RetrogeneDB ID: retro_tbel_1746

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: GeneScaffold_5625:78306..79049(+)
• Located in intron of: ENSTBEG00000008151

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSTBEG00000011678
• Aliases: None
• Description: None

Sequence

>retro_tbel_1746
ATATCTTGAAGGTATAACTCCAGGGCCACTATATTTTCTCTAGAAGGTCACTTATACCAAGCGGAATATGCCATGGAAGC
TATTGGACACACAGGCACCTGTTTGGGAATTTTAGCAATGATGGGGCTTTGCTTACAGCTGAGAGATGCAACATCCACAT
GCTTCTTGATGCTGTCTTTTTTCTGAAAAGATTTATAAACTCAATGAGGAAATAGTGTGCAGTGTGGCAGGCGTAACCTC
TGATGCCAGTGTCCTGACTAATGAACTGAGGCTCATTGCTCAAAGGTATTTATTGCAGTATGAGGAGCCCATTCCTTGTG
AGCAGTTGGTTACGGCACTGTGTGATACCAAACAAGCTTACACACAGTTTAGAGGAAAACGTCCCTTTGGTGTTTCTTTG
CTGTACATTGGTTGGGATAAACACCATGACTTTCAACTCTTATCAGAGTGACCCTAATGAAAATTATGGGGGCTGGAAAG
GCACGTGCATTGAAAATAACAACGCCACAGCCATGTCAATGTTGAAGCAAGATTACAAAGAAGGAGGAATGACTCTGAAA
TCGGCACTTGCATCAACTATCAAAGTACTAAATAAGCCTACGGATGTTAGTAAACTGTATGCTGGAAAAGTAGAAATTGC
CACATTGACAAGAAAGAACAGAAAGATGGTGATCAGAGTTTTCAAACAAAAGGAGGTGGAGCAGTTGATCAAAAACCATG
AGGAAGAAGAAGCCCAAGCTGAG

Alignment

ORF - retro_tbel_1746 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.67 %
• Parental protein coverage: 95.02 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MSRRYDSRTTIFSPEGRLYQVEYAMEAIGHAGTCLGILA-NDGVLLAAERRNIHKLLDEVFF-SEKIYKL
          .S.RY.SR.TIFS.EG.LYQ.EYAMEAIGH.GTCLGILA.NDG.LL.AER.NIH.LLD.VFF.SEKIYKL
Retrocopy IS*RYNSRATIFSLEGHLYQAEYAMEAIGHTGTCLGILA<NDGALLTAERCNIHMLLDAVFF<SEKIYKL

Parental  NEDMACSVAGITSDANVLTNELRLIAQRYLLQYQEPIPCEQLVTALCDIKQAYTQFGGKRPFGVSLLYIG
          NE...CSVAG.TSDA.VLTNELRLIAQRYLLQY.EPIPCEQLVTALCD.KQAYTQF.GKRPFGVSLLYIG
Retrocopy NEEIVCSVAGVTSDASVLTNELRLIAQRYLLQYEEPIPCEQLVTALCDTKQAYTQFRGKRPFGVSLLYIG

Parental  WDKHYGFQL-YQSDPSGNYGGWKATCIGNNSAAAVSMLKQDYKEGEMTLKSALALAIKVLNKTMDVSKLS
          WDKH..FQL.YQSDP..NYGGWK.TCI.NN.A.A.SMLKQDYKEG.MTLKSALA..IKVLNK..DVSKL.
Retrocopy WDKHHDFQL>YQSDPNENYGGWKGTCIENNNATAMSMLKQDYKEGGMTLKSALASTIKVLNKPTDVSKLY

Parental  AEKVEIATLTRENGKTVIRVLRQKEVEQLIKNHEEEEAKAE
          A.KVEIATLTR.N.K.VIRV..QKEVEQLIKNHEEEEA.AE
Retrocopy AGKVEIATLTRKNRKMVIRVFKQKEVEQLIKNHEEEEAQAE

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_1746 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_1746 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 6 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000010369	1 retrocopy	retro_cjac_58,
Myotis lucifugus	ENSMLUG00000027860	1 retrocopy	retro_mluc_1404,
Mus musculus	ENSMUSG00000032301	2 retrocopies	retro_mmus_1035, retro_mmus_1707,
Pteropus vampyrus	ENSPVAG00000009182	2 retrocopies	retro_pvam_1229, retro_pvam_824,
Tupaia belangeri	ENSTBEG00000011678	5 retrocopies	retro_tbel_1746 , retro_tbel_2953, retro_tbel_3324, retro_tbel_4164, retro_tbel_614,
Tarsius syrichta	ENSTSYG00000011745	1 retrocopy	retro_tsyr_21,