RetrogeneDB ID: retro_tbel_247

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: GeneScaffold_1549:461684..462201(+)
• Located in intron of: ENSTBEG00000015383

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_247
TGGACCACGCGGTATGGTGAGCAAGATCAAGCTGTCCACCTCTGGAGGTAAGAAGGAGGCCATCCAGCCCTCACAGAGTT
CATGAATAAACTCAAAGAAAATCAGGAATTTACAGAATTTCGTAAAGCAAGGAGCAACATGCTTCTCTCCAGAAAGAATC
AGCTGCTCCTGGTGTTCAGTTTCTGGAATGAGCCCGTCGCATGGTCAGGACCGAATGTATATGAGCTCAGGTCTCACCAA
CTCCGGCCAGGAGCCATGATCGAATGGGCCAGTTCCTGGGCTTGTGCTGTTTGCTTCAGGCAGGACAGTAATGAAGCAGG
GGGCGGGTTCTTCTCTCAGATGGGCAGCTGTCTACAGTGTACCAGCTTTGGGTTTACAGGGATCGTCAGACCCGGGAAGA
CATACGGAATGCAGCGTGGCATAACATGGCTGGGAAGACCTGGTCTATTACACGGTCCCACCTGTTCAGGAAACGGAATC
CAGAATCGTGATCCCACTGAAGACCTCACCCCTCCAG

Alignment

ORF - retro_tbel_247 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64. %
• Parental protein coverage: 69.2 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  WNTWYGEQDQAVHLWRFSGGYPALMDCMNKLKNNKEYLEFRKERSQMLLSRRNQLLLEFSFWNEPQPRAG
          W.T.YGEQDQAVHLWR..GG.PAL...MNKLK.N.E..EFRK.RS.MLLSR.NQLLL.FSFWNEP....G
Retrocopy WTTRYGEQDQAVHLWR*EGGHPALTEFMNKLKENQEFTEFRKARSNMLLSRKNQLLLVFSFWNEPVAWSG

Parental  PNIYELRTYKLKPGTMIEWGNNWARAIKYRQENQEAVGGFFSQI-GELYVVHHLWAYKDLQSREETRNAA
          PN.YELR...L.PG.MIEW...WA.A...RQ...EA.GGFFSQ..G.L..V..LW.Y.D.Q.RE..RNAA
Retrocopy PNVYELRSHQLRPGAMIEWASSWACAVCFRQDSNEAGGGFFSQM<GQLSTVYQLWVYRDRQTREDIRNAA

Parental  WRK-RGWDENVYYTVPLVRHMESRIMIPLKISPLQ
          W....GW...VYYTVP.V...ESRI.IPLK.SPLQ
Retrocopy WHN<HGWEDLVYYTVPPVQETESRIVIPLKTSPLQ

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_247 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_247 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,