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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCCCTTGAAAAGCAGAGCTGCCAAGGCAATCGGATTCATTGAGAAGATGATCGATTACTCCAAGGCAAACTCTCCCCTGCAAAGAGATCTCGAAGCTGgtgcgttaaaaactttggcttggcttgcttggtttgcttacttcgctatatactcttttcgcacag

Basic information

species Selaginella moellendorffii
transcript EFJ10940
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ10940 (Selaginella moellendorffii), 5'ss of exon 10
lower sequence: LOC_Os08g23810.1 (Oryza sativa), 5'ss of exon 12
GTCCCTTGAAAAGCAGAGCTGCCAAGGCAATCGGATTCATTGAGAAGATGATCGATTACTCCAAGGCAAACTCTCCCCTGCAAAGAGATCTCGAAGCTGgtgcgttaaaaactttggcttggcttgcttggtttgcttacttcgctatatact----cttttcgcacag------------------------------------
|||| |||  |||| |||||||||||||||| |||||||||||||||||||| || |||||  | |  ||  | ||  |||| | ||| ||    || ||| |   |    |||     |   || | |    | |||  ||   |  | |      ||||||   |||                                    
GTCCTTTGGGAAGCCGAGCTGCCAAGGCAATTGGATTCATTGAGAAGATGATAGAATACTCTTATGTTAATGCACCGTTGCAGAAAGAACTGTTGGCAGgtccaaaaccgccttatttctctgttacatatgcttcttgttttatttaaaagaacaacttttcatccagatatactctaacgaaagcattttgtatgtcgaacag

upper sequence: EFJ10940 (Selaginella moellendorffii), 5'ss of exon 10
lower sequence: GRMZM2G070422_T03 (Zea mays), 5'ss of exon 11
GTCCCTTGAAAAGCAGAGCTGCCAAGGCAATCGGATTCATTGAGAAGATGATCGATTACTCCAAGGCAAACTCTCCCCTGCAAAGAGATCTCGAAGCTGgt--gcgttaaaaactttggcttggcttgct-tggtttgct----tacttcgctatata------------ctcttttcgcacag----------------------------------------
| ||  |    ||| ||||||| |||||||| ||||| |||||||||||||| || |||||  | |  ||  | ||  |||| |  || ||    ||||||  | |||   |    |  ||| | |   | ||  |||||     |   | |||| |             || |||   |||||                                        
GCCCTCTTGGGAGCCGAGCTGCTAAGGCAATTGGATTTATTGAGAAGATGATAGAGTACTCATATGTTAATGCACCATTGCAGAAGGAGCTGTTGGCTGgtcagagttttgactcctccctttgttacttgtgacttgctgtttcatccccctatttgaaaggtggcaacctttttcttcacagtgctctcttttttcttaacaagtatgctcttgttgaacag
















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|169109266|gb|FE514068.1|FE514068
EST:     GATCGATTACTCCAAGGCAAACTCTCCCCTGCAAAGAGATCTCGAAGCTG                         ATGATATTGGAAACGCAGCCACTTTCCTCGCCTCGCCACTTGCGTCGGCCA
genomic: GATCGATTACTCCAAGGCAAACTCTCCCCTGCAAAGAGATCTCGAAGCTGgtgcgttaaa ... tttcgcacagATGATATTGGAAACGCAGCCACTTTCCTCGCCTCGCCACTTGCGTCGGCCA
EST: gi|169029497|gb|FE438897.1|FE438897
EST:     GATCGATTACTCCAAGGCAAATTCTCCCCTGCAAAGAGATCTCGAAGCTG                         ATGATATTGGAAACGCAGCCACTTTCCTCGCCTCGCCACTGGCGTCGGCCA
genomic: GATCGATTACTCCAAGGCAAACTCTCCCCTGCAAAGAGATCTCGAAGCTGgtgcgttaaa ... tttcgcacagATGATATTGGAAACGCAGCCACTTTCCTCGCCTCGCCACTTGCGTCGGCCA
EST: gi|169041054|gb|FE450354.1|FE450354
EST:     GATCGATTACTCCAAGGCAAATTCTCCCCTGCAAAGAGATCTCGAAGCTG                         ATGATATTGGAAACGCAGCCACTTTCCTCGCCTCGCCACTGGCGTCGGCCA
genomic: GATCGATTACTCCAAGGCAAACTCTCCCCTGCAAAGAGATCTCGAAGCTGgtgcgttaaa ... tttcgcacagATGATATTGGAAACGCAGCCACTTTCCTCGCCTCGCCACTTGCGTCGGCCA
EST: gi|169024460|gb|FE434385.1|FE434385
EST:     GATCGATTACTCCAAGGCAAATTCTCCCCTGCAAAGAGATCTCGAAGCTG                         ATGATATTGGAAACGCAGCCACTTTCCTCGCCTCGCCACTGGCGTCGGCCA
genomic: GATCGATTACTCCAAGGCAAACTCTCCCCTGCAAAGAGATCTCGAAGCTGgtgcgttaaa ... tttcgcacagATGATATTGGAAACGCAGCCACTTTCCTCGCCTCGCCACTTGCGTCGGCCA
EST: gi|169106433|gb|FE507445.1|FE507445
EST:     GATCGATTACTCCAAGGCAAACTCTCCCCTGCAAAGAGATCTCGAAGCTG                         ATGATATTGGAAACGCAGCCACTTTCCTCGCCTCGCCACTTGCGTCGGCCA
genomic: GATCGATTACTCCAAGGCAAACTCTCCCCTGCAAAGAGATCTCGAAGCTGgtgcgttaaa ... tttcgcacagATGATATTGGAAACGCAGCCACTTTCCTCGCCTCGCCACTTGCGTCGGCCA
EST: gi|169069401|gb|FE480524.1|FE480524
EST:     GATCGATTACTCCAAGGCAAATTCTCCCCTGCAAAGAGATCTCGAAGCTG                         ATGATATTGGAAACGCAGCCACTTTCCTCGCCTCGCCACTGGCGTCGGCCA
genomic: GATCGATTACTCCAAGGCAAACTCTCCCCTGCAAAGAGATCTCGAAGCTGgtgcgttaaa ... tttcgcacagATGATATTGGAAACGCAGCCACTTTCCTCGCCTCGCCACTTGCGTCGGCCA
EST: gi|169083532|gb|FE495876.1|FE495876
EST:     GATCGATTACTCCAAGGCAAACTCTCCCCTGCAAAGAGATCTCGAAGCTG                         ATGATATTGGAAACGCAGCCACTTTCCTCGCCTCGCCACTTGCGTCGGCCA
genomic: GATCGATTACTCCAAGGCAAACTCTCCCCTGCAAAGAGATCTCGAAGCTGgtgcgttaaa ... tttcgcacagATGATATTGGAAACGCAGCCACTTTCCTCGCCTCGCCACTTGCGTCGGCCA
EST: gi|169069400|gb|FE480523.1|FE480523
EST:     GATCGATTACTCCAAGGCAAATTCTCCCCTGCAAAGAGATCTCGAAGCTG                         ATGATATTGGAAACGCAGCCACTTTCCTCGCCTCGCCACTGGCGTCGGCCA
genomic: GATCGATTACTCCAAGGCAAACTCTCCCCTGCAAAGAGATCTCGAAGCTGgtgcgttaaa ... tttcgcacagATGATATTGGAAACGCAGCCACTTTCCTCGCCTCGCCACTTGCGTCGGCCA
EST: gi|169035072|gb|FE444881.1|FE444881
EST:     GATCGATTACTCCAAGGCAAATTCTCCCCTGCAAAGAGATCTCGAAGCTG                         ATGATATTGGAAACGCAGCCACTTTCCTCGCCTCGCCACTGGCGTCGGCCA
genomic: GATCGATTACTCCAAGGCAAACTCTCCCCTGCAAAGAGATCTCGAAGCTGgtgcgttaaa ... tttcgcacagATGATATTGGAAACGCAGCCACTTTCCTCGCCTCGCCACTTGCGTCGGCCA
EST: gi|169113335|gb|FE515286.1|FE515286
EST:     GATCGATTACTCCAAGGCAAACTCTCCCCTGCAAAGAGATCTCGAAGCTG                         ATGATATTGGAAACGCAGCCACTTTCCTCGCCTCGCCACTTGCGTCGGCCA
genomic: GATCGATTACTCCAAGGCAAACTCTCCCCTGCAAAGAGATCTCGAAGCTGgtgcgttaaa ... tttcgcacagATGATATTGGAAACGCAGCCACTTTCCTCGCCTCGCCACTTGCGTCGGCCA

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: 31 (upstream exon), 33 (downstream exon)
Score: 21

GTCCCTTGAAAAGCAGAGCTGCCAAGGCAATCGGATTCATTGAGAAGATGATCGATTACTCCAAGGCAAACTCTCCCCTGCAAAGAGATCTCGAAGCTGgtgcgttaaa ... tttcgcacagATGATATTGGAAACGCAGCCACTTTCCTCGCCTCGCCACTTGCGTCGGCCATCTCCGGAACCGTGTTCTACGTAGACAATGGGCTTCACACAATGGGAAT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTCCCTTGAAAAGCAGAGCTGCCAAGGCAATCGGATTCATTGAGAAGATGATCGATTACTCCAAGGCAAACTCTCCCCTGCAAAGAGATCTCGAAGCTGgtgcgttaaaaactttggcttggcttgcttggtttgcttacttcgctatatactcttttcgcacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG