RetrogeneDB ID: retro_tbel_3393

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_139224:11904..12211(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSTBEG00000013836
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: NABP1
• Ensembl ID: ENSTBEG00000001158
• Aliases: None
• Description: nucleic acid binding protein 1 [Source:HGNC Symbol;Acc:26232]

Sequence

>retro_tbel_3393
TTCATGAAAGATATCGAGCTCTGGCTCAAGAACCTGAATCGTATTTTCAATGTGCTGGAGACAGGCCAGTGACAGAAACA
AAGAACAGGCACGAGGTTTGGACCTGCAAAGTGGCAGACAAAACAGAAGCATAATTATCTCAATCTGGGACAATGTGTAC
AACTTGACCCAGCCTGGAGACATTCTCAACAAGAGATATGCCTCAGTGTTCAAAGGTTGTCTGACACAGTACACTGGCCA
TGGAGGTGATCTGCAGGAAACTGGAGAATTCTATCTGGTTTATTCCAAGCTTCCCAACTTCAGTGAG

Alignment

ORF - retro_tbel_3393 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.75 %
• Parental protein coverage: 51.47 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  FIKDIKPRLKNLNVVFIVLKIGR-VTKTKDGHEVRSCKVADKTG-SITISVWDEIGGLIQPGDIIRLTRG
          F.KDI...LKNLN..F.VL..G..VT.TK..HEV..CKVADKT..SI.IS.WD....L.QPGDI..L...
Retrocopy FMKDIELWLKNLNRIFNVLETGQ<VTETKNRHEVWTCKVADKTE<SIIISIWDNVYNLTQPGDI--LNKR

Parental  YASMWKGCLTLYSGRGGELQKIGEFCMVYSEVPNFSE
          YAS..KGCLT.Y.G.GG.LQ..GEF..VYS..PNFSE
Retrocopy YASVFKGCLTQYTGHGGDLQETGEFYLVYSKLPNFSE

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_3393 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_3393 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 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000011862	1 retrocopy	retro_mdom_1393,
Oryctolagus cuniculus	ENSOCUG00000017546	2 retrocopies	retro_ocun_1146, retro_ocun_991,
Procavia capensis	ENSPCAG00000012746	1 retrocopy	retro_pcap_297,
Tupaia belangeri	ENSTBEG00000001158	1 retrocopy	retro_tbel_3393 ,