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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacctggccaaagttttagatggttagcgatcgatcgagcgagcgaaaaacgagcaagccagcagcattcttacttcttttttggtatctccgtgcagTACATCCTTGACACCAGCGTCTATCCCCGGGAGCCGGCTCCTTTGAAAGGACTGCGAGAGATGACAGCCCACCATCCATG

Basic information

species Selaginella moellendorffii
transcript EFJ11728
intron # 1
splice site 3'
intron type U2

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|169106716|gb|FE506753.1|FE506753
EST:     ACTCGCAAGTCGGGCACAAGAGCGTCCTCAAGAGCGACAAGTTGTATCAG                         TACATCCTTGACACCAGCGTCTATCCCCGGGAGCCGGCTCCTTTGAAAGGA
genomic: ACTCGCAAGTCGGGCACAAGAGCGTCCTCAAGAGCGACAAGTTGTATCAGgtacctggcc ... ctccgtgcagTACATCCTTGACACCAGCGTCTATCCCCGGGAGCCGGCTCCTTTGAAAGGA
EST: gi|169066692|gb|FE475448.1|FE475448
EST:     ACTCGCAAGTCGGGCACAAGAGCGTCCTCAAGAGCGACAAGTTGTATCAG                         TACATCCTTGACACCAGCGTCTATCCCCGGGAGCCGGCTCCTTTGAAAGGA
genomic: ACTCGCAAGTCGGGCACAAGAGCGTCCTCAAGAGCGACAAGTTGTATCAGgtacctggcc ... ctccgtgcagTACATCCTTGACACCAGCGTCTATCCCCGGGAGCCGGCTCCTTTGAAAGGA
EST: gi|169075572|gb|FE481958.1|FE481958
EST:     ACTCGCAAGTCGGGCACAAGAGCGTCCTCAAGAGCGACAAGTTGTATCAG                         TACATCCTTGACACCAGCGTCTATCCCCGGGAGCCGGCTCCTTTGAAAGGA
genomic: ACTCGCAAGTCGGGCACAAGAGCGTCCTCAAGAGCGACAAGTTGTATCAGgtacctggcc ... ctccgtgcagTACATCCTTGACACCAGCGTCTATCCCCGGGAGCCGGCTCCTTTGAAAGGA
EST: gi|169059287|gb|FE467468.1|FE467468
EST:     ACTCGCAAGTCGGGCACAAGAGCGTCCTCAAGAGCGACAAGTTGTATCAG                         TACATCCTTGACACCAGCGTCTATCCCCGGGAGCCGGCTCCTTTGAAAGGA
genomic: ACTCGCAAGTCGGGCACAAGAGCGTCCTCAAGAGCGACAAGTTGTATCAGgtacctggcc ... ctccgtgcagTACATCCTTGACACCAGCGTCTATCCCCGGGAGCCGGCTCCTTTGAAAGGA
EST: gi|169108255|gb|FE513564.1|FE513564
EST:     ACTCGCAAGTCGGGCACAAGAGCGTCCTCAAGAGCGACAAGTTGTATCAG                         TACATCCTTGACACCAGCGTCTATCCCCGGGAGCCGGCTCCTTTGAAAGGA
genomic: ACTCGCAAGTCGGGCACAAGAGCGTCCTCAAGAGCGACAAGTTGTATCAGgtacctggcc ... ctccgtgcagTACATCCTTGACACCAGCGTCTATCCCCGGGAGCCGGCTCCTTTGAAAGGA
EST: gi|169070774|gb|FE477321.1|FE477321
EST:     ACTCGCAAGTCGGGCACAAGAGCGTCCTCAAGAGCGACAAGTTGTATCAG                         TACATCCTTGACACCAGCGTCTATCCCCGGGAGCCGGCTCCTTTGAAAGGA
genomic: ACTCGCAAGTCGGGCACAAGAGCGTCCTCAAGAGCGACAAGTTGTATCAGgtacctggcc ... ctccgtgcagTACATCCTTGACACCAGCGTCTATCCCCGGGAGCCGGCTCCTTTGAAAGGA
EST: gi|169107109|gb|FE507263.1|FE507263
EST:     ACTCGCAAGTCGGGCACAAGAGCGTCCTCAAGAGCGACAAGTTGTATCAG                         TACATCCTTGACACCAGCGTCTATCCCCGGGAGCCGGCTCCTTTGAAAGGA
genomic: ACTCGCAAGTCGGGCACAAGAGCGTCCTCAAGAGCGACAAGTTGTATCAGgtacctggcc ... ctccgtgcagTACATCCTTGACACCAGCGTCTATCCCCGGGAGCCGGCTCCTTTGAAAGGA
EST: gi|169104300|gb|FE503714.1|FE503714
EST:     ACTCGCAAGTCGGGCACAAGAGCGTCCTCAAGAGCGACAAGTTGTATCAG                         TACATCCTTGACACCAGCGTCTATCCCCGGGAGCCGGCTCCTTTGAAAGGA
genomic: ACTCGCAAGTCGGGCACAAGAGCGTCCTCAAGAGCGACAAGTTGTATCAGgtacctggcc ... ctccgtgcagTACATCCTTGACACCAGCGTCTATCCCCGGGAGCCGGCTCCTTTGAAAGGA
EST: gi|169115444|gb|FE516185.1|FE516185
EST:     ACTCGCAAGTCGGGCACAAGAGCGTCCTCAAGAGCGACAAGTTGTATCAG                         TACATCCTTGACACCAGCGTCTATCCCCGGGAGCCGGCTCCTTTGAAAGGA
genomic: ACTCGCAAGTCGGGCACAAGAGCGTCCTCAAGAGCGACAAGTTGTATCAGgtacctggcc ... ctccgtgcagTACATCCTTGACACCAGCGTCTATCCCCGGGAGCCGGCTCCTTTGAAAGGA

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 35 (upstream exon), 35 (downstream exon)
Score: 349

CGTGAGCAGTGTGGAAGTTTCGAGCGACAATGCCAACAAGGCCGGCAAGCACTCGCAAGTCGGGCACAAGAGCGTCCTCAAGAGCGACAAGTTGTATCAGgtacctggcc ... ctccgtgcagTACATCCTTGACACCAGCGTCTATCCCCGGGAGCCGGCTCCTTTGAAAGGACTGCGAGAGATGACAGCCCACCATCCATG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgaaaaacgagcaagccagcagcattcttacttcttttttggtatctccgtgcagTACATCCTTGACACCAGCGTCTATCCCCGGGAGCCGGCTCCTTTGAAAGGACTGCGAGAGATGACAGCCCACCATCCATG
                        ttcttac  putative branch site (score: 349)
                                          tatctcc  putative PPT
                               ttctttttt  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacctggccaaagttttagatggttagcgatcgatcgagcgagcgaaaaacgagcaagccagcagcattcttacttcttttttggtatctccgtgcagTACATCCTTGACACCAGCGTCTATCCCCGGGAGCCGGCTCCTTTGAAAGGACTGCGAGAGATGACAGCCCACCATCCATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG