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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacatatgagtagatagcgattgcagctttaacctcaaagtaacgttatcacagATTTGCAACAAGCAAAAGGCAATCCTTCTAGCTGATATGGCTCATATAAGCGGACTTGTAGCTGCTGGTGTCGTGCCATCTCCATTCGACGTTGCAGACG

Basic information

species Selaginella moellendorffii
transcript EFJ32604
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ32604 (Selaginella moellendorffii), 3'ss of exon 8
lower sequence: GRMZM2G135283_T03 (Zea mays), 3'ss of exon 8
---------------------------------------------------------------------------gtacatatgagtagatagcga--ttgcagctttaacc--tcaaa-------gtaacgttatc-----acagATTTGCAACAAGCAAAAGGCAATCCTTCTAGCTGATATGGCTCATATAAGCGGACTTGTAGCTGCTGGTGTCGTGCCATCTCCATTCGACGTTGCAGACG
                                                                            |||| |  | |  |  ||||  ||     ||| | |  |||||        ||| |||||      |||||| ||||||||||| |||||||| |||||||| || ||||| ||||| || || ||||| || |||||||| || |||||||| || ||   |||||| |
gcaaggtttctttccacgatagtattttttctccaagatgcaagggagctgcacattattatattacagagaactatacagaacattgaaccgcgatctttttttttttatcaatcaaataattccataatgttatgtgtcgacagATATGCAACAAGCAGAAGGCAATACTTCTAGCAGACATGGCACATATTAGTGGGCTTGTTGCAGCTGGTGTTGTTCCATCTCCTTTTGATTATGCAGATG
















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|169115018|gb|FE516383.1|FE516383
EST:     CTGGAGCCAGCGCCTACTCTCGGCATTATGATTATGCACGAATGCGTCAG                         ATTTGCAACAAGCAAAAGGCAATCCTTCTAGCTGATATGGCTCATATAAGC
genomic: CCGGAGCCAGCGCCTACTCTCGGCATTATGATTATGCACGAATGCGTCAGgtacatatga ... gttatcacagATTTGCAACAAGCAAAAGGCAATCCTTCTAGCTGATATGGCTCATATAAGC
EST: gi|169070247|gb|FE478068.1|FE478068
EST:     CACGAATGCGTCAG                         ATTTGCAACAAGCAAAAGGCAATCCTTCTAGCTGATATGGCTCATATAAGC
genomic: CACGAATGCGTCAGgtacatatga ... gttatcacagATTTGCAACAAGCAAAAGGCAATCCTTCTAGCTGATATGGCTCATATAAGC
EST: gi|169051134|gb|FE458681.1|FE458681
EST:     CCGGAGCCAGCGCCTACTCTCGGCATTATGATTATGCACGAATGCGTCAG                         ATTTTGCA-CAAGCAAAAGGCAATCCTTCTAGCTGATATGG
genomic: CCGGAGCCAGCGCCTACTCTCGGCATTATGATTATGCACGAATGCGTCAGgtacatatga ... gttatcacagATTT-GCAACAAGCAAAAGGCAATCCTTCTAGCTGATATGG
EST: gi|169048578|gb|FE454447.1|FE454447
EST:     CTGGAGCCAGCGCCTACTCTCGGCATTATGATTATGCACGAATGCGTCAG                         ATTTGCAACAAGCAAAAGGCAATCCTTCTAGCTGATATGGCTCATATAAGC
genomic: CCGGAGCCAGCGCCTACTCTCGGCATTATGATTATGCACGAATGCGTCAGgtacatatga ... gttatcacagATTTGCAACAAGCAAAAGGCAATCCTTCTAGCTGATATGGCTCATATAAGC
EST: gi|169019270|gb|FE428183.1|FE428183
EST:     CCGGAGCCAGCGCCTACTCTCGGCATTATGATTATGCACGAATGCGTCAG                         ATTTGCAACAAGCAAAAGGCAATCCTTCTAGCTGATATGGCTCATATAAGC
genomic: CCGGAGCCAGCGCCTACTCTCGGCATTATGATTATGCACGAATGCGTCAGgtacatatga ... gttatcacagATTTGCAACAAGCAAAAGGCAATCCTTCTAGCTGATATGGCTCATATAAGC
EST: gi|169087154|gb|FE493101.1|FE493101
EST:     CCGGAGCCAGCGCCTACTCTCGGCATTATGATTATGCACGAATGCGTCAG                         ATTTGCAACAAGCAAAAGGCAATCCTTCTAGCTGATATGGCTCATATAAGC
genomic: CCGGAGCCAGCGCCTACTCTCGGCATTATGATTATGCACGAATGCGTCAGgtacatatga ... gttatcacagATTTGCAACAAGCAAAAGGCAATCCTTCTAGCTGATATGGCTCATATAAGC
EST: gi|169098871|gb|FE502268.1|FE502268
EST:     CTGGAGCCAGCGCCTACTCTCGGCATTATGATTATGCACGAATGCGTCAG                         ATTTGCAACAAGCAAAAGGCAATCCTTCTAGCTGATATGGCTCATATAAGC
genomic: CCGGAGCCAGCGCCTACTCTCGGCATTATGATTATGCACGAATGCGTCAGgtacatatga ... gttatcacagATTTGCAACAAGCAAAAGGCAATCCTTCTAGCTGATATGGCTCATATAAGC
EST: gi|169080654|gb|FE487175.1|FE487175
EST:     CTGGAGCCAGCGCCTACTCTCGGCATTATGATTATGCACGAATGCGTCAG                         ATTTNNGCA-CA-GCAAAAGGCAATCCTTCTAGCTGATATGGCTCA
genomic: CCGGAGCCAGCGCCTACTCTCGGCATTATGATTATGCACGAATGCGTCAGgtacatatga ... gttatcacagATTT--GCAACAAGCAAAAGGCAATCCTTCTAGCTGATATGGCTCA
EST: gi|169113402|gb|FE514729.1|FE514729
EST:     CTGGAGCCAGCGCCTACTCTCGGCATTATGATTATGCACGAATGCGTCAG                         ATTTGCAACAAGCAAAAGGCAATCCTTCTAGCTGATATGGCTCATATAAGC
genomic: CCGGAGCCAGCGCCTACTCTCGGCATTATGATTATGCACGAATGCGTCAGgtacatatga ... gttatcacagATTTGCAACAAGCAAAAGGCAATCCTTCTAGCTGATATGGCTCATATAAGC
EST: gi|169113160|gb|FE514406.1|FE514406
EST:     CACGAATGCGTCAG                         ATTTGCAACAAGCAAAAGGCAATCCTTCTAGCTGATATGGCTCATATAAGC
genomic: CACGAATGCGTCAGgtacatatga ... gttatcacagATTTGCAACAAGCAAAAGGCAATCCTTCTAGCTGATATGGCTCATATAAGC
EST: gi|169030300|gb|FE440025.1|FE440025
EST:     CCGGAGCCAGCGCCTACTCTCGGCATTATGATTATGCACGAATGCGTCAG                         ATTTGCAACAAGC
genomic: CCGGAGCCAGCGCCTACTCTCGGCATTATGATTATGCACGAATGCGTCAGgtacatatga ... gttatcacagATTTGCAACAAGC
EST: gi|169035576|gb|FE445346.1|FE445346
EST:     CTGGAGCCAGCGCCTACTCTCGGCATTATGATTATGCACGAATGCGTCAG                         ATTTGCAACAAGCAAAAGGCAATCCTTCTAGCTGATATGGCTCA
genomic: CCGGAGCCAGCGCCTACTCTCGGCATTATGATTATGCACGAATGCGTCAGgtacatatga ... gttatcacagATTTGCAACAAGCAAAAGGCAATCCTTCTAGCTGATATGGCTCA
EST: gi|169019686|gb|FE427489.1|FE427489
EST:     CACGAATGCGTCAG                         ATTTGCAACAAGCAAAAGGCAATCCTTCTAGCTGATATGGCTCATATAAGC
genomic: CACGAATGCGTCAGgtacatatga ... gttatcacagATTTGCAACAAGCAAAAGGCAATCCTTCTAGCTGATATGGCTCATATAAGC
EST: gi|169044083|gb|FE451669.1|FE451669
EST:     CCGGAGCCAGCGCCTACTCTCGGCATTATGATTATGCACGAATGCGTCAG                         ATTTGCAACAAGCAAAAGGCAATCCTTCTAGCTGATATGGCTCATATAAGC
genomic: CCGGAGCCAGCGCCTACTCTCGGCATTATGATTATGCACGAATGCGTCAGgtacatatga ... gttatcacagATTTGCAACAAGCAAAAGGCAATCCTTCTAGCTGATATGGCTCATATAAGC

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), 34 (downstream exon)
Score: 47

CTTGAAAAAAGCGCGACACTCTTCCGGCCAAAACTCATCGTGGCCGGAGCCAGCGCCTACTCTCGGCATTATGATTATGCACGAATGCGTCAGgtacatatga ... gttatcacagATTTGCAACAAGCAAAAGGCAATCCTTCTAGCTGATATGGCTCATATAAGCGGACTTGTAGCTGCTGGTGTCGTGCCATCTCCATTCGACGTTGCAGACG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtacatatgagtagatagcgattgcagctttaacctcaaagtaacgttatcacagATTTGCAACAAGCAAAAGGCAATCCTTCTAGCTGATATGGCTCATATAAGCGGACTTGTAGCTGCTGGTGTCGTGCCATCTCCATTCGACGTTGCAGACG
                                      aagtaac  putative branch site (score: 47)
                                     aaagtaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacatatgagtagatagcgattgcagctttaacctcaaagtaacgttatcacagATTTGCAACAAGCAAAAGGCAATCCTTCTAGCTGATATGGCTCATATAAGCGGACTTGTAGCTGCTGGTGTCGTGCCATCTCCATTCGACGTTGCAGACG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT