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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTCTATGCAAACTATGCCATTGGCAAAGACGTTCAAGCGATGAAAGCTGTCGTGGGAGAAGAAGCGCTGTCATCTGAAGATCTGgtaaagcaccagttttgctttttgatgccagtatgttaaccaactgtgttccttccctgcag

Basic information

species Selaginella moellendorffii
transcript EFJ13375
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ13375 (Selaginella moellendorffii), 5'ss of exon 13
lower sequence: LOC_Os01g51380.2 (Oryza sativa), 5'ss of exon 14
CTCTATGCAAACTATGCCATTGGCAAAGACGTTCAAGCGATGAAAGCTGTCGTGGGAGAAGAAGCGCTGTCATCTGAAGATCTGgtaaagcaccagttttgcttt---ttgatgccagtatgttaaccaactgtgttccttccctgcag--------------------------------
|| ||||| || || ||||| ||||| ||||| || |||||||| || || || ||||| |||||||||||||| || || |||||||  | |  |  |  | |    ||| |     ||   |    || | | ||   |     |                                  
CTGTATGCCAATTACGCCATAGGCAAGGACGTACAGGCGATGAAGGCAGTGGTTGGAGAGGAAGCGCTGTCATCAGAGGACCTGgtaaccctcatgcatgacctgacattgttattcttaaactccttaattattttaagttttaacctcctaatcaactgatctatgaaaaaaatgacag

upper sequence: EFJ13375 (Selaginella moellendorffii), 5'ss of exon 13
lower sequence: GLYMA09G38110.1 (Glycine max), 5'ss of exon 14
CTCTATGCAAACTATGCCATTGGCAAAGACGTTCAAGCGATGAAAGCTGTCGTGGGAGAAGAAGCGCTGTCATCTGAAGATCTGgtaaagcaccagttttgctttttgatgccagtatgttaaccaactgtgttccttccctgcag--------------------------------------
||||||||||| ||||||||||| || || || || || ||||||||||| || ||||||||||| || |||||||| || |||||     || | |||| || || |       | | | |      ||||||  | || || ||                                      
CTCTATGCAAATTATGCCATTGGAAAGGATGTCCAGGCAATGAAAGCTGTGGTCGGAGAAGAAGCACTTTCATCTGAGGACCTGgtctc-tactactttt-ctcttgggaattcttgtttgagtatggtgtgtttgt-ccttgaagtggtggtactaattaattttattctttttgatcaacag

upper sequence: EFJ13375 (Selaginella moellendorffii), 5'ss of exon 13
lower sequence: GLYMA18G48280.1 (Glycine max), 5'ss of exon 14
CTCTATGCAAACTATGCCATTGGCAAAGACGTTCAAGCGATGAAAGCTGTCGTGGGAGAAGAAGCGCTGTCATCTGAAGATCTGgtaaagcaccagttttgctttttgatgccagtatgttaaccaactgtgttccttccctgcag---------------------------------------
 |||||||||| ||||||||||| || || || || || |||||||| || || ||||||||||| || |||||||| || |||||     || | |||| || || |       | | | |    | || | |  | || || ||                                       
-TCTATGCAAATTATGCCATTGGAAAGGATGTCCAGGCAATGAAAGCCGTGGTCGGAGAAGAAGCACTTTCATCTGAGGACCTGGtctc-tactactttt-ctcttgggaattcttgtttgagtgtagtgagattgt-ccttgaagtggtggtactaattaagtttattctttatgatcaacagc

upper sequence: EFJ13375 (Selaginella moellendorffii), 5'ss of exon 13
lower sequence: GLYMA20G24070.1 (Glycine max), 5'ss of exon 15
CTCTATGCAAACTATGCCATTGGCAAAGACGTTCAAGCGATGAAAGCTGTCGTGGGAGAAGAAGCGCTGTCATCTGAAGATCTGgtaaagcaccagttttgctttttgatgc-cagtatgttaaccaact----gtgttccttccctgcag---------------------------------------
||||||||||| ||||| ||||| || || || || || |||||||| || || ||||||||||| || |||||||| || |||||     |  |  |||   | |||||    | ||| ||      ||    |||    ||||||  |                                        
CTCTATGCAAATTATGCTATTGGAAAGGATGTCCAGGCAATGAAAGCAGTGGTTGGAGAAGAAGCACTTTCATCTGAGGACCTGgtctc-taataactttctatcttgataagtactatattttgtttcttcaagtgaaatttcccttgaagtggtactaatggaactccccctccccttttattaacag

upper sequence: EFJ13375 (Selaginella moellendorffii), 5'ss of exon 13
lower sequence: AT1G20260.1 (Arabidopsis thaliana), 5'ss of exon 14
CTCTATGCAAACTATGCCATTGGCAAAGACGTTCAAGCGATGAAAGCTGTCGTGGGAGAAGAAGCGCTGTCATCTGAAGATCTGgtaaagc-----------accagt-tttgctttttgatgccagta-tgt-taaccaactgtgttccttccctgcag-----------------------
|| || ||||| ||||| || || ||||| |||||||| ||||||||||| || ||||||||||| ||||| || || |||||||||   |           |||| | || |  ||   ||     || ||| ||  ||||  |  |   || |  ||                        
CTATACGCAAATTATGCAATCGGAAAAGATGTTCAAGCCATGAAAGCTGTTGTTGGAGAAGAAGCTCTGTCTTCCGAGGATCTGgtacctctctctgacttcaccaatattcgtgttcctatcaagatactgtatatgcaacaataattactcacaacaatttattgtgttgtgtgtttgtag

upper sequence: EFJ13375 (Selaginella moellendorffii), 5'ss of exon 13
lower sequence: Vv03s0038g02760.t01 (Vitis vinifera), 5'ss of exon 14
CTCTATGCAAACTATGCCATTGGCAAAGACGTTCAAGCGATGAAAGCTGTCGTGGGAGAAGAAGCGCTGTCATCTGAAGATCTGgtaaagcaccagttttgctttttgatgccagtatgttaacc-aactgtgttccttccctgcag---------------------------------------
||||||||||| ||||| ||||| || || |||||||| ||||||||||| || ||||||||||| || || ||||| ||||||||| |       | |  || ||  |    |  || | | |  || ||  | |||    |                                           
CTCTATGCAAATTATGCAATTGGGAAGGATGTTCAAGCAATGAAAGCTGTGGTTGGAGAAGAAGCACTTTCTTCTGAGGATCTGgtaca-------tctcactcttataaattatcatttcatctgaaatgaatccctattgtaagaaaacaactaacaggttgtccgacccttcactggaaacag

upper sequence: EFJ13375 (Selaginella moellendorffii), 5'ss of exon 13
lower sequence: PP1S100_117V6.1 (Physcomitrella patens), 5'ss of exon 14
CTCTATGCAAACTATGCCATTGGCAAAGACGTTCAAGCGATGAAAGCTGTCGTGGGAGAAGAAGCGCTGTCATCTGAAGATCTGgtaaagcaccagttttgctttttgatgccagtatg-------ttaaccaactgt-gttccttccctgcag-----------------------------------------------------------------------
 | ||||| || ||||||||||| || || |||||||| ||||| |||||||| ||||| |||||  |||| || ||||||||||||          |   | | |   ||| || |         ||   ||| | |  ||   ||| ||| |                                                                       
TTGTATGCTAATTATGCCATTGGAAAGGATGTTCAAGCAATGAAGGCTGTCGTTGGAGAGGAAGCTTTGTCTTCAGAAGATCTGgtaccctcgtgaatactcctgtgactgcaagcagaactcaatttgttcaatttttatttaatccatgccgctcatttccgtgcatactccgctatgtcaactctatttgttgcttacatcctcacttgttttgttttccag

upper sequence: EFJ13375 (Selaginella moellendorffii), 5'ss of exon 13
lower sequence: PP1S425_12V6.1 (Physcomitrella patens), 5'ss of exon 13
CTCTATGCAAACTATGCCATTGGCAAAGACGTTCAAGCGATGAAAGCTGTCGTGGGAGAAGAAGCGCTGTCATCTGAAGATCTGgtaaagcaccagttttgctt-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|169083324|gb|FE491368.1|FE491368
EST:     AAGCGATGAAAGCTGTCGTGGGAGAAGAAGCGCTGTCATCTGAAGATCTG                         CTGTACTTGGAGTTTTTAGACAAATTCGAGAGAAAATTTGTCAGTCAAAGC
genomic: AAGCGATGAAAGCTGTCGTGGGAGAAGAAGCGCTGTCATCTGAAGATCTGgtaaagcacc ... ttccctgcagCTGTACTTGGAGTTCTTAGACAAATTCGAGAGAAAATTTGTCAGTCAAAGC
EST: gi|169083325|gb|FE491369.1|FE491369
EST:     AAGCGATGAAAGCTGTCGTGGGAGAAGAAGCGCTGTCATCTGAAGATCTG                         CTGTACTTGGAGTTCTTAGACAAATTCGAGAGAAAATTTGTCAGTCAAAGC
genomic: AAGCGATGAAAGCTGTCGTGGGAGAAGAAGCGCTGTCATCTGAAGATCTGgtaaagcacc ... ttccctgcagCTGTACTTGGAGTTCTTAGACAAATTCGAGAGAAAATTTGTCAGTCAAAGC

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), 30 (downstream exon)
Score: 48

CTCTATGCAAACTATGCCATTGGCAAAGACGTTCAAGCGATGAAAGCTGTCGTGGGAGAAGAAGCGCTGTCATCTGAAGATCTGgtaaagcacc ... ttccctgcagCTGTACTTGGAGTTCTTAGACAAATTCGAGAGAAAATTTGTCAGTCAAAGCGCTTACGACACAAGAGACATCTTCCAGTCCTTGGACTTGGCGTGGACTT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTCTATGCAAACTATGCCATTGGCAAAGACGTTCAAGCGATGAAAGCTGTCGTGGGAGAAGAAGCGCTGTCATCTGAAGATCTGgtaaagcaccagttttgctttttgatgccagtatgttaaccaactgtgttccttccctgcag

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