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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTTATGCAAACTATGCCATTGGCAAAGACGTTCAAGCGATGAAAGCTGTCGTGGGAGAAGAAGCGCTGTCATCTGAAGATCTGgtaaagcaccagttttgctttttgatgccagtatgttaaccaactgtgttccttccctgcag

Basic information

species Selaginella moellendorffii
transcript EFJ11911
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ11911 (Selaginella moellendorffii), 5'ss of exon 13
lower sequence: LOC_Os01g51380.2 (Oryza sativa), 5'ss of exon 14
CTTTATGCAAACTATGCCATTGGCAAAGACGTTCAAGCGATGAAAGCTGTCGTGGGAGAAGAAGCGCTGTCATCTGAAGATCTGgtaaagcaccagttttgcttt---ttgatgccagtatgttaaccaactgtgttccttccctgcag--------------------------------
|| ||||| || || ||||| ||||| ||||| || |||||||| || || || ||||| |||||||||||||| || || |||||||  | |  |  |  | |    ||| |     ||   |    || | | ||   |     |                                  
CTGTATGCCAATTACGCCATAGGCAAGGACGTACAGGCGATGAAGGCAGTGGTTGGAGAGGAAGCGCTGTCATCAGAGGACCTGgtaaccctcatgcatgacctgacattgttattcttaaactccttaattattttaagttttaacctcctaatcaactgatctatgaaaaaaatgacag

upper sequence: EFJ11911 (Selaginella moellendorffii), 5'ss of exon 13
lower sequence: GLYMA09G38110.1 (Glycine max), 5'ss of exon 14
CTTTATGCAAACTATGCCATTGGCAAAGACGTTCAAGCGATGAAAGCTGTCGTGGGAGAAGAAGCGCTGTCATCTGAAGATCTGgtaaagcaccagttttgctttttgatgccagtatgttaaccaactgtgttccttccctgcag--------------------------------------
|| |||||||| ||||||||||| || || || || || ||||||||||| || ||||||||||| || |||||||| || |||||     || | |||| || || |       | | | |      ||||||  | || || ||                                      
CTCTATGCAAATTATGCCATTGGAAAGGATGTCCAGGCAATGAAAGCTGTGGTCGGAGAAGAAGCACTTTCATCTGAGGACCTGgtctc-tactactttt-ctcttgggaattcttgtttgagtatggtgtgtttgt-ccttgaagtggtggtactaattaattttattctttttgatcaacag

upper sequence: EFJ11911 (Selaginella moellendorffii), 5'ss of exon 13
lower sequence: GLYMA18G48280.1 (Glycine max), 5'ss of exon 14
CTTTATGCAAACTATGCCATTGGCAAAGACGTTCAAGCGATGAAAGCTGTCGTGGGAGAAGAAGCGCTGTCATCTGAAGATCTGgtaaagcaccagttttgctttttgatgccagtatgttaaccaactgtgttccttccctgcag---------------------------------------
 | |||||||| ||||||||||| || || || || || |||||||| || || ||||||||||| || |||||||| || |||||     || | |||| || || |       | | | |    | || | |  | || || ||                                       
-TCTATGCAAATTATGCCATTGGAAAGGATGTCCAGGCAATGAAAGCCGTGGTCGGAGAAGAAGCACTTTCATCTGAGGACCTGGtctc-tactactttt-ctcttgggaattcttgtttgagtgtagtgagattgt-ccttgaagtggtggtactaattaagtttattctttatgatcaacagc

upper sequence: EFJ11911 (Selaginella moellendorffii), 5'ss of exon 13
lower sequence: AT1G20260.1 (Arabidopsis thaliana), 5'ss of exon 14
CTTTATGCAAACTATGCCATTGGCAAAGACGTTCAAGCGATGAAAGCTGTCGTGGGAGAAGAAGCGCTGTCATCTGAAGATCTGgtaaagc-----------accagt-tttgctttttgatgccagta-tgt-taaccaactgtgttccttccctgcag-----------------------
|| || ||||| ||||| || || ||||| |||||||| ||||||||||| || ||||||||||| ||||| || || |||||||||   |           |||| | || |  ||   ||     || ||| ||  ||||  |  |   || |  ||                        
CTATACGCAAATTATGCAATCGGAAAAGATGTTCAAGCCATGAAAGCTGTTGTTGGAGAAGAAGCTCTGTCTTCCGAGGATCTGgtacctctctctgacttcaccaatattcgtgttcctatcaagatactgtatatgcaacaataattactcacaacaatttattgtgttgtgtgtttgtag

upper sequence: EFJ11911 (Selaginella moellendorffii), 5'ss of exon 13
lower sequence: Vv03s0038g02760.t01 (Vitis vinifera), 5'ss of exon 14
CTTTATGCAAACTATGCCATTGGCAAAGACGTTCAAGCGATGAAAGCTGTCGTGGGAGAAGAAGCGCTGTCATCTGAAGATCTGgtaaagcaccagttttgctttttgatgccagtatgttaacc-aactgtgttccttccctgcag---------------------------------------
|| |||||||| ||||| ||||| || || |||||||| ||||||||||| || ||||||||||| || || ||||| ||||||||| |       | |  || ||  |    |  || | | |  || ||  | |||    |                                           
CTCTATGCAAATTATGCAATTGGGAAGGATGTTCAAGCAATGAAAGCTGTGGTTGGAGAAGAAGCACTTTCTTCTGAGGATCTGgtaca-------tctcactcttataaattatcatttcatctgaaatgaatccctattgtaagaaaacaactaacaggttgtccgacccttcactggaaacag

upper sequence: EFJ11911 (Selaginella moellendorffii), 5'ss of exon 13
lower sequence: PP1S100_117V6.1 (Physcomitrella patens), 5'ss of exon 14
CTTTATGCAAACTATGCCATTGGCAAAGACGTTCAAGCGATGAAAGCTGTCGTGGGAGAAGAAGCGCTGTCATCTGAAGATCTGgtaaagcaccagttttgctttttgatgccagtatg-------ttaaccaactgt-gttccttccctgcag-----------------------------------------------------------------------
 | ||||| || ||||||||||| || || |||||||| ||||| |||||||| ||||| |||||  |||| || ||||||||||||          |   | | |   ||| || |         ||   ||| | |  ||   ||| ||| |                                                                       
TTGTATGCTAATTATGCCATTGGAAAGGATGTTCAAGCAATGAAGGCTGTCGTTGGAGAGGAAGCTTTGTCTTCAGAAGATCTGgtaccctcgtgaatactcctgtgactgcaagcagaactcaatttgttcaatttttatttaatccatgccgctcatttccgtgcatactccgctatgtcaactctatttgttgcttacatcctcacttgttttgttttccag

upper sequence: EFJ11911 (Selaginella moellendorffii), 5'ss of exon 13
lower sequence: PP1S425_12V6.1 (Physcomitrella patens), 5'ss of exon 13
CTTTATGCAAACTATGCCATTGGCAAAGACGTTCAAGCGATGAAAGCTGTCGTGGGAGAAGAAGCGCTGTCATCTGAAGATCTGgtaaagcaccagttttgctt-tttgatgc-cagtatgttaaccaactgtgttccttccctgcag---------------------------------------------------------------------------------------
 | || ||||||||||| ||||| || || || ||||| ||||| ||||| ||||||||||||||  |||| || || |||||||||     |   || |  ||    | | | ||||  |  | || ||  ||     ||| |                                                                                           
TTGTACGCAAACTATGCGATTGGAAAGGATGTACAAGCCATGAAGGCTGTGGTGGGAGAAGAAGCCTTGTCTTCAGAGGATCTGgtatccatctcattctatttgcccgttacgcagtg-gacatcctacaatgaaatctccatatgttgatggttttgaacattatctctagtacgttatctctggtctgaagcttttcactccctaatgacactctcaaccggctctatgcag

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|169108145|gb|FE512518.1|FE512518
EST:     AAGCGATGAAAGCTGTCGTGGGAGAAGAAGCGCTGTCATCTGAAGATCTG                         CTGTACTTGGAATTCTTAGACAAATTCGAGAAAAAATTTGTCAGTCAAAGC
genomic: AAGCGATGAAAGCTGTCGTGGGAGAAGAAGCGCTGTCATCTGAAGATCTGgtaaagcacc ... ttccctgcagCTGTACTTGGAATTCTTAGACAAATTCGAGAAAAAATTTGTCAGTCAAAGC
EST: gi|169093628|gb|FE492360.1|FE492360
EST:     AAGCGATGAAAGCTGTCGTGGGAGAAGAAGCGCTGTCATCTGAAGATCTG                         CTGTACTTGGAATTCTTAGACAAATTCGAGAAAAAATTTGTCAGTCAAAGC
genomic: AAGCGATGAAAGCTGTCGTGGGAGAAGAAGCGCTGTCATCTGAAGATCTGgtaaagcacc ... ttccctgcagCTGTACTTGGAATTCTTAGACAAATTCGAGAAAAAATTTGTCAGTCAAAGC
EST: gi|169057425|gb|FE465729.1|FE465729
EST:     AAGCGATGAAAGCTGTCGTGGGAGAAGAAGCGCTGTCATCTGAAGATCTG                         CTGTACTTGGAGTTCTTAGACAAATTCGAGAGAAAATTTGTCAGTCAAAGC
genomic: AAGCGATGAAAGCTGTCGTGGGAGAAGAAGCGCTGTCATCTGAAGATCTGgtaaagcacc ... ttccctgcagCTGTACTTGGAATTCTTAGACAAATTCGAGAAAAAATTTGTCAGTCAAAGC
EST: gi|169049332|gb|FE458243.1|FE458243
EST:     AAGCGATGAAAGCTGTCGTGGGAGAAGAAGCGCTGTCATCTGAAGATCTG                         CTGTACTTGGAGTTCTTAGACAAATTCGAGAGAAAATTTGTCAGTCAAAGC
genomic: AAGCGATGAAAGCTGTCGTGGGAGAAGAAGCGCTGTCATCTGAAGATCTGgtaaagcacc ... ttccctgcagCTGTACTTGGAATTCTTAGACAAATTCGAGAAAAAATTTGTCAGTCAAAGC
EST: gi|169031673|gb|FE437474.1|FE437474
EST:     AAGCGATGAAAGCTGTCGTGGGAGAAGAAGCGCTGTCATCTGAAGATCTG                         CTGTACTTGGAATTCTTAGACAAATTCGAGAAAAAATTTGTCAGTCAAAGC
genomic: AAGCGATGAAAGCTGTCGTGGGAGAAGAAGCGCTGTCATCTGAAGATCTGgtaaagcacc ... ttccctgcagCTGTACTTGGAATTCTTAGACAAATTCGAGAAAAAATTTGTCAGTCAAAGC
EST: gi|169035380|gb|FE444318.1|FE444318
EST:     AAGCGATGAAAGCTGTCGTGGGAGAAGAAGCGCTGTCATCTGAAGATCTG                         CTGTACTTGGAATTCTTAGACAAATTCGAGAAAAAATTTGTCAGTCAAAGC
genomic: AAGCGATGAAAGCTGTCGTGGGAGAAGAAGCGCTGTCATCTGAAGATCTGgtaaagcacc ... ttccctgcagCTGTACTTGGAATTCTTAGACAAATTCGAGAAAAAATTTGTCAGTCAAAGC
EST: gi|169092668|gb|FE496262.1|FE496262
EST:     AAGCGATGAAAGCTGTCGTGGGAGAAGAAGCGCTGTCATCTGAAGATCTG                         CTGTACTTGGAATTCTTAGACAAATTCGAGAAAAAATTTGTCAGTCAAAGC
genomic: AAGCGATGAAAGCTGTCGTGGGAGAAGAAGCGCTGTCATCTGAAGATCTGgtaaagcacc ... ttccctgcagCTGTACTTGGAATTCTTAGACAAATTCGAGAAAAAATTTGTCAGTCAAAGC
EST: gi|169104893|gb|FE509037.1|FE509037
EST:     AAGCGATGAAAGCTGTCGTGGGAGAAGAAGCGCTGTCATCTGAAGATCTG                         CTGTACTTGGAATTCTTAGACAAATTCGAGAAAAAATTTGTCAGTCAAAGC
genomic: AAGCGATGAAAGCTGTCGTGGGAGAAGAAGCGCTGTCATCTGAAGATCTGgtaaagcacc ... ttccctgcagCTGTACTTGGAATTCTTAGACAAATTCGAGAAAAAATTTGTCAGTCAAAGC
EST: gi|169088664|gb|FE491524.1|FE491524
EST:     AAGCGATGAAAGCTGTCGTGGGAGAAGAAGCGCTGTCATCTGAAGATCTG                         CTGTACTTGGAGTTCTTAGACAAATTCGAGAGAAAATTTGTCAGTCAAAGC
genomic: AAGCGATGAAAGCTGTCGTGGGAGAAGAAGCGCTGTCATCTGAAGATCTGgtaaagcacc ... ttccctgcagCTGTACTTGGAATTCTTAGACAAATTCGAGAAAAAATTTGTCAGTCAAAGC
EST: gi|169114882|gb|FE515831.1|FE515831
EST:     AAGCGATGAAAGCTGTCGTGGGAGAAGAAGCGCTGTCATCTGAAGATCTG                         CTGTACTTGGAATTCTTAGACAAATTCGAGAAAAAATTTGTCAGTCAAAGC
genomic: AAGCGATGAAAGCTGTCGTGGGAGAAGAAGCGCTGTCATCTGAAGATCTGgtaaagcacc ... ttccctgcagCTGTACTTGGAATTCTTAGACAAATTCGAGAAAAAATTTGTCAGTCAAAGC
EST: gi|169028054|gb|FE435932.1|FE435932
EST:     AAGCGATGAAAGCTGTCGTGGGAGAAGAAGCGCTGTCATCTGAAGATCTG                         CTGTACTTGGAGTTCTTAGACAAATTCGAGAGAAAATTTGTCAGTCAAAGC
genomic: AAGCGATGAAAGCTGTCGTGGGAGAAGAAGCGCTGTCATCTGAAGATCTGgtaaagcacc ... ttccctgcagCTGTACTTGGAATTCTTAGACAAATTCGAGAAAAAATTTGTCAGTCAAAGC
EST: gi|169059084|gb|FE468229.1|FE468229
EST:     AAGCGATGAAAGCTGTCGTGGGAGAAGAAGCGCTGTCATTTGAAGATTTG                         CTGTACTTGGAATTTTTAGACAAATTCGAGAAAAAATTTGTCAGTCAAAGC
genomic: AAGCGATGAAAGCTGTCGTGGGAGAAGAAGCGCTGTCATCTGAAGATCTGgtaaagcacc ... ttccctgcagCTGTACTTGGAATTCTTAGACAAATTCGAGAAAAAATTTGTCAGTCAAAGC

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: 30 (upstream exon), 34 (downstream exon)
Score: 37

CTTTATGCAAACTATGCCATTGGCAAAGACGTTCAAGCGATGAAAGCTGTCGTGGGAGAAGAAGCGCTGTCATCTGAAGATCTGgtaaagcacc ... ttccctgcagCTGTACTTGGAATTCTTAGACAAATTCGAGAAAAAATTTGTCAGTCAAAGCGCTTACGACACAAGAGACATCTTCCAGTCCTTGGACTTGGCGTGGACTT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTTTATGCAAACTATGCCATTGGCAAAGACGTTCAAGCGATGAAAGCTGTCGTGGGAGAAGAAGCGCTGTCATCTGAAGATCTGgtaaagcaccagttttgctttttgatgccagtatgttaaccaactgtgttccttccctgcag

- - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA