AGATAGNIPPPPPGCPPNAAQL

Parental  A-VMQGANVLVTQRKGNFFM-GGSDGGYTIW
          A.VMQG..VLVTQRKGNFFM.GGS.GGYTIW
Retrocopy A>VMQGSHVLVTQRKGNFFM>GGSMGGYTIW

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_3228 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_3228 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 8 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000298	1 retrocopy	retro_chof_85,
Dasypus novemcinctus	ENSDNOG00000009306	1 retrocopy	retro_dnov_1772,
Equus caballus	ENSECAG00000007313	1 retrocopy	retro_ecab_286,
Myotis lucifugus	ENSMLUG00000009959	1 retrocopy	retro_mluc_351,
Mus musculus	ENSMUSG00000000346	1 retrocopy	retro_mmus_1073,
Sorex araneus	ENSSARG00000003823	1 retrocopy	retro_sara_632,
Tupaia belangeri	ENSTBEG00000013232	1 retrocopy	retro_tbel_3228 ,
Vicugna pacos	ENSVPAG00000001156	2 retrocopies	retro_vpac_314, retro_vpac_568,