RetrogeneDB ID: retro_tbel_4296

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_758:154298..154622(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSTBEG00000007272
• Aliases: None
• Description: None

Sequence

>retro_tbel_4296
GCCATAGGTAAAAGTTGTCTATTGATCAGTTATACAATCAATGCCTTCCCTGGAGAATATATTCTTACTGTCTTTGATAA
CTATTCTGCCAATGTTATGATGGATGGAAAACCAGTGACTCTGGGTTTATGAGATATAGCTGGACAAGAAGATTATGACA
GATTACACCCCCTATCCTATACACAGACAGATATATTCTTAATTTGCTTTTCCCTTGTGAGTTCTGCATCATTCAAAAAT
GTCCATGCAAAGTGGTATCCTGAAGTACGACACCATTGTCCCAGTACTTCCATCATTCTAGTGGGAACTAAACTTGATCT
TCAG

Alignment

ORF - retro_tbel_4296 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.56 %
• Parental protein coverage: 97.22 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AVGKTCLLISYTTNAFPGEYIPTVFDNYSANVMVDGKPVNLGLWDTAGQEDYDRLRPLSYPQTDVFLICF
          A.GK.CLLISYT.NAFPGEYI.TVFDNYSANVM.DGKPV.LGL.D.AGQEDYDRL.PLSY.QTD.FLICF
Retrocopy AIGKSCLLISYTINAFPGEYILTVFDNYSANVMMDGKPVTLGL*DIAGQEDYDRLHPLSYTQTDIFLICF

Parental  SLVSPASFENVRAK-YP-VRHHCPHTPILL-GTKLDLR
          SLVS.ASF.NV.AK.YP.VRHHCP.T.I.L.GTKLDL.
Retrocopy SLVSSASFKNVHAKWYPEVRHHCPSTSIILVGTKLDLQ

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_4296 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_4296 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 29 parental genes, and 67 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017364	1 retrocopy	retro_amel_1104,
Bos taurus	ENSBTAG00000009233	2 retrocopies	retro_btau_1601, retro_btau_332,
Canis familiaris	ENSCAFG00000015716	1 retrocopy	retro_cfam_496,
Callithrix jacchus	ENSCJAG00000018194	1 retrocopy	retro_cjac_2687,
Cavia porcellus	ENSCPOG00000013861	1 retrocopy	retro_cpor_18,
Echinops telfairi	ENSETEG00000012902	3 retrocopies	retro_etel_1565, retro_etel_1645, retro_etel_42,
Felis catus	ENSFCAG00000011361	2 retrocopies	retro_fcat_1632, retro_fcat_717,
Felis catus	ENSFCAG00000011671	1 retrocopy	retro_fcat_431,
Homo sapiens	ENSG00000136238	6 retrocopies	retro_hsap_1256, retro_hsap_1925, retro_hsap_28, retro_hsap_3036, retro_hsap_3072, retro_hsap_4910,
Gorilla gorilla	ENSGGOG00000026733	2 retrocopies	retro_ggor_2110, retro_ggor_217,
Loxodonta africana	ENSLAFG00000012844	1 retrocopy	retro_lafr_818,
Macropus eugenii	ENSMEUG00000006196	1 retrocopy	retro_meug_201,
Myotis lucifugus	ENSMLUG00000009701	1 retrocopy	retro_mluc_1059,
Macaca mulatta	ENSMMUG00000021075	4 retrocopies	retro_mmul_1310, retro_mmul_1964, retro_mmul_2642, retro_mmul_721,
Mus musculus	ENSMUSG00000001847	2 retrocopies	retro_mmus_1372, retro_mmus_234,
Oryctolagus cuniculus	ENSOCUG00000009956	1 retrocopy	retro_ocun_305,
Otolemur garnettii	ENSOGAG00000012467	1 retrocopy	retro_ogar_2140,
Oreochromis niloticus	ENSONIG00000017151	1 retrocopy	retro_onil_34,
Procavia capensis	ENSPCAG00000009949	1 retrocopy	retro_pcap_16,
Pongo abelii	ENSPPYG00000008763	2 retrocopies	retro_pabe_1047, retro_pabe_2546,
Pan troglodytes	ENSPTRG00000018910	4 retrocopies	retro_ptro_1288, retro_ptro_3044, retro_ptro_3274, retro_ptro_36,
Rattus norvegicus	ENSRNOG00000001068	1 retrocopy	retro_rnor_230,
Ictidomys tridecemlineatus	ENSSTOG00000006784	1 retrocopy	retro_itri_1503,
Tupaia belangeri	ENSTBEG00000002614	17 retrocopies	retro_tbel_1091, retro_tbel_1379, retro_tbel_1697, retro_tbel_1711, retro_tbel_183, retro_tbel_2320, retro_tbel_2447, retro_tbel_2721, retro_tbel_4016, retro_tbel_4168, retro_tbel_4184, retro_tbel_4273, retro_tbel_4427, retro_tbel_584, retro_tbel_585, retro_tbel_860, retro_tbel_873,
Tupaia belangeri	ENSTBEG00000007272	4 retrocopies	retro_tbel_1796, retro_tbel_2564, retro_tbel_4296 , retro_tbel_9,
Takifugu rubripes	ENSTRUG00000004543	1 retrocopy	retro_trub_12,
Takifugu rubripes	ENSTRUG00000016201	1 retrocopy	retro_trub_15,
Tarsius syrichta	ENSTSYG00000001618	2 retrocopies	retro_tsyr_2027, retro_tsyr_2068,
Xenopus tropicalis	ENSXETG00000027593	1 retrocopy	retro_xtro_1,