RetrogeneDB ID: retro_tbel_4673

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_97525:43050..43487(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NIPSNAP1
• Ensembl ID: ENSTBEG00000004614
• Aliases: None
• Description: nipsnap homolog 1 (C. elegans) [Source:HGNC Symbol;Acc:7827]

Sequence

>retro_tbel_4673
ATGAATAAACTCAAAAGAAAATCAGGAAATTACAGAATTTCGTAAAGCAAGGAGCAACACGCTTCTCTCCAGAAAGAATC
AGCTGCTCCTGGTGTTCAGTTTCTGGAATGAGCCCGTCGCATGGTCAGGACCGAATGTATATGAGCTCAGGTCTCACCAA
CTCTGGCCAGGAGCCATGATCGAATGGGCCAGTTCCTGGGCTTGTGCTGTTTGCTTCAGGCAGGACAGTAATGAAGCAGG
GGGCGGGTTCTTCTCTCAGATGGGCAGCTGTCTACAGTGTACCAGCTTTGGGTTTACAGGGATCGTCAGACCCGGGAAGA
CATACGGAATGCAGCGTGGCATAACATGGCTGGGAAGACCTGGTCTATTACACGGTCCCACCTGTTCAGGAAACGGAATC
CAGAATCGTGATCCCACTGAAGACCTCACCCCTCCAG

Alignment

ORF - retro_tbel_4673 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.74 %
• Parental protein coverage: 58.4 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MNKLKN-NKEYLEFRKERSQMLLSRRNQLLLEFSFWNEPQPRAGPNIYELRTYKLKPGTMIEWGNNWARA
          MNKLK..N.E..EFRK.RS..LLSR.NQLLL.FSFWNEP....GPN.YELR...L.PG.MIEW...WA.A
Retrocopy MNKLKR>NQEITEFRKARSNTLLSRKNQLLLVFSFWNEPVAWSGPNVYELRSHQLWPGAMIEWASSWACA

Parental  IKYRQENQEAVGGFFSQI-GELYVVHHLWAYKDLQSREETRNAAWRK-RGWDENVYYTVPLVRHMESRIM
          ...RQ...EA.GGFFSQ..G.L..V..LW.Y.D.Q.RE..RNAAW....GW...VYYTVP.V...ESRI.
Retrocopy VCFRQDSNEAGGGFFSQM<GQLSTVYQLWVYRDRQTREDIRNAAWHN<HGWEDLVYYTVPPVQETESRIV

Parental  IPLKISPLQ
          IPLK.SPLQ
Retrocopy IPLKTSPLQ

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_4673 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_4673 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 7 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000012291	1 retrocopy	retro_cfam_2091,
Macaca mulatta	ENSMMUG00000031041	1 retrocopy	retro_mmul_1211,
Otolemur garnettii	ENSOGAG00000012167	1 retrocopy	retro_ogar_2741,
Pongo abelii	ENSPPYG00000011693	1 retrocopy	retro_pabe_1429,
Pteropus vampyrus	ENSPVAG00000017876	1 retrocopy	retro_pvam_675,
Sus scrofa	ENSSSCG00000009988	1 retrocopy	retro_sscr_615,
Tupaia belangeri	ENSTBEG00000004614	3 retrocopies	retro_tbel_247, retro_tbel_4673 , retro_tbel_968,