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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGAGGGATTCTATGAACATTATGATCCGAACTTTATTTCAATCCGAACAAAAGCACGTGAAGTGCTACAAAGAGAAGACGATCTAAACGAGATTGTTCAGgtacgtgaactggtgagagattcaaagtcagtattttcttttcacag

Basic information

species Selaginella moellendorffii
transcript EFJ30330
intron # 16
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ30330 (Selaginella moellendorffii), 5'ss of exon 16
lower sequence: LOC_Os06g45120.1 (Oryza sativa), 5'ss of exon 15
GGAGGGATTCTATGAACATTATGATCCGAACTTTATTTCAATCCGAACAAAAGCACGTGAAGTGCTACAAAGAGAAGACGATCTAAACGAGATTGTTCAGgtacgtg-----aactggtgagag----attcaaagtcagtattttcttttcacag--------------------------------------------
|||    ||||||||  | | |||||   | || |||   ||  |||||||||| ||||||||| |||| ||||| ||||||||||| || ||||| ||||||  |      | || |||  ||    ||       |   ||||  |  |   ||                                            
GGAATCCTTCTATGAGAAGTTTGATCAAGATTTCATTGATATTAGAACAAAAGCTCGTGAAGTGTTACAGAGAGAGGACGATCTAAATGAAATTGTCCAGgtattttttttcaccttgtgcaaggatgatctgttccctagatttagtcgtagaagcaatagtttgaacttggaccacttaaacatggtgtttttgtttt
















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|169116507|gb|FE517532.1|FE517532
EST:     AAGCACGTGAAGTGCTACAAAGAGAAGACGATCTAAACGAGATTGTTCAG                         CTTGTCGGCAAAGATGCGCTGGCCGAGGGAGATAAGATTATTCTTGAGACG
genomic: AAGCACGTGAAGTGCTACAAAGAGAAGACGATCTAAACGAGATTGTTCAGgtacgtgaac ... cttttcacagCTTGTCGGCAAAGATGCGCTGGCCGAGGGAGATAAGATTATTCTTGAGACG
EST: gi|169094896|gb|FE491630.1|FE491630
EST:     AAGCACGTGAAGTGCTACAAAGAGAAGACGATCTAAACGAGATTGTTCAG                         CTTGTCGGCAAAGATGCGCTGGCCGAGGGAGATAAGATTATTCTTGAGACG
genomic: AAGCACGTGAAGTGCTACAAAGAGAAGACGATCTAAACGAGATTGTTCAGgtacgtgaac ... cttttcacagCTTGTCGGCAAAGATGCGCTGGCCGAGGGAGATAAGATTATTCTTGAGACG
EST: gi|169105223|gb|FE504895.1|FE504895
EST:     AAGCACGTGAAGTGCTACAAAGAGAAGACGATCTAAACGAGATTGTTCAG                         CTTGTCGGCAAAGATGCGCTGGCCGAGGGAGATAAGATTATTCTTGAGACG
genomic: AAGCACGTGAAGTGCTACAAAGAGAAGACGATCTAAACGAGATTGTTCAGgtacgtgaac ... cttttcacagCTTGTCGGCAAAGATGCGCTGGCCGAGGGAGATAAGATTATTCTTGAGACG
EST: gi|169034854|gb|FE444043.1|FE444043
EST:     AAGCACGTGAAGTGCTACAAAGAGAAGACGATCTAAACGAGATTGTTCAG                         CTTGTCGGCAAAGATGCGCTGGCCGAGGGAGATAAGATTATTCTTGAGACG
genomic: AAGCACGTGAAGTGCTACAAAGAGAAGACGATCTAAACGAGATTGTTCAGgtacgtgaac ... cttttcacagCTTGTCGGCAAAGATGCGCTGGCCGAGGGAGATAAGATTATTCTTGAGACG
EST: gi|169075917|gb|FE482836.1|FE482836
EST:     AAGCACGTGAAGTGCTACAAAGAGAAGACGATCTAAACGAGATTGTTCAG                         CTTGTCGGCAAAGATGCGCTGGCCGAGGGAGATAAGATTATTCTTGAGACG
genomic: AAGCACGTGAAGTGCTACAAAGAGAAGACGATCTAAACGAGATTGTTCAGgtacgtgaac ... cttttcacagCTTGTCGGCAAAGATGCGCTGGCCGAGGGAGATAAGATTATTCTTGAGACG
EST: gi|169058960|gb|FE467728.1|FE467728
EST:     AAGCACGTGAAGTGCTACAAAGAGAAGACGATCTAAACGAGATTGTTCAG                         CTTGTCGGCAAAGATGCGCTGGCCGAGGGAGATAAGATTATTCTTGAGACG
genomic: AAGCACGTGAAGTGCTACAAAGAGAAGACGATCTAAACGAGATTGTTCAGgtacgtgaac ... cttttcacagCTTGTCGGCAAAGATGCGCTGGCCGAGGGAGATAAGATTATTCTTGAGACG
EST: gi|169116508|gb|FE517533.1|FE517533
EST:     AAGCACGTGAAGTGCTACAAAGAGAAGACGATCTAAACGAGATTGTTCAG                         CTTGTCGGCAAAGATGCGCTGGCCGAGGGAGATAAGATTATTCTTGAGACG
genomic: AAGCACGTGAAGTGCTACAAAGAGAAGACGATCTAAACGAGATTGTTCAGgtacgtgaac ... cttttcacagCTTGTCGGCAAAGATGCGCTGGCCGAGGGAGATAAGATTATTCTTGAGACG
EST: gi|169055454|gb|FE465852.1|FE465852
EST:     AAGCACGTGAAGTGCTACAAAGAGAAGACGATCTAAACGAGATTGTTCAG                         CTTGTCGGCAAAGATGCGCTGGCCGAGGGAGATAAGATTATTCTTGAGACG
genomic: AAGCACGTGAAGTGCTACAAAGAGAAGACGATCTAAACGAGATTGTTCAGgtacgtgaac ... cttttcacagCTTGTCGGCAAAGATGCGCTGGCCGAGGGAGATAAGATTATTCTTGAGACG
EST: gi|169074665|gb|FE480895.1|FE480895
EST:     AAGCACGTGAAGTGCTACAAAGAGAAGACGATCTAAACGAGATTGTTCAG                         CTTGTCGGCAAAGATGCGCTGGCCGAGGGAGATAAGATTATTCTTGAGACG
genomic: AAGCACGTGAAGTGCTACAAAGAGAAGACGATCTAAACGAGATTGTTCAGgtacgtgaac ... cttttcacagCTTGTCGGCAAAGATGCGCTGGCCGAGGGAGATAAGATTATTCTTGAGACG
EST: gi|169026429|gb|FE434742.1|FE434742
EST:     CGATCTAAAACGAGATT-TTCAG                         CTTGTCGGCAAAGATGCGCTGGCCGAGGGAGATAAGATTATTCTTGAGACG
genomic: CGATCT-AAACGAGATTGTTCAGgtacgtgaac ... cttttcacagCTTGTCGGCAAAGATGCGCTGGCCGAGGGAGATAAGATTATTCTTGAGACG
EST: gi|169026425|gb|FE435778.1|FE435778
EST:     AAGCACGTGAAGTGCTACAAAGAGAAGACGATCTAAACGAGATTGTTCAG                         CTTGTCGGCAAAGATGCGCTGGCCGAGGGAGATAAGATTATTCTTGAGACG
genomic: AAGCACGTGAAGTGCTACAAAGAGAAGACGATCTAAACGAGATTGTTCAGgtacgtgaac ... cttttcacagCTTGTCGGCAAAGATGCGCTGGCCGAGGGAGATAAGATTATTCTTGAGACG
EST: gi|169083647|gb|FE495380.1|FE495380
EST:     AAGCACGTGAAGTGCTACAAAGAGAAGACGATCTAAACGAGATTGTTCAG                         CTTGTCGGCAAAGATGCGCTGGCCGAGGGAGATAAGATTATTCTTGAGACG
genomic: AAGCACGTGAAGTGCTACAAAGAGAAGACGATCTAAACGAGATTGTTCAGgtacgtgaac ... cttttcacagCTTGTCGGCAAAGATGCGCTGGCCGAGGGAGATAAGATTATTCTTGAGACG
EST: gi|169038845|gb|FE446988.1|FE446988
EST:     AAGCACGTGAAGTGCTACAAAGAGAAGACGATCTAAACGAGATTGTTCAG                         CTTGTCGGCAAAGATGCGCTGGCCGAGGGAGATAAGATTATTCTTGAGACG
genomic: AAGCACGTGAAGTGCTACAAAGAGAAGACGATCTAAACGAGATTGTTCAGgtacgtgaac ... cttttcacagCTTGTCGGCAAAGATGCGCTGGCCGAGGGAGATAAGATTATTCTTGAGACG
EST: gi|169067637|gb|FE475314.1|FE475314
EST:     AAGCACGTGAAGTGCTACAAAGAGAAGACGATCTAAACGAGATTGTTCAG                         CTTGTCGGCAAAGATGCGCTGGCCGAGGGAGATAAGATTATTCTTGAGACG
genomic: AAGCACGTGAAGTGCTACAAAGAGAAGACGATCTAAACGAGATTGTTCAGgtacgtgaac ... cttttcacagCTTGTCGGCAAAGATGCGCTGGCCGAGGGAGATAAGATTATTCTTGAGACG
EST: gi|169047686|gb|FE454854.1|FE454854
EST:     AAGCACGTGAAGTGCTACAAAGAGAAGACGATCTAAACGAGATTGTTCAG                         CTTGTCGGCAAAGATGCGCTGGCCGAGGGAGATAAGATTATTCTTGAGACG
genomic: AAGCACGTGAAGTGCTACAAAGAGAAGACGATCTAAACGAGATTGTTCAGgtacgtgaac ... cttttcacagCTTGTCGGCAAAGATGCGCTGGCCGAGGGAGATAAGATTATTCTTGAGACG
EST: gi|169077658|gb|FE484920.1|FE484920
EST:     AAGCACGTGAAGTGCTACAAAGAGAAGACGATCTAAACGAGATTGTTCAG                         CTTGTCGGCAAAGATGCGCTGGCCGAGGGAGATAAGATTATTCTTGAGACG
genomic: AAGCACGTGAAGTGCTACAAAGAGAAGACGATCTAAACGAGATTGTTCAGgtacgtgaac ... cttttcacagCTTGTCGGCAAAGATGCGCTGGCCGAGGGAGATAAGATTATTCTTGAGACG
EST: gi|169045568|gb|FE452529.1|FE452529
EST:     AAGCACGTGAAGTGCTACAAAGAGAAGACGATCTAAACGAGATTGTTCAG                         CTTGTCGGCAAAGATGCGCTGGCCGAGGGAGATAAGATTATTCTTGAGACG
genomic: AAGCACGTGAAGTGCTACAAAGAGAAGACGATCTAAACGAGATTGTTCAGgtacgtgaac ... cttttcacagCTTGTCGGCAAAGATGCGCTGGCCGAGGGAGATAAGATTATTCTTGAGACG

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: 33 (upstream exon), 34 (downstream exon)
Score: 15

GGAGGGATTCTATGAACATTATGATCCGAACTTTATTTCAATCCGAACAAAAGCACGTGAAGTGCTACAAAGAGAAGACGATCTAAACGAGATTGTTCAGgtacgtgaac ... cttttcacagCTTGTCGGCAAAGATGCGCTGGCCGAGGGAGATAAGATTATTCTTGAGACGGCCAAGCTCTTGAGAGAGGATTATTTGGCGCAAAACGCTTTCAGTGT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGAGGGATTCTATGAACATTATGATCCGAACTTTATTTCAATCCGAACAAAAGCACGTGAAGTGCTACAAAGAGAAGACGATCTAAACGAGATTGTTCAGgtacgtgaactggtgagagattcaaagtcagtattttcttttcacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA