Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaggagaattttttttcttgagagaaagcttgcgatggttgctcttggcagGGAAATGTGGGACTTATCTTCACCAAAGGTGATCTCAAAGAAGTTCGCGAGGAAGTCGCGAAGTACAAG

Basic information

species Selaginella moellendorffii
transcript EFJ24514
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ13245 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: LOC_Os12g03880.1 (Oryza sativa), 3'ss of exon 1
------------------------------------gtaaggagaattttttttcttgagagaaagcttgcgatggttgctcttggcagGGAAATGTGGGACTTATCTTCACCAAAGGTGATCTCAAAGAAGTTCGCGAGGAAGTCGCGAAGTACAAG
                                     |   |   | | |||||| |||       | ||   |  ||| | || | |||| || || || || ||||||||||| ||||| ||||| || || |||||||| ||||| |||||||||
gtaagttcaccttcttcttccatgttcatacctaacctcgagtccactgtttttcctga-------cctgtttttcttgttgtttgtagGGTAACGTTGGTCTCATCTTCACCAAGGGTGACCTCAAGGAGGTCCGCGAGGAGGTCGCCAAGTACAAG
















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|169059624|gb|FE468858.1|FE468858
EST:     CCGAGAAGAGCGGCAACACGACTGTTCTCAGTCTCATGCCTCTTTTGGTG                         GGAAATGTGGGACTTATTTTCACCAAAGGTGATCTCAAAGAAGTTCGCGAG
genomic: CCGAGAAGAGCGGCAACACGACTGTTCTCAGTCTCATGCCTCTTTTGGTGgtaaggagaa ... ctcttggcagGGAAATGTGGGACTTATCTTCACCAAAGGTGATCTCAAAGAAGTTCGCGAG
EST: gi|169102451|gb|FE503893.1|FE503893
EST:     CCGAGAAGAGCGGCAACACGACTGTTCTCAGTCTCATGCCTCTTTTGGTG                         GGAAATGTGGGACTTATTTTCACCAAAGGTGATCTCAAAGAAGTTCGCGAG
genomic: CCGAGAAGAGCGGCAACACGACTGTTCTCAGTCTCATGCCTCTTTTGGTGgtaaggagaa ... ctcttggcagGGAAATGTGGGACTTATCTTCACCAAAGGTGATCTCAAAGAAGTTCGCGAG
EST: gi|169078881|gb|FE489653.1|FE489653
EST:     CCGAGAAGAGCGGCAACACGACTGTTCTCAGTCTCATGCCTCTTTTGGTG                         GGAAATGTGGGACTTATCTTCACCAAAGGTGATCTCAAAGAAGTTCGCGAG
genomic: CCGAGAAGAGCGGCAACACGACTGTTCTCAGTCTCATGCCTCTTTTGGTGgtaaggagaa ... ctcttggcagGGAAATGTGGGACTTATCTTCACCAAAGGTGATCTCAAAGAAGTTCGCGAG
EST: gi|169060805|gb|FE469220.1|FE469220
EST:     CCGAGAAGAGCGGCAACACGACTGTTCTCAGTCTCATGCCTCTTTTGGTG                         GGAAATGTGGGACTTATCTTCACCAAAGGTGATCTCAAAGAAGTTCGCGAG
genomic: CCGAGAAGAGCGGCAACACGACTGTTCTCAGTCTCATGCCTCTTTTGGTGgtaaggagaa ... ctcttggcagGGAAATGTGGGACTTATCTTCACCAAAGGTGATCTCAAAGAAGTTCGCGAG
EST: gi|169040256|gb|FE448971.1|FE448971
EST:     CCGAGAAGAGCGGCAACACGACTGTTCTCAGTCTCATGCCTCTTTTGGTG                         GGAAATGTGGGACTTATCTTCACCAAAGGTGATCTCAAAGAAGTTCGCGAG
genomic: CCGAGAAGAGCGGCAACACGACTGTTCTCAGTCTCATGCCTCTTTTGGTGgtaaggagaa ... ctcttggcagGGAAATGTGGGACTTATCTTCACCAAAGGTGATCTCAAAGAAGTTCGCGAG
EST: gi|169114856|gb|FE516117.1|FE516117
EST:     CCGAGAAGAGCGGCAACACGACTGTTCTCAGTCTCATGCCTCTTTTGGTG                         GGAAATGTGGGACTTATCTTCACCAAAGGTGATCTCAAAGAAGTTCGCGAG
genomic: CCGAGAAGAGCGGCAACACGACTGTTCTCAGTCTCATGCCTCTTTTGGTGgtaaggagaa ... ctcttggcagGGAAATGTGGGACTTATCTTCACCAAAGGTGATCTCAAAGAAGTTCGCGAG
EST: gi|169103625|gb|FE506822.1|FE506822
EST:     CCGAGAAGAGCGGCAACACGACTGTTCTCAGTCTCATGCCTCTTTTGGTG                         GGAAATGTGGGACTTATTTTCACCAAAGGTGATCTCAAAGAAGTTCGCGAG
genomic: CCGAGAAGAGCGGCAACACGACTGTTCTCAGTCTCATGCCTCTTTTGGTGgtaaggagaa ... ctcttggcagGGAAATGTGGGACTTATCTTCACCAAAGGTGATCTCAAAGAAGTTCGCGAG
EST: gi|169109253|gb|FE512820.1|FE512820
EST:     CCGAGAAGAGCGGCAACACGACTGTTCTCAGTCTCATGCCTCTTTTGGTG                         GGAAATGTGGGACTTATCTTCACCAAAGGTGATCTCAAAGAAGTTCGCGAG
genomic: CCGAGAAGAGCGGCAACACGACTGTTCTCAGTCTCATGCCTCTTTTGGTGgtaaggagaa ... ctcttggcagGGAAATGTGGGACTTATCTTCACCAAAGGTGATCTCAAAGAAGTTCGCGAG
EST: gi|169045016|gb|FE452758.1|FE452758
EST:     CCGAGAAGAGCGGCAACACGACTGTTCTCAGTCTCATGCCTCTTTTGGTG                         GGAAATGTGGGACTTATCTTCACCAAAGGTGATCTCAAAGAAGTTCGCGAG
genomic: CCGAGAAGAGCGGCAACACGACTGTTCTCAGTCTCATGCCTCTTTTGGTGgtaaggagaa ... ctcttggcagGGAAATGTGGGACTTATCTTCACCAAAGGTGATCTCAAAGAAGTTCGCGAG
EST: gi|169114855|gb|FE516116.1|FE516116
EST:     CCGAGAAGAGCGGCAACACGACTGTTCTCAGTCTCATGCCTCTTTTGGTG                         GGAAATGTGGGACTTATCTTCACCAAAGGTGATCTCAAAGAAGTTCGCGAG
genomic: CCGAGAAGAGCGGCAACACGACTGTTCTCAGTCTCATGCCTCTTTTGGTGgtaaggagaa ... ctcttggcagGGAAATGTGGGACTTATCTTCACCAAAGGTGATCTCAAAGAAGTTCGCGAG
EST: gi|169078880|gb|FE489652.1|FE489652
EST:     CCGAGAAGAGCGGCAACACGACTGTTCTCAGTCTCATGCCTCTTTTGGTG                         GGAAATGTGGGACTTATCTTCACCAAAGGTGATCTCAAAGAAGTTCGCGAG
genomic: CCGAGAAGAGCGGCAACACGACTGTTCTCAGTCTCATGCCTCTTTTGGTGgtaaggagaa ... ctcttggcagGGAAATGTGGGACTTATCTTCACCAAAGGTGATCTCAAAGAAGTTCGCGAG
EST: gi|169053546|gb|FE463315.1|FE463315
EST:     CCGAGAAGAGCGGCAACACGACTGTTCTCAGTCTCATGCCTCTTTTGGTG                         GGAAATGTGGGACTTATCTTCACCAAAGGTGATCTCAAAGAAGTTCGCGAG
genomic: CCGAGAAGAGCGGCAACACGACTGTTCTCAGTCTCATGCCTCTTTTGGTGgtaaggagaa ... ctcttggcagGGAAATGTGGGACTTATCTTCACCAAAGGTGATCTCAAAGAAGTTCGCGAG
EST: gi|169053686|gb|FE461505.1|FE461505
EST:     CCGAGAAGAGCGGCAACACGACTGTTCTCAGTCTCATGCCTCTTTTGGTG                         GGAAATGTGGGACTTATCTTCACCAAAGGTGATCTCAAAGAAGTTCGCGAG
genomic: CCGAGAAGAGCGGCAACACGACTGTTCTCAGTCTCATGCCTCTTTTGGTGgtaaggagaa ... ctcttggcagGGAAATGTGGGACTTATCTTCACCAAAGGTGATCTCAAAGAAGTTCGCGAG
EST: gi|169035320|gb|FE443764.1|FE443764
EST:     CCGAGAAGAGCGGCAACACGACTGTTCTCAGTCTCATGCCTCTTTTGGTG                         GGAAATGTGGGACTTATTTTCACCAAAGGTGATCTCAAAGAAGTTCGCGAG
genomic: CCGAGAAGAGCGGCAACACGACTGTTCTCAGTCTCATGCCTCTTTTGGTGgtaaggagaa ... ctcttggcagGGAAATGTGGGACTTATCTTCACCAAAGGTGATCTCAAAGAAGTTCGCGAG
EST: gi|169074146|gb|FE481871.1|FE481871
EST:     CCGAGAAGAGCGGCAACACGACTGTTCTCAGTCTCATGCCTCTTTTGGTG                         GGAAATGTGGGACTTATTTTCACCAAAGGTGATCTCAAAGAAGTTCGCGAG
genomic: CCGAGAAGAGCGGCAACACGACTGTTCTCAGTCTCATGCCTCTTTTGGTGgtaaggagaa ... ctcttggcagGGAAATGTGGGACTTATCTTCACCAAAGGTGATCTCAAAGAAGTTCGCGAG

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: 34 (upstream exon), 35 (downstream exon)
Score: 67

GGTTCTCATGGGGAAGAACACTCTCATGAAGCGGACGATCAGGACTTACGCCGAGAAGAGCGGCAACACGACTGTTCTCAGTCTCATGCCTCTTTTGGTGgtaaggagaa ... ctcttggcagGGAAATGTGGGACTTATCTTCACCAAAGGTGATCTCAAAGAAGTTCGCGAGGAAGTCGCGAAGTACAAG




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtaaggagaattttttttcttgagagaaagcttgcgatggttgctcttggcagGGAAATGTGGGACTTATCTTCACCAAAGGTGATCTCAAAGAAGTTCGCGAGGAAGTCGCGAAGTACAAG
                                           ttgctctt  CT-rich tract
        agaattttttttctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaggagaattttttttcttgagagaaagcttgcgatggttgctcttggcagGGAAATGTGGGACTTATCTTCACCAAAGGTGATCTCAAAGAAGTTCGCGAGGAAGTCGCGAAGTACAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT