Introduction
Welcome to Trans-SAMap. You can retrieve and download all of trans-NAT pair. Here, A step-by-step introduction to Trans-SAMap website, You can click to browse every subject, or choose search keywords.

A: You just input gene symbols you are interested in to look for trans-SAs.
       But you can only input our internal IDs. If you wanna retrieve genes, please click 'search' on the menu bar.

Then you can gain detail transcript's information, which will descript in the 'Transcript Entry' page.
B:View the absolute number of trans-SAs in ten species.
C:View the relative abundance of trans-SAs in ten species.

About
The 'about Trans-SAMap' page introducts Trans-SAMap by subjects below: introduction, pipeline, , softwares, databases and reference. Combination with pipilien, in introduction, we show how we develop Trans-SAMap and the content of Trans-SAMap, Here also show softwares and database (click to view detailed info and link to their websites) we used in the pipeline. The references are also list in our manuscript.






Browse
There are two main approaches to search natural antisense transcripts you are interested in.

Browse Approaches:

Browse Result:

Take the first row as an example.
The 1st field hs_0_m.0 is the TU's ID (TU, that is transcript unit, equal to gene).    The 'hs' indicates that it is from human species.   The '0' means a chromosone's locus.    The '_m' refers to this gene transcripted from the minus DNA strand.

The 2nd field '-' is the gene's orientation.    '-' is in minus strand, while '+' is in plus strand. Click the T ID and then the web browser will turn to 'Transcript Entry' page.

The 3rd field hs_0_m.0.118692 is the T ID (Transcript ID).    These transcripts are predicted by   SVAP . The 'hs_0_m.0' is TU ID. The last '.0' is a marker of transcript. Different transcripts from a gene have different IDs.

The 4th field is the chromosonal location of the transcript.

The 5th field is all exon numbers of the transcript



Transcripts description
Click T ID in the Browse Result Page to browse all predicted Trans-NATs or their targets on chromosomes. Here show known Trans-NATs on chromosome in graph and in text.


Click 'Fetch Sequence' in the 1st field, you can get the fasta format of transcript sequence.

Click the TU-ID in the 2nd field, the browser will turn to 'Gene entry' page described next.

Links to UCSC in Trans-NATs entry: 'View in the Genome Browser' in the 4th field links to GoldenPath in UCSC.We generate .BED file for every transcript / isoform embeding our predicted isoforms into UCSC genome browser. The goals are: (1) to help users compare our isoforms with UCSC annotation.(2) to avoid our TUs are mistaken as noisy transcription.

The 5th field of 'Evidence' is the supporting sequences of this transcript. We have uploaded all the predicted transcripts onto NATsDB . You can retrieve all the supporting sequences and predicted transcripts in NATsDB.

"One Color, One HSP". In the 6th field, we show the complementary regions of Trans-NAT and its partners. The black block represents exons, the dashed line intron. Other blocks of various color (by default, red color) different form black means the complementary regions. Even one transcript has more than one color block, which indicates it has more than one HSP to complement with its partners. Many transcripts have more than one target transcript. In this case, there are two complementary regions: the first one is colored with dark red while the second one with scarlet.

Click ID besides triangle icon The ID besides triangle icon stands for the other partner. Click this ID and the browser will turn to the page describing information on this partner.

In the 7th field, 'Other variant in the same TU' refers to those transcripts belonging to the same genes, that is, one gene's alternative splicing isoforms.



Transcript Unit description
Click 'TU ID' in the 2nd field of the 'Transcript Entry' Page and the 'Gene Entry' page will describe the gene's information in graph and in text, including chromosomal location and all its isoforms.


We assigned Descritpion, EntrezGene ID and Gene Symbols from NCBI to every TU to confirm the real transcription and correct orientation prediction.
Cluster ID: is more high level genomic organization than Transcriptional Unit-segments of the genome where ESTs/mRNAs overlapped in their genomic coordinates, regardless of their orientations. One transcriptional unit belongs to only one Cluster while one Cluster may include multiple TUs. We link the Cluster ID to NATsDB, where the browser displays Exon/intron structure, poly(A) signals and tails, CpG island and First Exon prediction to support the transcript's orientation. More information is provided in NATsDB but users should read Help file in NATsDB first.

Link to NCBI EntrezGene:You can click Gene ID and the Page will turn to NCBI. The gene annotation including gene orientation and real transcription confirms our correct prediction and inexistence of 'noisy' transcription.

Links to UCSC in Trans-NATs Gene entry: 'View in the Genome Browser' in the 6th field links to GoldenPath in UCSC. We generate .BED file for every TU embeding our predicted TUs into UCSC genome browser. The goals are: (1) to help users compare our TU genomic structure with UCSC annotation.(2) to avoid our TUs are mistaken as noisy transcription.

In the 7th field, 'Variants' included all isoforms of this gene, due to alternative splicing, predicted by SVAP. The black box represents exon and the gray line means intro. Only those which contain the marker '(target)' have trans-SA partners. In this graph, we show the relationship between alternative splicing events and trans-NAT pairs.

Click ID besides triangle icon We assign a unique ID to every splicing isoform. Only those isoforms having trans-antisense targets, which are marked as "(target)" have links to their page. Just Click ID besides triangle icon and with "(target)" mark. The browser will turn to the page describing information on this isoform.




Search
Here, you can search in the search page via text search, chromosome location search and sequence search.





Statistics

We show the statistics of identification and analysis.





Download

    We provide supplementary data including two parts : Identification data and Analysis data, in Download Page.
    In identification part, we provide all the sense transcript and trans_NAT sequence in fasta format to download. In every file, you can copy the display id (our internal id) of each transcript fasta and paste it to the search box in our website. You can retrieve the related information of this transcript.
    In analysis part, we provide four files, every of which is explained clearly in the download page.