RetrogeneDB ID: retro_tbel_4154

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_68951:5118..5556(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSTBEG00000017716
• Aliases: None
• Description: None

Sequence

>retro_tbel_4154
AGACGTTCAAGAAGCTGAAGTTATGAAAGAAGGAGATCAAGAAGTCAGTCTTTTGATTACAACTATAGAAGATCTTATAG
TCCTAGAAACAGTAGACCGACTGGAAGACCACGACGTAGCAGAAGTCATTCCGACAATGATAGATTCAAACACTGAAATC
GATCTTTTTCAAGATCTAAATACAATTCAAGATCATGATCCAAGTCCCAGCCCAAGAAATAAATGAAGGCTAAATCACAT
TCTAGGTCTGTGTCTCACACCAAAACTAGAGGCACCTCTAAAACAGATTCCAAAACACAGTATAAGTCTGCCTCAAGATA
TGAAAAGGAATAGAGGAAAAAAGAACCACCTAGATCCAAATCTCAGTCAAGATCACACTCTAGGTCTAGGTCCAAGTCTA
GATCCAGGTCATGGACCAGCCCTAAGTCCAGCGGCCAC

Alignment

ORF - retro_tbel_4154 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.78 %
• Parental protein coverage: 64.16 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RRSRSRSYERRRSRSRSFDYNYRRSYSPRNSRPTGRPRRSRSHSDNDRFKHRNRSFSRSS-NSRSRSKSQ
          RRSRS.SYERRRSRS.SFDYNYRRSYSPRNSRPTGRPRRSRSHSDNDRFKH.NRSFSRS..NSRS.SKSQ
Retrocopy RRSRS*SYERRRSRSQSFDYNYRRSYSPRNSRPTGRPRRSRSHSDNDRFKH*NRSFSRSKYNSRS*SKSQ

Parental  PKKEMKAKSRSRSASHTKTRGTSKTDSKTHYKSASRYEKESRKKEPPRSKSQSRSQSRSRSKSRSRSWTS
          PKK.MKAKS.SRS.SHTKTRGTSKTDSKT.YKSASRYEKE.RKKEPPRSKSQSRS.SRSRSKSRSRSWTS
Retrocopy PKK*MKAKSHSRSVSHTKTRGTSKTDSKTQYKSASRYEKE*RKKEPPRSKSQSRSHSRSRSKSRSRSWTS

Parental  PKSSGH
          PKSSGH
Retrocopy PKSSGH

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_4154 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_4154 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 11 parental genes, and 25 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000004836	1 retrocopy	retro_chof_7,
Callithrix jacchus	ENSCJAG00000020883	9 retrocopies	retro_cjac_1126, retro_cjac_1170, retro_cjac_2176, retro_cjac_2595, retro_cjac_2638, retro_cjac_3852, retro_cjac_628, retro_cjac_705, retro_cjac_864,
Cavia porcellus	ENSCPOG00000024533	1 retrocopy	retro_cpor_1098,
Dasypus novemcinctus	ENSDNOG00000008699	3 retrocopies	retro_dnov_1327, retro_dnov_1809, retro_dnov_2244,
Dipodomys ordii	ENSDORG00000009136	1 retrocopy	retro_dord_667,
Erinaceus europaeus	ENSEEUG00000014286	1 retrocopy	retro_eeur_522,
Homo sapiens	ENSG00000188529	5 retrocopies	retro_hsap_1343, retro_hsap_1940, retro_hsap_2445, retro_hsap_3054, retro_hsap_4295,
Myotis lucifugus	ENSMLUG00000028520	1 retrocopy	retro_mluc_89,
Oryctolagus cuniculus	ENSOCUG00000029326	1 retrocopy	retro_ocun_717,
Tupaia belangeri	ENSTBEG00000015120	1 retrocopy	retro_tbel_31,
Tupaia belangeri	ENSTBEG00000017716	1 retrocopy	retro_tbel_4154 ,