RetrogeneDB ID: retro_tbel_968

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: GeneScaffold_3450:166410..166828(+)
• Located in intron of: ENSTBEG00000012802

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_968
AATCAGGAAAGTGTAGAATTCCGTAAGGCAAGAAACAACATGTCTCTCTCCAGAAAGAACCAGTTGCTACTGGAATTTAG
CCTTTGGAATGCGCCCGTCCCATGGTCAGGATCTAATACATATGAACTCAGGTCTTACCTACTCTGACCAGGAGCCGATA
CTAAATGGGGTGAATTCCTGGGCTCAAGCAATTTTTTTCAGGCAGGACGGTAATGAAGCTGTTGGACAATTTTTCTCAGG
GTGGGCAGCTGTCTATGGTGCATCATCTTTGGGCGTACAAGGATCTTTAGACCAGGAAGATATATGGAATGCAGCATGGC
ATCAACATGGCTGGGAAGAACTGGTCTATTATACGGTCCCACTTATTCCAGAAATGGAATCCAGAACTATGATCCCTCTG
AAGACCTCATCCCTCCAG

Alignment

ORF - retro_tbel_968 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.81 %
• Parental protein coverage: 56.0 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  NKEYLEFRKERSQMLLSRRNQLLLEFSFWNEPQPRAGPNIYELRTYKLKPGTMIEWG-NNWARAIKYRQE
          N.E..EFRK.R..M.LSR.NQLLLEFS.WN.P.P..G.N.YELR.Y.L.PG....WG.N.WA.AI..RQ.
Retrocopy NQESVEFRKARNNMSLSRKNQLLLEFSLWNAPVPWSGSNTYELRSYLL*PGADTKWG>NSWAQAIFFRQD

Parental  NQEAVGGFFS-QIG-ELYVVHHLWAYKDLQSR-EETRNAAWRKRGWDENVYYTVPLVRHMESRIMIPLKI
          ..EAVG.FFS...G..L..VHHLWAYKDL..R.E...NAAW...GW.E.VYYTVPL...MESR.MIPLK.
Retrocopy GNEAVGQFFS<RVG<QLSMVHHLWAYKDL*TR<EDIWNAAWHQHGWEELVYYTVPLIPEMESRTMIPLKT

Parental  SPLQ
          S.LQ
Retrocopy SSLQ

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_968 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_968 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 ,