RetrogeneDB ID: retro_tbel_1396

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: GeneScaffold_4594:10304..11016(-)
• Located in intron of: ENSTBEG00000017558

Retrocopy information

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

Parental gene information

• Parental gene symbol: MFSD1
• Ensembl ID: ENSTBEG00000013974
• Aliases: None
• Description: major facilitator superfamily domain containing 1 [Source:HGNC Symbol;Acc:25874]

Sequence

>retro_tbel_1396
CTCATGGGATGGCTGTATTCTGAGATTGAAGCTTCTTTGGGTTCTGCTGGTCACACAACCATTGGTGTCACACTTATGCT
TGGGGGTATAACCTGCATTCTTTCACTTATCTGTGCCTTGGCTTTTGCTTACTTGATCAGAGAGCAGAGAGAATTCTTCA
TAAATAACAAGAAAAAACAGGTGGAATTATTAAATTAATCGATGTGAAGGACTTCTTAGCCCTCTGGCTCCTATTTATCA
TCTGTGTCTGCTATTATGTTCCTGTGTTCTCTTTTATTGGACTTGGGAAAATTTTCTTTATAGAGAAATTTGAATTTTCT
TCCCAGGCATCAAGTGCAATTAACAATGTCGTATATGTCTTATCAGCTCCCATGTCCCCAGTACTTGGGCTCCTGGTGAT
AAAACAGGGAGGAACATCATCTGGGTTCTGTGTGCAGTGGCGGCCACTCTTGAGTCTCACGTGACACTGCCCTTTACGAT
GTAGAACCCTTGGATTGCTGTGTGTCTTCTGGGAATCTCCTACTCATTGCTGGCTTGTGCGCTGTGGCTGATGGTGGCAT
TTGTAGTTCCTGAGCTTCAGCTGAGAACTGCATATGGCTTCATGCAGTCCATTCAGAATCTCGGGCTGGCAGTCATTTCC
ATCATTGCCGGCATGATATTGTATACTAGAGGCTATATGTTTTTAGAAGTTCTCTTCGCTGCCTTTGTTTCT

Alignment

ORF - retro_tbel_1396 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.4 %
• Parental protein coverage: 51.4 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LMGWLYSEIEASLGSTGHTTLGVTLMLGSISCLLSLICAFALAYL-DQRAERILHKEQGKTGEVIKLTDV
          LMGWLYSEIEASLGS.GHTT.GVTLMLG.I.C.LSLICA.A.AYL.DQRAERILHK.Q.KTG..IKL.DV
Retrocopy LMGWLYSEIEASLGSAGHTTIGVTLMLGGITCILSLICALAFAYL<DQRAERILHK*QEKTGGIIKLIDV

Parental  KDFSLALWLIFIICVCYYVAVFPFIGLGKIFFIEKFEFSSQAASAINSVVYVISAPMSPVFGLLV-DKTG
          KDF.LALWL.FIICVCYYV.VF.FIGLGKIFFIEKFEFSSQA.SAIN.VVYV.SAPMSPV.GLLV.DKTG
Retrocopy KDF-LALWLLFIICVCYYVPVFSFIGLGKIFFIEKFEFSSQASSAINNVVYVLSAPMSPVLGLLV<DKTG

Parental  RNIIWVLCAVAATLVSHMMLAFTMWNPWIAMCLLGVSYSLLACALWPMVAFVVPEHQLGTAYGFMQSIQN
          RNIIWVLCAVAATL.SH..L.FTM.NPWIA.CLLG.SYSLLACALW.MVAFVVPE.QL.TAYGFMQSIQN
Retrocopy RNIIWVLCAVAATLESHVTLPFTM*NPWIAVCLLGISYSLLACALWLMVAFVVPELQLRTAYGFMQSIQN

Parental  LGLAIIAIIAGMILDSRGYLFLEVFFIACVS
          LGLA.I.IIAGMIL..RGY.FLEV.F.A.VS
Retrocopy LGLAVISIIAGMILYTRGYMFLEVLFAAFVS

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_1396 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_1396 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 8 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000009263	1 retrocopy	retro_btau_1323,
Dasypus novemcinctus	ENSDNOG00000005048	1 retrocopy	retro_dnov_1121,
Macaca mulatta	ENSMMUG00000023510	1 retrocopy	retro_mmul_1210,
Oryctolagus cuniculus	ENSOCUG00000001272	1 retrocopy	retro_ocun_1528,
Pongo abelii	ENSPPYG00000014247	1 retrocopy	retro_pabe_1427,
Tupaia belangeri	ENSTBEG00000013974	1 retrocopy	retro_tbel_1396 ,
Tursiops truncatus	ENSTTRG00000002207	2 retrocopies	retro_ttru_1119, retro_ttru_1271,
Drosophila melanogaster	FBgn0031636	1 retrocopy	retro_dmel_45,