RetrogeneDB ID: retro_tbel_4688

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_97792:11328..12034(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RNPS1
• Ensembl ID: ENSTBEG00000009098
• Aliases: None
• Description: RNA binding protein S1, serine-rich domain [Source:HGNC Symbol;Acc:10080]

Sequence

>retro_tbel_4688
ACCAACCGCAAAGACCACTCTGATAAAAAGTCCAAGCAGCACAGTAAAGATCAAGGGGACACCAAGGACCACGGCAGGAT
AAGACTCGGAAGAGGCACAGTGCTTCTGGGGGTGGCAGCAGTACCGGTGCAAGGTCCACACGGCCTGCAGTTCGGGTTCC
AGTCCTAGCACAGGCTCCAGCAGCGGCTCCAGCTCCCCCTCAGCATCCAGCTGCCCAGGAAGTCCCCGCACATCCCACAG
TTCCAGCTGTTCCTCTGGCTCTCTGAGCCCCTCTCAGCACAGATGTGACAACAGGCTGCACTCCTGATCCAAATCCAAGC
CACCTAAATAGATAAAAAGGAGAGGAAAAGGTGGAGTTATTCCCCTGAACCCACAAAAGTGCATAATGGGAGGCTCACCA
GAAATGTGACCAGGGATCACATCATGGAGACATTTTCCACCTGTGAGGAAATTGAAATGATGGACATGCCCATAGAAAGG
ATGCACCCCCATCTGTCCAAGGGCTATGCCTACGTGGGGTTGGAGAATCCAGATGAAGCTGAGAAGGTGCTGAAGCACAT
GGAGGAAGGACAAATGGATGGCCAGGACATAACCGCCACTGCTGTGTGGCCCCCTGGCCTCAGCCACCTCCCCAGTGACT
CAGCCCTCCCAGGAGATTGCTGCCACCCCTCCCATGTGGCGCAGGTCACCCCCACTGATGAGGAGA

Alignment

ORF - retro_tbel_4688 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.44 %
• Parental protein coverage: 87.5 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  SDEKSKDRSKDKGATKESSE-KDRGR-DKTRKRRSASSGSSSTRSRSS-STSSSGSSTSTGSSSGSSSSS
          ...K.....K.K...K.....KD.GR.DKTRKR.SAS.G.SST..RS.....SSGSS.STGSSSGSSS.S
Retrocopy TNRKDHSDKKSKQHSKDQGDTKDHGR<DKTRKRHSASGGGSSTGARST<TACSSGSSPSTGSSSGSSSPS

Parental  ASSRSGSSSTSRSSSSSSSSGSPSPSRRRHDNRRRSRSKSKPPK-RDEKERKRRSPSPKPTKVHIGRLTR
          ASS..GS..TS.SSS.SS..GS.SPS..R.DNR..S.SKSKPPK..D.KERKR.S.SP.PTKVH.GRLTR
Retrocopy ASSCPGSPRTSHSSSCSS--GSLSPSQHRCDNRLHS*SKSKPPK<IDKKERKRWSYSPEPTKVHNGRLTR

Parental  NVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKHMDGGQIDGQEITATAV-L
          NVT.DHIME.FST...I.M.DMP.ERMHPHLSKGYAYV..ENPDEAEK.LKHM..GQ.DGQ.ITATAV..
Retrocopy NVTRDHIMETFSTCEEIEMMDMPIERMHPHLSKGYAYVGLENPDEAEKVLKHMEEGQMDGQDITATAV<V

Parental  APWPRPPPRRFSPPRRMLPP-PPMWRRSPPRMRR
          APWP.PPP...SPPRR.LPP.PPMWRRSPP.MRR
Retrocopy APWPQPPPQ*LSPPRRLLPP<PPMWRRSPPLMRR

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_4688 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_4688 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 19 parental genes, and 43 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017861	1 retrocopy	retro_amel_194,
Bos taurus	ENSBTAG00000009969	7 retrocopies	retro_btau_1187, retro_btau_1239, retro_btau_1283, retro_btau_1515, retro_btau_764, retro_btau_776, retro_btau_85,
Canis familiaris	ENSCAFG00000019397	1 retrocopy	retro_cfam_449,
Equus caballus	ENSECAG00000023288	1 retrocopy	retro_ecab_524,
Felis catus	ENSFCAG00000007690	1 retrocopy	retro_fcat_248,
Homo sapiens	ENSG00000205937	1 retrocopy	retro_hsap_2911,
Gorilla gorilla	ENSGGOG00000014275	1 retrocopy	retro_ggor_2016,
Macropus eugenii	ENSMEUG00000008882	1 retrocopy	retro_meug_1996,
Myotis lucifugus	ENSMLUG00000016808	3 retrocopies	retro_mluc_2237, retro_mluc_2618, retro_mluc_643,
Macaca mulatta	ENSMMUG00000019238	1 retrocopy	retro_mmul_794,
Monodelphis domestica	ENSMODG00000015891	1 retrocopy	retro_mdom_1171,
Mus musculus	ENSMUSG00000034681	1 retrocopy	retro_mmus_173,
Otolemur garnettii	ENSOGAG00000031582	1 retrocopy	retro_ogar_3241,
Rattus norvegicus	ENSRNOG00000008703	4 retrocopies	retro_rnor_1537, retro_rnor_2135, retro_rnor_2988, retro_rnor_649,
Sarcophilus harrisii	ENSSHAG00000016951	1 retrocopy	retro_shar_390,
Ictidomys tridecemlineatus	ENSSTOG00000013200	1 retrocopy	retro_itri_1160,
Tupaia belangeri	ENSTBEG00000009098	8 retrocopies	retro_tbel_1262, retro_tbel_1851, retro_tbel_2132, retro_tbel_2154, retro_tbel_2216, retro_tbel_3193, retro_tbel_3286, retro_tbel_4688 ,
Tarsius syrichta	ENSTSYG00000001629	1 retrocopy	retro_tsyr_957,
Tursiops truncatus	ENSTTRG00000008220	7 retrocopies	retro_ttru_1010, retro_ttru_1033, retro_ttru_1558, retro_ttru_1808, retro_ttru_1809, retro_ttru_203, retro_ttru_986,