RetrogeneDB ID: retro_tbel_1872

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: GeneScaffold_5912:241351..241906(+)
• Located in intron of: ENSTBEG00000016902

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSTBEG00000000209
• Aliases: None
• Description: None

Sequence

>retro_tbel_1872
ATGGCAGTGGCCAAGGCAGGGTCCTAGCAGTCTGCTGACTACAAAGGACAACCCAGAACATGGTGCCGGTGGGTGTGTGA
ACAGTCTGTCATGTTACCTAGGACATGCTCCCAGGGCCCTATTATAAGACCACAGAAAAAAAAGGCCCCACCACTAAGAA
GTATAATTTGTGCATGGAAGTCTACAAGCCTTACCTGTTTGATGGCATGGGGTATGGTTTCTACCCAAAGCTCCCTAACT
GCTTACAGAGGAGGAGGATCCATGGTATGACTGGGACTACTCAGATCTGAGATTGAACTGGGGTGAACCGATACACTGGG
ACCTAGACATGTATATCAGAAACGGTGTGGAACATCCCCTACACCTGTTTCCTGGAATGTCATGTGTAAACAGCTCTTTA
GGTTTGTGGCCTTCATGATGTTCATGTTCTAGGAGGGAGAGAATTACCCCTCCTACCAACCAATGGGGCCAAAGCAGTAT
CTTTATAATGATCTGTACCTGGAATGAGGCAGTGATCTCACCAAAGAACCTGAGGTGGTGGTTCACTCTGAGATC

Alignment

ORF - retro_tbel_1872 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.37 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MAAARAG-VLGIRWLQRATRNVVPLGARTASHVTKDMLPGPYPKTPEERAAAAKKYNMRVEDYEPYPDDG
          MA.A.AG.VL....LQR.T.N.VP.G..T..HVT.DMLPGPY.KT........KKYN...E.Y.PY..DG
Retrocopy MAVAKAG<VLAVC*LQRTTQNMVPVGV*TVCHVT*DMLPGPYYKTTXXXGPTTKKYNLCMEVYKPYLFDG

Parental  MGYGDYPKLPDHSQ-QERDPWYDWDHSDLRMNWGEPIHWDLDMYIRNRVD-TSPTPVSWNVMCKHLFGFV
          MGYG.YPKLP...Q..E.DPWYDWD.SDLR.NWGEPIHWDLDMYIRN.V..TSPTPVSWNVMCK.LF.FV
Retrocopy MGYGFYPKLPNCLQ<EEEDPWYDWDYSDLRLNWGEPIHWDLDMYIRNGVE<TSPTPVSWNVMCKQLFRFV

Parental  AFMMFMFWLGENYPSYLPAGPKQYPYNDLYLERGGDPTKEPEPVVHYEI
          AFMMFMF..GENYPSY.P.GPKQY.YNDLYLE.G.D.TKEPE.VVH.EI
Retrocopy AFMMFMF*EGENYPSYQPMGPKQYLYNDLYLE*GSDLTKEPEVVVHSEI

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_1872 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_1872 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 20 parental genes, and 49 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006651	3 retrocopies	retro_amel_1460, retro_amel_1467, retro_amel_931,
Bos taurus	ENSBTAG00000000091	1 retrocopy	retro_btau_1844,
Canis familiaris	ENSCAFG00000009698	2 retrocopies	retro_cfam_1405, retro_cfam_1947,
Callithrix jacchus	ENSCJAG00000037906	1 retrocopy	retro_cjac_870,
Dasypus novemcinctus	ENSDNOG00000003661	1 retrocopy	retro_dnov_65,
Felis catus	ENSFCAG00000006453	2 retrocopies	retro_fcat_501, retro_fcat_856,
Homo sapiens	ENSG00000166136	3 retrocopies	retro_hsap_1363, retro_hsap_1772, retro_hsap_770,
Gorilla gorilla	ENSGGOG00000027239	3 retrocopies	retro_ggor_1062, retro_ggor_2240, retro_ggor_639,
Microcebus murinus	ENSMICG00000001341	1 retrocopy	retro_mmur_859,
Myotis lucifugus	ENSMLUG00000015094	1 retrocopy	retro_mluc_1830,
Macaca mulatta	ENSMMUG00000006636	5 retrocopies	retro_mmul_1098, retro_mmul_1232, retro_mmul_1620, retro_mmul_415, retro_mmul_753,
Monodelphis domestica	ENSMODG00000019356	1 retrocopy	retro_mdom_1543,
Mustela putorius furo	ENSMPUG00000016959	1 retrocopy	retro_mputfur_1259,
Mus musculus	ENSMUSG00000025204	2 retrocopies	retro_mmus_1995, retro_mmus_2909,
Nomascus leucogenys	ENSNLEG00000014774	3 retrocopies	retro_nleu_1068, retro_nleu_2810, retro_nleu_398,
Otolemur garnettii	ENSOGAG00000030711	3 retrocopies	retro_ogar_1237, retro_ogar_152, retro_ogar_2593,
Pongo abelii	ENSPPYG00000002570	3 retrocopies	retro_pabe_1131, retro_pabe_1541, retro_pabe_756,
Pan troglodytes	ENSPTRG00000002851	3 retrocopies	retro_ptro_1186, retro_ptro_539, retro_ptro_936,
Sus scrofa	ENSSSCG00000006166	2 retrocopies	retro_sscr_1092, retro_sscr_444,
Tupaia belangeri	ENSTBEG00000000209	8 retrocopies	retro_tbel_1872 , retro_tbel_2950, retro_tbel_3122, retro_tbel_322, retro_tbel_3696, retro_tbel_4042, retro_tbel_4718, retro_tbel_540,