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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTCCTCGAGTGGTGTTACAGAGGTGGACAAGGATAGCTTCTGGCCGCTCGTTGATGGAGCTGGAGACAAGGTCGTGGTGCTCGACATGTACACCCAATGgtaaacttctctccctttttttccggaagcttgacacagaaaaacgctttttttcttcgctctttag

Basic information

species Selaginella moellendorffii
transcript EFJ10424
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ10424 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: LOC_Os01g68480.1 (Oryza sativa), 5'ss of exon 1
-CTTCCTCGAGTGGTGTTACAGAGGTGGACAAGGATAGCTTCTGGCCGCTCGTTGATGGAGCTGGAGACAAGGTCGTGGTGCTCGACATGTACACCCAATGgta-----------------aacttctctccctttttttccggaagcttgacacagaaaaacgctttttttcttcgctctttag---------------------------------------------------------------------------------------------------------------
 | |   || |  | || || |||||| ||||||||| |||||||||  | ||  |    || ||   ||||||||| || |||||||||||||||||||||||                 |||| | ||    | ||  |   || ||  |   |  ||        |    |    |||| ||                                                                                                               
CCGTGACCGGGCAG-GTGACGGAGGTGAACAAGGATACCTTCTGGCCAATTGTCAAGTCGGCAGGGCCCAAGGTCGTCGTCCTCGACATGTACACCCAATGgtacttcacaaaagccacaaaactccactgatctcttcgcgtcaatctccattgatgaactgttgcctcgcatgaattcttcagtcttatcacgagctggatttattttgaaatgagcggcgtgaataagaaagggaacagatctcatcccactgctcagtgtaataactgtaaaactgactggttgatttgcag

upper sequence: EFJ10424 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: GRMZM2G025954_T01 (Zea mays), 5'ss of exon 1
-CTTCCTCGAGTGGTGTTACAGAGGTGGACAAGGATAGCTTCTGGCCGCTCGTTGATGGAGCTGGAGACAAGGTCGTGGTGCTCGACATGTACACCCAATGgtaaacttctctccctttttttccggaagcttgacacagaaaaacgctttttt-----tcttcgctctttag-------------------------------------------------------------------------------------
 | ||  || |  | || || |||||  ||||||| | |||||||||  |||| || |  || || ||||||||||| || ||||||||||||||| |||||||   | |   | | |       |    || ||   ||   ||  | ||        |  | |  |  ||                                                                                      
CCGTCACCGGGCAG-GTCACGGAGGTCAACAAGGACACCTTCTGGCCCATCGTCGAGGCCGCCGGCGACAAGGTCGTCGTCCTCGACATGTACACCGAATGgtacg-tacgtacgcgtgcaaagtgatgcctcgatctagctcaagtcgttccaggagattgtagaaccatatatcctgagacgacgacgacagtacgtgttgcattgcagtacatactgatatactgcgcgcgttgtggtgtgtttgcatcatgcag

upper sequence: EFJ10424 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: GRMZM2G017419_T01 (Zea mays), 5'ss of exon 1
-CTTCCTCGAGTGGTGTTACAGAGGTGGACAAGGATAGCTTCTGGCCGCTCGTTGATGGAGCTGGAGACAAGGTCGTGGTGCTCGACATGTACACCCAATGgt--------------aaacttctctccctttttttccggaagcttgacacagaaaaacgctttttttctt--cgctctttag-----------------
 | ||  || |  | || || |||||  ||||||| | |||||||||  |||| || |  || || ||||||||||| || ||||||||||||||| ||||||              | |  | ||| | | || |||    |    | |    |  ||   |  ||| |||    ||  | |                  
CCGTCACCGGGCAG-GTCACGGAGGTCAACAAGGACACCTTCTGGCCCATCGTCGAGGCCGCCGGCGACAAGGTCGTCGTCCTCGACATGTACACCGAATGgtgcgtacactacaatatatatatcttcttcttcttcttccattcggtctttaacgaattttagtttacttactactaatcaagacacacaaatagatat

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|169098004|gb|FE498801.1|FE498801
EST:     GTTGATGGAGCTGGAGACAAGGTCGTGGTGCTCGACATGTACACCCAATG                         GTGTGGCCCTTGCAAAATGATGTTTCCAAAGATCGTGGAGCTCTCTTCCAG
genomic: GTTGATGGAGCTGGAGACAAGGTCGTGGTGCTCGACATGTACACCCAATGgtaaacttct ... cgctctttagGTGTGGCCCTTGCAAAATGATGTTTCCAAAGATCGTGGAGCTCTCTTCCAG
EST: gi|70670019|gb|DN838596.1|DN838596
EST:     GTTGATGGAGCTGGAGACAAGGTCGTGGTGCTCGACATGTACACCCAATG                         GTGTGGCCCTTGCAAAATGATGTTTCCAAAGATCGTGGAGCTCTCTTCCAG
genomic: GTTGATGGAGCTGGAGACAAGGTCGTGGTGCTCGACATGTACACCCAATGgtaaacttct ... cgctctttagGTGTGGCCCTTGCAAAATGATGTTTCCAAAGATCGTGGAGCTCTCTTCCAG
EST: gi|169067165|gb|FE474933.1|FE474933
EST:     GTTGATGGAGCTGGAGACAAGGTCGTGGTGCTCGACATGTACACCCAATG                         GTGTGGCCCTTGCAAAATGATGTTTCCAAAGATCGTGGAGCTCTCTTCCAG
genomic: GTTGATGGAGCTGGAGACAAGGTCGTGGTGCTCGACATGTACACCCAATGgtaaacttct ... cgctctttagGTGTGGCCCTTGCAAAATGATGTTTCCAAAGATCGTGGAGCTCTCTTCCAG
EST: gi|169056604|gb|FE465909.1|FE465909
EST:     GTTGATGGAGCTGGAGACAAGGTCGTGGTGCTCGACATGTACACCCAATG                         GTGTGGCCCTTGCAAAATGATGTTTCCAAAGATCGTGGAGCTCTCTTCCAG
genomic: GTTGATGGAGCTGGAGACAAGGTCGTGGTGCTCGACATGTACACCCAATGgtaaacttct ... cgctctttagGTGTGGCCCTTGCAAAATGATGTTTCCAAAGATCGTGGAGCTCTCTTCCAG
EST: gi|169072114|gb|FE478726.1|FE478726
EST:     GTTGATGGAGCTGGAGACAAGGTCGTGGTGCTCGACATGTACACCCAATG                         GTGTGGCCCTTGCAAAATGATGTTTCCAAAGATCGTGGAGCTCTCTTCCAG
genomic: GTTGATGGAGCTGGAGACAAGGTCGTGGTGCTCGACATGTACACCCAATGgtaaacttct ... cgctctttagGTGTGGCCCTTGCAAAATGATGTTTCCAAAGATCGTGGAGCTCTCTTCCAG
EST: gi|169111450|gb|FE510310.1|FE510310
EST:     GTTGATGGAGCTGGAGACAAGGTCGTGGTGCTCGACATGTACACCCAATG                         GTGTGGCCCTTGCAAAATGATGTTTCCAAAGATCGTGGAGCTCTCTTCCAG
genomic: GTTGATGGAGCTGGAGACAAGGTCGTGGTGCTCGACATGTACACCCAATGgtaaacttct ... cgctctttagGTGTGGCCCTTGCAAAATGATGTTTCCAAAGATCGTGGAGCTCTCTTCCAG
EST: gi|169059592|gb|FE468826.1|FE468826
EST:     GTTGATGGAGCTGGAGACAAGGTCGTGGTGCTCGACATGTACACCCAATG                         GTGTGGCCCTTGCAAAATGATGTTTCCAAAGATCGTGGAGCTCTCTTCCAG
genomic: GTTGATGGAGCTGGAGACAAGGTCGTGGTGCTCGACATGTACACCCAATGgtaaacttct ... cgctctttagGTGTGGCCCTTGCAAAATGATGTTTCCAAAGATCGTGGAGCTCTCTTCCAG
EST: gi|169098003|gb|FE498800.1|FE498800
EST:     GTTGATGGAGCTGGAGACAAGGTCGTGGTGCTCGACATGTACACCCAATG                         GTGTGGCCCTTGCAAAATGATGTTTCCAAAGATCGTGGAGCTCTCTTCCAG
genomic: GTTGATGGAGCTGGAGACAAGGTCGTGGTGCTCGACATGTACACCCAATGgtaaacttct ... cgctctttagGTGTGGCCCTTGCAAAATGATGTTTCCAAAGATCGTGGAGCTCTCTTCCAG
EST: gi|169102742|gb|FE508097.1|FE508097
EST:     GTTGATGGAGCTGGAGACAAGGTCGTGGTGCTCGACATGTACACCCAATG                         GTGTGGCCCTTGCAAAATGATGTTTCCAAAGATCGTGGAGCTCTCTTCCAG
genomic: GTTGATGGAGCTGGAGACAAGGTCGTGGTGCTCGACATGTACACCCAATGgtaaacttct ... cgctctttagGTGTGGCCCTTGCAAAATGATGTTTCCAAAGATCGTGGAGCTCTCTTCCAG
EST: gi|169109796|gb|FE513843.1|FE513843
EST:     GTTGATGGAGCTGGGGACAAGGTCGTGGTGCTCGACATGTACACCCAATG                         GTGTGGCCCTTGCAAAATGATGTTTCCAAAGATCGTGGAGCTCTCTTCCAG
genomic: GTTGATGGAGCTGGAGACAAGGTCGTGGTGCTCGACATGTACACCCAATGgtaaacttct ... cgctctttagGTGTGGCCCTTGCAAAATGATGTTTCCAAAGATCGTGGAGCTCTCTTCCAG
EST: gi|169097804|gb|FE498233.1|FE498233
EST:     GTTGATGGAGCTGGAGACAAGGTCGTGGTGCTCGACATGTACACCCAATG                         GTGTGGCCCTTGCGAAATGATGTTTCCAAAGATCGTGGAGCTCTCTTCCAG
genomic: GTTGATGGAGCTGGAGACAAGGTCGTGGTGCTCGACATGTACACCCAATGgtaaacttct ... cgctctttagGTGTGGCCCTTGCAAAATGATGTTTCCAAAGATCGTGGAGCTCTCTTCCAG
EST: gi|169074397|gb|FE484306.1|FE484306
EST:     GTTGATGGAGCTGGAGACAAGGTCGTGGTGCTCGACATGTACACCCAATG                         GTGTGGCCCTTGCAAAATGATGTTTCCAAAGATCGTGGAGCTCTCTTCCAG
genomic: GTTGATGGAGCTGGAGACAAGGTCGTGGTGCTCGACATGTACACCCAATGgtaaacttct ... cgctctttagGTGTGGCCCTTGCAAAATGATGTTTCCAAAGATCGTGGAGCTCTCTTCCAG
EST: gi|169040657|gb|FE449788.1|FE449788
EST:     GTTGATGGAGCTGGAGACAAGGTCGTGGTGCTCGACATGTACACCCAATG                         GTGTGGCCCTTGCAAAATGATGTTTCCAAAGATCGTGGAGCTCTCTTCCAG
genomic: GTTGATGGAGCTGGAGACAAGGTCGTGGTGCTCGACATGTACACCCAATGgtaaacttct ... cgctctttagGTGTGGCCCTTGCAAAATGATGTTTCCAAAGATCGTGGAGCTCTCTTCCAG
EST: gi|169075726|gb|FE481800.1|FE481800
EST:     GTTGATGGAGCTGGAGACAAGGTCGTGGTGCTCGACATGTACACCCAATG                         GTGTGGCCCTTGCAAAATGATGTTTCCAAAGATCGTGGAGCTCTCTTCCAG
genomic: GTTGATGGAGCTGGAGACAAGGTCGTGGTGCTCGACATGTACACCCAATGgtaaacttct ... cgctctttagGTGTGGCCCTTGCAAAATGATGTTTCCAAAGATCGTGGAGCTCTCTTCCAG
EST: gi|169107637|gb|FE514298.1|FE514298
EST:     GTTGATGGAGCTGGAGACAAGGTCGTGGTGCTCGACATGTACACCCAATG                         GTGTGGCCCTTGCAAAATGATGTTTCCAAAGATCGTGGAGCTCTCTTCCAG
genomic: GTTGATGGAGCTGGAGACAAGGTCGTGGTGCTCGACATGTACACCCAATGgtaaacttct ... cgctctttagGTGTGGCCCTTGCAAAATGATGTTTCCAAAGATCGTGGAGCTCTCTTCCAG
EST: gi|169107636|gb|FE514297.1|FE514297
EST:     GTTGATGGAGCTGGAGACAAGGTCGTGGTGCTCGACATGTACACCCAATG                         GTGTGGCCCTTGCAAAATGATGTTTCCAAAGATCGTGGAGCTCTCTTCCAG
genomic: GTTGATGGAGCTGGAGACAAGGTCGTGGTGCTCGACATGTACACCCAATGgtaaacttct ... cgctctttagGTGTGGCCCTTGCAAAATGATGTTTCCAAAGATCGTGGAGCTCTCTTCCAG
EST: gi|169083438|gb|FE494823.1|FE494823
EST:     GTTGATGGAGCTGGAGACAAGGTCGTGGTGCTCGACATGTACACCCAATG                         GTGTGGCCCTTGCAAAATGATGTTTCCAAAGATCGTGGAGCTCTCTTCCAG
genomic: GTTGATGGAGCTGGAGACAAGGTCGTGGTGCTCGACATGTACACCCAATGgtaaacttct ... cgctctttagGTGTGGCCCTTGCAAAATGATGTTTCCAAAGATCGTGGAGCTCTCTTCCAG
EST: gi|169040658|gb|FE449789.1|FE449789
EST:     GTTGATGGAGCTGGAGACAAGGTCGTGGTGCTCGACATGTACACCCAATG                         GTGTGGCCCTTGCAAAATGATGTTTCCAAAGATCGTGGAGCTCTCTTCCAG
genomic: GTTGATGGAGCTGGAGACAAGGTCGTGGTGCTCGACATGTACACCCAATGgtaaacttct ... cgctctttagGTGTGGCCCTTGCAAAATGATGTTTCCAAAGATCGTGGAGCTCTCTTCCAG

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: 22

CTTCCTCGAGTGGTGTTACAGAGGTGGACAAGGATAGCTTCTGGCCGCTCGTTGATGGAGCTGGAGACAAGGTCGTGGTGCTCGACATGTACACCCAATGgtaaacttct ... cgctctttagGTGTGGCCCTTGCAAAATGATGTTTCCAAAGATCGTGGAGCTCTCTTCCAGATACTCGGACGTGATGTTTCTCAAGCTGGATTGCAACCAAGAGAATAAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTTCCTCGAGTGGTGTTACAGAGGTGGACAAGGATAGCTTCTGGCCGCTCGTTGATGGAGCTGGAGACAAGGTCGTGGTGCTCGACATGTACACCCAATGgtaaacttctctccctttttttccggaagcttgacacagaaaaacgctttttttcttcgctctttag

- - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA