RetrogeneDB ID: retro_tbel_3560

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_144786:163321..163891(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PPA1
• Ensembl ID: ENSTBEG00000008947
• Aliases: None
• Description: pyrophosphatase (inorganic) 1 [Source:HGNC Symbol;Acc:9226]

Sequence

>retro_tbel_3560
GAAAAAGGACAATATATATCTCCATTTCATGATATTCCAATTTATTCAGATAAGGATGTGTTCCACCTGGTGGTTGAAGT
GCCACGTTGGTCTAATGCAAAAATGGAGATTGCTACAAAGGATCCTTTAAACCCAATTAAACAAGATGTGAAAAAAGGAA
AACCCCGCTATGTTGCAAATTTGTTTCCTTATAAAGGATACATCTGGAACTATGGTGCCATTCCTCAGACTTGGGAAGAC
CCAGGACACAGTGACAAGCATACTGGCTGTTGTGGCGACAATGACCCGATTGATGTGTGTGAAATTGGAAGCAAGGTTTG
TTCAAGAGGTGAAATAATTGGGGTGAAACTTCTGGGCATACTGGCCATGACTGACGAAGGGGAAACTGACTGGAAAGTCA
TTGCCATTAATGTGGAGGACCCTGATGCCGCCAATTATAATGACATTAATGACGTGAAACGCCTGAAACCTGGCTACCTA
GAAGCTACTGTGGACTGGTTTAGAAGGTACAAGGTTCCTGATGGAAAACCAGAAAATGAGTTTGCTTTCAATGCAGAATT
TAAAGATAAG

Alignment

ORF - retro_tbel_3560 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.26 %
• Parental protein coverage: 65.74 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EKGQYISPFHDIPIYSDKDVFHMVAGVPRWSNAKMEIATKDPLNPIKQDVKKGKLRYVANLFPYKGYIWN
          EKGQYISPFHDIPIYSDKDVFH.V..VPRWSNAKMEIATKDPLNPIKQDVKKGK.RYVANLFPYKGYIWN
Retrocopy EKGQYISPFHDIPIYSDKDVFHLVVEVPRWSNAKMEIATKDPLNPIKQDVKKGKPRYVANLFPYKGYIWN

Parental  YGAIPQTWEDPGHNDKHTGCCGDNDPIDVCEIGSKVCARGEIIGVKVLGILAMIDEGETDWKVIAINVDD
          YGAIPQTWEDPGH.DKHTGCCGDNDPIDVCEIGSKVC.RGEIIGVK.LGILAM.DEGETDWKVIAINV.D
Retrocopy YGAIPQTWEDPGHSDKHTGCCGDNDPIDVCEIGSKVCSRGEIIGVKLLGILAMTDEGETDWKVIAINVED

Parental  PDAANYNDINDVKRLKPGYLEATVDWFRRYKVPDGKPENEFAFNAEFKDK
          PDAANYNDINDVKRLKPGYLEATVDWFRRYKVPDGKPENEFAFNAEFKDK
Retrocopy PDAANYNDINDVKRLKPGYLEATVDWFRRYKVPDGKPENEFAFNAEFKDK

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_3560 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_3560 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 12 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000014023	1 retrocopy	retro_cpor_615,
Homo sapiens	ENSG00000180817	2 retrocopies	retro_hsap_2756, retro_hsap_3267,
Loxodonta africana	ENSLAFG00000004048	1 retrocopy	retro_lafr_990,
Myotis lucifugus	ENSMLUG00000017790	1 retrocopy	retro_mluc_2469,
Macaca mulatta	ENSMMUG00000006397	1 retrocopy	retro_mmul_1540,
Nomascus leucogenys	ENSNLEG00000016098	1 retrocopy	retro_nleu_7,
Oryctolagus cuniculus	ENSOCUG00000016001	2 retrocopies	retro_ocun_1373, retro_ocun_883,
Procavia capensis	ENSPCAG00000006788	1 retrocopy	retro_pcap_247,
Pongo abelii	ENSPPYG00000029405	1 retrocopy	retro_pabe_37,
Pan troglodytes	ENSPTRG00000002585	2 retrocopies	retro_ptro_1864, retro_ptro_2210,
Tupaia belangeri	ENSTBEG00000008947	3 retrocopies	retro_tbel_3560 , retro_tbel_3561, retro_tbel_848,
Tarsius syrichta	ENSTSYG00000005511	1 retrocopy	retro_tsyr_1856,