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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCCATCCTACTTGAAGGGAGAGTTTCCTGGCGATTATGGCTGGGACACTGCCGGACTCTCCGCTGATCCAGAGGCCTTTGCTCGCAACCGCGCTCTCGAGgtacgctcatttagttccaagaactttggaagaacttccaaacttcttggaactcttatcgtgttcgtaagtttggaaaccaacttgttgtttcttttctttttgataaacaaaccag

Basic information

species Selaginella moellendorffii
transcript EFJ32176
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ32176 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: PP1S254_3V6.1 (Physcomitrella patens), 5'ss of exon 2
TCCATCCTACTTGAAGGGAGAGTTTCCTGGCGATTATGGCTGGGACACTGCCGGACTCTCCGCTGATCCAGAGGCCTTTGCTCGCAACCGCGCTCTCGAGgtacgctcatttagttccaagaactttggaagaacttccaaacttcttggaactcttatcgtgttcgtaagtttggaaaccaacttgttgtttcttttctttttgataaacaaaccag--------------------
 || |||||||||||||| ||||| ||||| || || || ||||||||||| ||||||||||| || || ||| | ||||| || ||||| ||||| |||||||   || ||  | |  | |    | |||  |||  | |   |||||  |  ||     ||     | |  ||    || ||   |      | | |  |  |   |   |   ||                    
CCCCTCCTACTTGAAGGGCGAGTTCCCTGGTGACTACGGATGGGACACTGCTGGACTCTCCGCCGACCCCGAGTCATTTGCCCGGAACCGTGCTCTTGAGgtac---cacttt-tcctgacattgattgaactactcaccattctcttgataacctaccactgggttaagggctgtgcccccacaattcaccaatatgcgctgggtgtagggattgagttgttaaattgtatgcgcag
















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|169059514|gb|FE468540.1|FE468540
EST:     CCGGACTCTCCGCTGATCCAGAGGCCTTTGCTCGCAACCGCGCTCTCGAG                         CTGATCCACGGACGCTGGGCGATGCTGGGAGCTCTTGGCTGCGTCTTCCCG
genomic: CCGGACTCTCCGCTGATCCAGAGGCCTTTGCTCGCAACCGCGCTCTCGAGgtacgctcat ... aacaaaccagCTGATCCACGGACGCTGGGCGATGCTGGGAGCTCTTGGCTGCGTCTTCCCG
EST: gi|169059515|gb|FE468541.1|FE468541
EST:     CCGGACTCTCCGCTGATCCAGAGGCCTTTGCTCGCAACCGCGCTCTCGAG                         CTGATCCACGGACGCTGGGCGATGCTGGGAGCTCTTGGCTGCGTCTTCCCG
genomic: CCGGACTCTCCGCTGATCCAGAGGCCTTTGCTCGCAACCGCGCTCTCGAGgtacgctcat ... aacaaaccagCTGATCCACGGACGCTGGGCGATGCTGGGAGCTCTTGGCTGCGTCTTCCCG
EST: gi|169051420|gb|FE457692.1|FE457692
EST:     CCGGACTCTCCGCTGATCCAGAGGCCTTTGCTCGCAACCGCGCTCTCGAG                         CTGATCCACGGACGCTGGGCGATGCTGGGAGCTCTTGGCTGCGTCTTCCCG
genomic: CCGGACTCTCCGCTGATCCAGAGGCCTTTGCTCGCAACCGCGCTCTCGAGgtacgctcat ... aacaaaccagCTGATCCACGGACGCTGGGCGATGCTGGGAGCTCTTGGCTGCGTCTTCCCG
EST: gi|169066315|gb|FE472991.1|FE472991
EST:     CCGGACTCTCCGCTGATCCAGAGGCCTTTGCTCGCAACCGCGCTCTCGAG                         CTGATCCACGGACGCTGGGCGATGCTGGGAGCTCTTGGCTGCGTCTTCCCG
genomic: CCGGACTCTCCGCTGATCCAGAGGCCTTTGCTCGCAACCGCGCTCTCGAGgtacgctcat ... aacaaaccagCTGATCCACGGACGCTGGGCGATGCTGGGAGCTCTTGGCTGCGTCTTCCCG
EST: gi|169114834|gb|FE516095.1|FE516095
EST:     CCGGACTCTCCGCTGATCCAGAGGCCTTTGCTCGCAACCGCGCTCTCGAG                         CTGATCCACGGACGCTGGGCGATGCTGGGAGCTCTTGGCTGCGTCTTCCCG
genomic: CCGGACTCTCCGCTGATCCAGAGGCCTTTGCTCGCAACCGCGCTCTCGAGgtacgctcat ... aacaaaccagCTGATCCACGGACGCTGGGCGATGCTGGGAGCTCTTGGCTGCGTCTTCCCG
EST: gi|169080816|gb|FE486648.1|FE486648
EST:     CCGGACTCTCCGCTGATCCAGAGGCCTTTGCTCGCAACCGCGCTCTCGAG                         CTGATCCACGGACGCTGGGCGATGCTGGGAGCTCTTGGCTGCGTCTTCCCG
genomic: CCGGACTCTCCGCTGATCCAGAGGCCTTTGCTCGCAACCGCGCTCTCGAGgtacgctcat ... aacaaaccagCTGATCCACGGACGCTGGGCGATGCTGGGAGCTCTTGGCTGCGTCTTCCCG
EST: gi|169102356|gb|FE505826.1|FE505826
EST:     CCGGACTCTCCGCTGATCCAGAGGCCTTTGCTCGCAACCGCGCTCTCGAG                         CTGATCCACGGACGCTGGGCGATGCTGGGAGCTCTTGGCTGCGTCTTCCCG
genomic: CCGGACTCTCCGCTGATCCAGAGGCCTTTGCTCGCAACCGCGCTCTCGAGgtacgctcat ... aacaaaccagCTGATCCACGGACGCTGGGCGATGCTGGGAGCTCTTGGCTGCGTCTTCCCG
EST: gi|169096663|gb|FE496793.1|FE496793
EST:     CCGGACTCTCCGCTGATCCAGAGGCCTTTGCTCGCAACCGCGCTCTCGAG                         CTGATCCACGGACGCTGGGCGATGCTGGGAGCTCTTGGCTGCGTCTTCCCG
genomic: CCGGACTCTCCGCTGATCCAGAGGCCTTTGCTCGCAACCGCGCTCTCGAGgtacgctcat ... aacaaaccagCTGATCCACGGACGCTGGGCGATGCTGGGAGCTCTTGGCTGCGTCTTCCCG
EST: gi|169066314|gb|FE472990.1|FE472990
EST:     CCGGACTCTCCGCTGATCCAGAGGCCTTTGCTCGCAACCGCGCTCTCGAG                         CTGATCCACGGACGCTGGGCGATGCTGGGAGCTCTTGGCTGCGTCTTCCCG
genomic: CCGGACTCTCCGCTGATCCAGAGGCCTTTGCTCGCAACCGCGCTCTCGAGgtacgctcat ... aacaaaccagCTGATCCACGGACGCTGGGCGATGCTGGGAGCTCTTGGCTGCGTCTTCCCG
EST: gi|169051421|gb|FE457693.1|FE457693
EST:     CCGGACTCTCCGCTGATCCAGAGGCCTTTGCTCGCAACCGCGCTCTCGAG                         CTGATCCACGGACGCTGGGCGATGCTGGGAGCTCTTGGCTGCGTCTTCCCG
genomic: CCGGACTCTCCGCTGATCCAGAGGCCTTTGCTCGCAACCGCGCTCTCGAGgtacgctcat ... aacaaaccagCTGATCCACGGACGCTGGGCGATGCTGGGAGCTCTTGGCTGCGTCTTCCCG
EST: gi|169029229|gb|FE439409.1|FE439409
EST:     CCGGACTCTCCGCTGATCCAGAGGCCTTTGCTCGCAACCGCGCTCTCGAG                         CTGATCCACGGACGCTGGGCGATGCTGGGAGCTCTTGGCTGCGTCTTCCCG
genomic: CCGGACTCTCCGCTGATCCAGAGGCCTTTGCTCGCAACCGCGCTCTCGAGgtacgctcat ... aacaaaccagCTGATCCACGGACGCTGGGCGATGCTGGGAGCTCTTGGCTGCGTCTTCCCG
EST: gi|169108630|gb|FE512041.1|FE512041
EST:     CCGGACTCTCCGCTGATCCAGAGGCCTTTGCTCGCAACCGCGCTCTCGAG                         CTGATCCACGGACGCTGGGCGATGCTGGGAGCTCTTGGCTGCGTCTTCCCG
genomic: CCGGACTCTCCGCTGATCCAGAGGCCTTTGCTCGCAACCGCGCTCTCGAGgtacgctcat ... aacaaaccagCTGATCCACGGACGCTGGGCGATGCTGGGAGCTCTTGGCTGCGTCTTCCCG
EST: gi|169108629|gb|FE512040.1|FE512040
EST:     CCGGACTCTCCGCTGATCCAGAGGCCTTTGCTCGCAACCGCGCTCTCGAG                         CTGATCCACGGACGCTGGGCGATGCTGGGAGCTCTTGGCTGCGTCTTCCCG
genomic: CCGGACTCTCCGCTGATCCAGAGGCCTTTGCTCGCAACCGCGCTCTCGAGgtacgctcat ... aacaaaccagCTGATCCACGGACGCTGGGCGATGCTGGGAGCTCTTGGCTGCGTCTTCCCG
EST: gi|169029228|gb|FE439408.1|FE439408
EST:     CCGGACTCTCCGCTGATCCAGAGGCCTTTGCTCGCAACCGCGCTCTCGAG                         CTGATCCACGGACGCTGGGCGATGCTGGGAGCTCTTGGCTGCGTCTTCCCG
genomic: CCGGACTCTCCGCTGATCCAGAGGCCTTTGCTCGCAACCGCGCTCTCGAGgtacgctcat ... aacaaaccagCTGATCCACGGACGCTGGGCGATGCTGGGAGCTCTTGGCTGCGTCTTCCCG
EST: gi|169060049|gb|FE468659.1|FE468659
EST:     CCGGACTCTCCGCTGATCCAGAGGCCTTTGCTCGCAACCGCGCTCTCGAG                         CTGATCCACGGACGCTGGGCGATGCTGGGAGCTCTTGGCTGCGTCTTCCCG
genomic: CCGGACTCTCCGCTGATCCAGAGGCCTTTGCTCGCAACCGCGCTCTCGAGgtacgctcat ... aacaaaccagCTGATCCACGGACGCTGGGCGATGCTGGGAGCTCTTGGCTGCGTCTTCCCG
EST: gi|169043794|gb|FE453486.1|FE453486
EST:     CCGGACTCTCCGCTGATCCAGAGGCCTTTGCTCGCAACCGCGCTCTCGAG                         CTGATCCACGGACGCTGGGCGATGCTGGGAGCTCTTGGCTGCGTCTTCCCG
genomic: CCGGACTCTCCGCTGATCCAGAGGCCTTTGCTCGCAACCGCGCTCTCGAGgtacgctcat ... aacaaaccagCTGATCCACGGACGCTGGGCGATGCTGGGAGCTCTTGGCTGCGTCTTCCCG
EST: gi|169018599|gb|FE427512.1|FE427512
EST:     CCGGATTATCCGCTGATCCAGAGGCCTTTGCTTGCAACCGCGCTCTCGAG                         TTGATCCACGGACGCTGGGCGATGCTGGGAGCTCTTGGCTGCGTCTTCCCG
genomic: CCGGACTCTCCGCTGATCCAGAGGCCTTTGCTCGCAACCGCGCTCTCGAGgtacgctcat ... aacaaaccagCTGATCCACGGACGCTGGGCGATGCTGGGAGCTCTTGGCTGCGTCTTCCCG
EST: gi|169096664|gb|FE496794.1|FE496794
EST:     CCGGACTCTCCGCTGATCCAGAGGCCTTTGCTCGCAACCGCGCTCTCGAG                         CTGATCCACGGACGCTGGGCGATGCTGGGAGCTCTTGGCTGCGTCTTCCCG
genomic: CCGGACTCTCCGCTGATCCAGAGGCCTTTGCTCGCAACCGCGCTCTCGAGgtacgctcat ... aacaaaccagCTGATCCACGGACGCTGGGCGATGCTGGGAGCTCTTGGCTGCGTCTTCCCG
EST: gi|169101520|gb|FE501493.1|FE501493
EST:     CCGGACTCTCCGCTGATCCAGAGGCCTTTGCTCGCAACCGCGCTCTCGAG                         CTGATCCACGGACGCTGGGCGATGCTGGGAGCTCTTGGCTGCGTCTTCCCG
genomic: CCGGACTCTCCGCTGATCCAGAGGCCTTTGCTCGCAACCGCGCTCTCGAGgtacgctcat ... aacaaaccagCTGATCCACGGACGCTGGGCGATGCTGGGAGCTCTTGGCTGCGTCTTCCCG
EST: gi|169060050|gb|FE468660.1|FE468660
EST:     CCGGACTCTCCGCTGATCCAGAGGCCTTTGCTCGCAACCGCGCTCTCGAG                         CTGATCCACGGACGCTGGGCGATGCTGGGAGCTCTTGGCTGCGTCTTCCCG
genomic: CCGGACTCTCCGCTGATCCAGAGGCCTTTGCTCGCAACCGCGCTCTCGAGgtacgctcat ... aacaaaccagCTGATCCACGGACGCTGGGCGATGCTGGGAGCTCTTGGCTGCGTCTTCCCG

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: 60

TCCATCCTACTTGAAGGGAGAGTTTCCTGGCGATTATGGCTGGGACACTGCCGGACTCTCCGCTGATCCAGAGGCCTTTGCTCGCAACCGCGCTCTCGAGgtacgctcat ... aacaaaccagCTGATCCACGGACGCTGGGCGATGCTGGGAGCTCTTGGCTGCGTCTTCCCGGAGGTCCTCTCCAAATGGGTCGGTGTGGAGTTCAAGGAGAAAGTGTGGT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCCATCCTACTTGAAGGGAGAGTTTCCTGGCGATTATGGCTGGGACACTGCCGGACTCTCCGCTGATCCAGAGGCCTTTGCTCGCAACCGCGCTCTCGAGgtacgctcatttagttccaagaactttggaagaacttccaaacttcttggaactcttatcgtgttcgtaagtttggaaaccaacttgttgtttcttttctttttgataaacaaaccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT