RetrogeneDB ID: retro_tbel_930

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: GeneScaffold_334:156009..156552(-)
• Located in intron of: ENSTBEG00000013394

Retrocopy information

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

Parental gene information

• Parental gene symbol: HAX1
• Ensembl ID: ENSTBEG00000014445
• Aliases: None
• Description: HCLS1 associated protein X-1 [Source:HGNC Symbol;Acc:16915]

Sequence

>retro_tbel_930
CAGCCTCCCGAGGAATGTGGCTTCAGTTTTGGCTTCAGCCCATAGAAGAGGGATGCATTTCCATGATAACATCAGCTTTG
ATGATCTAGTATGGGATTTCAATAGCAGCTTCGTTGAGATGGAGGCCTCCACCTTGCCTTCCCACTCTCCTGAACTTCCG
GGTCTTGAGTCAGAGACACATGGTGAGAGAACTCAGGAAGGACAGACTCTTCAGGACTCCACATTTAAGTATCTAGGTAG
CCACTAGCCCAGGATCTTTGGGGGAGTCTTGGAGAGTAATAAAAGAACTGAATCCACCAAATCAGCACTAGACGGGCTCC
CAGAGACATTTTCAGAGGATTTTTGATATATGGCTTGTGACTCTCCCATCCTAGAGTCAGAGAGGACAATGATCTTGATT
CCCAGGTTTCCCAGGAGGGTCTTGGTCCATGTCTACAGCCCCAGCCCAAATTCTATTTCAGGAGCATCTCTGTGACCAAG
ATCGCTAAACCAGATGGGACAGTGAAGGAGCATCAGACTGTGGTAGATAATGAGGGCCAACAG

Alignment

ORF - retro_tbel_930 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.2 %
• Parental protein coverage: 69.62 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  QPPEEFGFSFSFSP-GGGMRFHDNFGFDDLVRDFNSIFSEMGAWTLPSHSPELPGVESETPGERPREGQT
          QPPEE.GFSF.FSP...GM.FHDN..FDDLV.DFNS.F.EM.A.TLPSHSPELPG.ESET.GER..EGQT
Retrocopy QPPEECGFSFGFSP>RRGMHFHDNISFDDLVWDFNSSFVEMEASTLPSHSPELPGLESETHGERTQEGQT

Parental  LRDSMLKYPDSHQPRIFGGVLESDERTEPPKPAPDWGSQRPF-QRFDDRWPVT-PHPRAREDNDLDSQVS
          L.DS..KY..SH.PRIFGGVLES..RTE..K.A.D.G....F.QR..D.W.VT..HPR.REDNDLDSQVS
Retrocopy LQDSTFKYLGSH*PRIFGGVLESNKRTESTKSALD-GLPETF>QRIFDIWLVT>SHPRVREDNDLDSQVS

Parental  QEGLGPVLQPQPKSYFKSISVTKITKPDGIVEERRTVVDSEGRR
          QEGLGP.LQPQPK.YF.SISVTKI.KPDG.V.E..TVVD.EG..
Retrocopy QEGLGPCLQPQPKFYFRSISVTKIAKPDGTVKEHQTVVDNEGQQ

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_930 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_930 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.

---

Parental genes homology:

Parental genes homology involve 11 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000009660	1 retrocopy	retro_cjac_1888,
Dasypus novemcinctus	ENSDNOG00000016727	1 retrocopy	retro_dnov_1537,
Dipodomys ordii	ENSDORG00000012587	1 retrocopy	retro_dord_769,
Homo sapiens	ENSG00000143575	1 retrocopy	retro_hsap_4912,
Microcebus murinus	ENSMICG00000010414	2 retrocopies	retro_mmur_1118, retro_mmur_1284,
Monodelphis domestica	ENSMODG00000017215	1 retrocopy	retro_mdom_433,
Mus musculus	ENSMUSG00000027944	3 retrocopies	retro_mmus_1306, retro_mmus_2000, retro_mmus_353,
Nomascus leucogenys	ENSNLEG00000011290	1 retrocopy	retro_nleu_2286,
Pan troglodytes	ENSPTRG00000001380	1 retrocopy	retro_ptro_3275,
Rattus norvegicus	ENSRNOG00000045647	1 retrocopy	retro_rnor_736,
Tupaia belangeri	ENSTBEG00000014445	1 retrocopy	retro_tbel_930 ,