RetrogeneDB ID: retro_tbel_1962

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: GeneScaffold_6071:320974..321285(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ARPC5
• Ensembl ID: ENSTBEG00000006295
• Aliases: None
• Description: actin related protein 2/3 complex, subunit 5, 16kDa [Source:HGNC Symbol;Acc:708]

Sequence

>retro_tbel_1962
ATGTCGAAGAACACCGTGTCGTCAGCGTGGTTCCGGAAGGTGGACGTGGATGAGTATGAGAACAAGTTTGTGGACGAGGA
GGACGGGGGACACCGCCAGGCTGGGCCCCACGAGGGCGAGGTGGACTCCTGCCTGTGGCAAGGAAACATGACAGCTGCCC
TACAGGCCGCTCTGAAAACTCTCTTCCATCAACACCAAGAGTCAGGCAGTGAAGGATCTGAGCAGGCAGCATTGTCTTGA
AGGTACTCATCTGTTTTAAAGCTAATGATATTGAAAAGGCTGTTCAGTCTTTGGACAGGAATGGCATGGAA

Alignment

ORF - retro_tbel_1962 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.44 %
• Parental protein coverage: 69.08 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MSKNTVSSARFRKVDVDEYDENKFVDEEDGGDGQAGPDEGEVAPRAEAGRNMTAALQAALKN-PPINTKS
          MSKNTVSSA.FRKVDVDEY.ENKFVDEEDGG..QAGP.EGEV......G.NMTAALQAALK....INTKS
Retrocopy MSKNTVSSAWFRKVDVDEY-ENKFVDEEDGGHRQAGPHEGEVDSCLWQG-NMTAALQAALKT>SSINTKS

Parental  QAVKDR-AGSIVLKVLISFKANDIEKAVQSLDKNGVD
          QAVKD..AGSIVLKVLI.FKANDIEKAVQSLD.NG..
Retrocopy QAVKDL>AGSIVLKVLICFKANDIEKAVQSLDRNGME

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_1962 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_1962 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 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000014969	1 retrocopy	retro_etel_1922,
Monodelphis domestica	ENSMODG00000007194	1 retrocopy	retro_mdom_968,
Mus musculus	ENSMUSG00000008475	1 retrocopy	retro_mmus_281,
Tupaia belangeri	ENSTBEG00000006295	8 retrocopies	retro_tbel_1822, retro_tbel_1933, retro_tbel_1962 , retro_tbel_2504, retro_tbel_3191, retro_tbel_3192, retro_tbel_3197, retro_tbel_3806,
Tupaia belangeri	ENSTBEG00000008398	1 retrocopy	retro_tbel_442,