Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatacgagtcattattgttatgatttgtcattgccttctattttttctcttagGTGACGACCACAATCGGATATGGTTCGCCGAACAAGGCCAATAGCTACAGTGTCCACGGCAGTGCACTAGGCTCGAAGGAAGTTGATGCTACGAGAAAGA

Basic information

species Selaginella moellendorffii
transcript EFJ07729
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ07676 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: PP1S72_25V6.1 (Physcomitrella patens), 3'ss of exon 4
------------------------------------------------------------------------------------------gtatacgagtcattattgttatgatttgtcattgc-------cttctattttttctcttagGTGACGACCACAATCGGATATGGTTCGCCGAACAAGGCCAATAGCTACAGTGTCCACGGCAGTGCACTAGGCTCGAAGGAAGTTGATGCTACGAGAAAGA
                                                                                           |  | |     ||  ||     | ||||  ||||       |||  ||  |     ||||||||| |||||||||||||||||||| || |||||||||||    |||  ||| || ||    || || ||  | || ||||| ||||| ||  |  | |
gtacacttaacagctttttatttatctacttttttaatatcttccgaatatcagcatcagatttctgttacttgtttattagtttctacatttcatgttgggttgctgcatgaacttgtatttgctgatattcttgaatcatgaaatttagGTGACAACCACAATCGGATATGGTTCACCAAACAAGGCCAACTCATACGCTGTGCATGGTGCCGCTCTGGGAACAAAAGAAGTAGATGCAACCCGCCAAA
















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|169113502|gb|FE515037.1|FE515037
EST:     CTGCCATTGCTGAAGCTAAGACGATTAAAGACAAGCCAACCATGATCAAG                         GTGACGACCACAATCGGATATGGTTCGCCGAACAAGGCCAATAGCTACAGT
genomic: CTGCCATTGCTGAAGCTAAGACGATTAAAGACAAGCCAACCATGATCAAGgtatacgagt ... tttctcttagGTGACGACCACAATCGGATATGGTTCGCCGAACAAGGCCAATAGCTACAGT
EST: gi|169065822|gb|FE476232.1|FE476232
EST:     CTGCCATTGCTGAAGCTAAGACGATTAAAGACAAGCCAACCATGATCAAG                         GTGACGACCACAATCGGATATGGTTCGCCGAACAAGGCCAATAGCTACAGT
genomic: CTGCCATTGCTGAAGCTAAGACGATTAAAGACAAGCCAACCATGATCAAGgtatacgagt ... tttctcttagGTGACGACCACAATCGGATATGGTTCGCCGAACAAGGCCAATAGCTACAGT
EST: gi|169076855|gb|FE484754.1|FE484754
EST:     CTGCCATTGCTGAAGCTAAGACGATTAAAGACAAGCCAACCATGATCAAG                         GTGACGACCACAATCGGATATGGTTCGCCGAACAAGGCCAATAGCTACAGT
genomic: CTGCCATTGCTGAAGCTAAGACGATTAAAGACAAGCCAACCATGATCAAGgtatacgagt ... tttctcttagGTGACGACCACAATCGGATATGGTTCGCCGAACAAGGCCAATAGCTACAGT
EST: gi|169081273|gb|FE488756.1|FE488756
EST:     CTGCCATTGCTGAAGCTAAGACGATTAAAGACAAGCCAACCATGATCAAG                         GTGACGACCACAATCGGATATGGTTCGCCGAACAAGGCCAATAGCTACAGT
genomic: CTGCCATTGCTGAAGCTAAGACGATTAAAGACAAGCCAACCATGATCAAGgtatacgagt ... tttctcttagGTGACGACCACAATCGGATATGGTTCGCCGAACAAGGCCAATAGCTACAGT
EST: gi|169029029|gb|FE437532.1|FE437532
EST:     CTGCCATTGCTGAAGCTAAGACGATTAAAGACAAGCCAACCATGATCAAG                         GTGACGACCACAATCGGATATGGTTCGCCGAACAAGGCCAATAGCTACAGT
genomic: CTGCCATTGCTGAAGCTAAGACGATTAAAGACAAGCCAACCATGATCAAGgtatacgagt ... tttctcttagGTGACGACCACAATCGGATATGGTTCGCCGAACAAGGCCAATAGCTACAGT
EST: gi|169040813|gb|FE447864.1|FE447864
EST:     CTGCCATTGCTGAAGCTAAGACGATTAAAGACAAGCCAACCATGATCAAG                         GTGACGACCACAATCGGATATGGTTCGCCGAACAAGGCCAATAGCTACAGT
genomic: CTGCCATTGCTGAAGCTAAGACGATTAAAGACAAGCCAACCATGATCAAGgtatacgagt ... tttctcttagGTGACGACCACAATCGGATATGGTTCGCCGAACAAGGCCAATAGCTACAGT
EST: gi|169065061|gb|FE474509.1|FE474509
EST:     CTGCCATTGCTGAAGCTAAGACGATTAAAGACAAGCCAACCATGATCAAG                         GTGACGACCACAATCGGATATGGTTCGCCGAACAAGGCCAATAGCTACAGT
genomic: CTGCCATTGCTGAAGCTAAGACGATTAAAGACAAGCCAACCATGATCAAGgtatacgagt ... tttctcttagGTGACGACCACAATCGGATATGGTTCGCCGAACAAGGCCAATAGCTACAGT
EST: gi|169045804|gb|FE453896.1|FE453896
EST:     CTGCCATTGCTGAAGCTAAGACGATTAAAGACAAGCCAACCATGATCAAG                         GTGACGACCACAATCGGATATGGTTCGCCGAACAAGGCCAATAGCTACAGT
genomic: CTGCCATTGCTGAAGCTAAGACGATTAAAGACAAGCCAACCATGATCAAGgtatacgagt ... tttctcttagGTGACGACCACAATCGGATATGGTTCGCCGAACAAGGCCAATAGCTACAGT
EST: gi|169067032|gb|FE475996.1|FE475996
EST:     CTGCCATTGCTGAAGCTAAGACGATTAAAGACAAGCCAACCATGATCAAG                         GTGACGACCACAATCGGATATGGTTCGCCGAACAAGGCCAATAGCTACAGT
genomic: CTGCCATTGCTGAAGCTAAGACGATTAAAGACAAGCCAACCATGATCAAGgtatacgagt ... tttctcttagGTGACGACCACAATCGGATATGGTTCGCCGAACAAGGCCAATAGCTACAGT
EST: gi|169044587|gb|FE450626.1|FE450626
EST:     CTGCCATTGCTGAAGCTAAGACGATTAAAGACAAGCCAACCATGATCAAG                         GTGACGACCACAATCGGATATGGTTCGCCGAACAAGGCCAATAGCTACAGT
genomic: CTGCCATTGCTGAAGCTAAGACGATTAAAGACAAGCCAACCATGATCAAGgtatacgagt ... tttctcttagGTGACGACCACAATCGGATATGGTTCGCCGAACAAGGCCAATAGCTACAGT
EST: gi|169026511|gb|FE434785.1|FE434785
EST:     CTGCCATTGCTGAAGCTAAGACGATTAAAGACAAGCCAACCATGATCAAG                         GTGACGACCACAATCGGATATGGTTCGCCGAACAAGGCCAATAGCTACAGT
genomic: CTGCCATTGCTGAAGCTAAGACGATTAAAGACAAGCCAACCATGATCAAGgtatacgagt ... tttctcttagGTGACGACCACAATCGGATATGGTTCGCCGAACAAGGCCAATAGCTACAGT
EST: gi|169019094|gb|FE427903.1|FE427903
EST:     CTGCCATTGCTGAAGCTAAGACGATTAAAGACAAGCCAACCATGATCAAG                         GTGACGACCACAATCGGATATGGTTCGCCGAACAAGGCCAATAGCTACAGT
genomic: CTGCCATTGCTGAAGCTAAGACGATTAAAGACAAGCCAACCATGATCAAGgtatacgagt ... tttctcttagGTGACGACCACAATCGGATATGGTTCGCCGAACAAGGCCAATAGCTACAGT
EST: gi|169055062|gb|FE462964.1|FE462964
EST:     CTGCCATTGCTGAAGCTAAGACGATTAAAGACAAGCCAACCATGATCAAG                         GTGACGACCACAATCGGATATGGTTCGCCGAACAAGGCCAATAGCTACAGT
genomic: CTGCCATTGCTGAAGCTAAGACGATTAAAGACAAGCCAACCATGATCAAGgtatacgagt ... tttctcttagGTGACGACCACAATCGGATATGGTTCGCCGAACAAGGCCAATAGCTACAGT
EST: gi|169102485|gb|FE508542.1|FE508542
EST:     CTGCCATTGCTGAAGCTAAGACGATTAAAGACAAGCCAACCATGATCAAG                         GTGACGACCACAATCGGATATGGTTCGCCGAACAAGGCCAATAGCTACAGT
genomic: CTGCCATTGCTGAAGCTAAGACGATTAAAGACAAGCCAACCATGATCAAGgtatacgagt ... tttctcttagGTGACGACCACAATCGGATATGGTTCGCCGAACAAGGCCAATAGCTACAGT
EST: gi|169020097|gb|FE428510.1|FE428510
EST:     CTGCCATTGCTGAAGCTAAGACGATTAAAGACAAGCCAACCATGATCAAG                         GTGACGACCACAATCGGATATGGTTCGCCGAACAAGGCCAATAGCTACAGT
genomic: CTGCCATTGCTGAAGCTAAGACGATTAAAGACAAGCCAACCATGATCAAGgtatacgagt ... tttctcttagGTGACGACCACAATCGGATATGGTTCGCCGAACAAGGCCAATAGCTACAGT
EST: gi|169063776|gb|FE472506.1|FE472506
EST:     CTGCCATTGCTGAAGCTAAGACGATTAAAGACAAGCCAACCATGATCAAG                         GTGACGACCACAATCGGATATGGTTCGCCGAACAAGGCCAATAGCTACAGT
genomic: CTGCCATTGCTGAAGCTAAGACGATTAAAGACAAGCCAACCATGATCAAGgtatacgagt ... tttctcttagGTGACGACCACAATCGGATATGGTTCGCCGAACAAGGCCAATAGCTACAGT
EST: gi|169115636|gb|FE517846.1|FE517846
EST:     CTGCCATTGCTGAAGCTAAGACGATTAAAGACAAGCCAACCATGATCAAG                         GTGACGACCACAATCGGATATGGTTCGCCGAACAAGGCCAATAGCTACAGT
genomic: CTGCCATTGCTGAAGCTAAGACGATTAAAGACAAGCCAACCATGATCAAGgtatacgagt ... tttctcttagGTGACGACCACAATCGGATATGGTTCGCCGAACAAGGCCAATAGCTACAGT
EST: gi|169080870|gb|FE486702.1|FE486702
EST:     CTGCCATTGCTGAAGCTAAGACGATTAAAGACAAGCCAACCATGATCAAG                         GTGACGACCACAATCGGATATGGTTCGCCGAACAAGGCCAATAGCTACAGT
genomic: CTGCCATTGCTGAAGCTAAGACGATTAAAGACAAGCCAACCATGATCAAGgtatacgagt ... tttctcttagGTGACGACCACAATCGGATATGGTTCGCCGAACAAGGCCAATAGCTACAGT
EST: gi|169104123|gb|FE507112.1|FE507112
EST:     CTGCCATTGCTGAAGCTAAGACGATTAAAGACAAGCCAACCATGATCAAG                         GTGACGACCACAATCGGATATGGTTCGCCGAACAAGGCCAATAGCTACAGT
genomic: CTGCCATTGCTGAAGCTAAGACGATTAAAGACAAGCCAACCATGATCAAGgtatacgagt ... tttctcttagGTGACGACCACAATCGGATATGGTTCGCCGAACAAGGCCAATAGCTACAGT
EST: gi|169071470|gb|FE479083.1|FE479083
EST:     CTGAAGCTAAGACGATTAAAGACAAGCCAACCATGATCAAG                         GTGACGACCACAATCGGATATGGTTCGCCGAACAAGGCCAATAGCTACAGT
genomic: CTGAAGCTAAGACGATTAAAGACAAGCCAACCATGATCAAGgtatacgagt ... tttctcttagGTGACGACCACAATCGGATATGGTTCGCCGAACAAGGCCAATAGCTACAGT
EST: gi|169114836|gb|FE516097.1|FE516097
EST:     CTGCCATTGCTGAAGCTAAGACGATTAAAGACAAGCCAACCATGATCAAG                         GTGACGACCACAATCGGATATGGTTCGCCGAACAAGGCCAATAGCTACAGT
genomic: CTGCCATTGCTGAAGCTAAGACGATTAAAGACAAGCCAACCATGATCAAGgtatacgagt ... tttctcttagGTGACGACCACAATCGGATATGGTTCGCCGAACAAGGCCAATAGCTACAGT
EST: gi|169098559|gb|FE497211.1|FE497211
EST:     CTGCCATTGCTGAAGCTAAGACGATTAAAGACAAGCCAACCATGATCAAG                         GTGACGACCACAATCGGATATGGTTCGCCGAACAAGGCCAATAGCTACAGT
genomic: CTGCCATTGCTGAAGCTAAGACGATTAAAGACAAGCCAACCATGATCAAGgtatacgagt ... tttctcttagGTGACGACCACAATCGGATATGGTTCGCCGAACAAGGCCAATAGCTACAGT
EST: gi|169050854|gb|FE459376.1|FE459376
EST:     GAAGCTAAGACGATTAAAGACAAGCCAACCATGATCAAG                         GTGACGACCACAATCGGATATGGTTCGCCGAACAAGGCCAATAGCTACAGT
genomic: GAAGCTAAGACGATTAAAGACAAGCCAACCATGATCAAGgtatacgagt ... tttctcttagGTGACGACCACAATCGGATATGGTTCGCCGAACAAGGCCAATAGCTACAGT
EST: gi|169075982|gb|FE480990.1|FE480990
EST:     GCTGAAGCTAAGACGATTAAAGACAAGCCAACCATGATCAAG                         GTGACGACCACAATCGGATATGGTTCGCCGAACAAGGCCAATAGCTACAGT
genomic: GCTGAAGCTAAGACGATTAAAGACAAGCCAACCATGATCAAGgtatacgagt ... tttctcttagGTGACGACCACAATCGGATATGGTTCGCCGAACAAGGCCAATAGCTACAGT
EST: gi|169079172|gb|FE488657.1|FE488657
EST:     CTGCCATTGCTGAAGCTAAGACGATTAAAGACAAGCCAACCATGATCAAG                         GTGACGACCACAATCGGATATGGTTCGCCGAACAAGGCCAATAGCTACAGT
genomic: CTGCCATTGCTGAAGCTAAGACGATTAAAGACAAGCCAACCATGATCAAGgtatacgagt ... tttctcttagGTGACGACCACAATCGGATATGGTTCGCCGAACAAGGCCAATAGCTACAGT
EST: gi|169026428|gb|FE434741.1|FE434741
EST:     CTGCCATTGCTGAAGCTAAGACGATTAAAGACAAGCCAACCATGATCAAG                         GTGACGACCACAATCGGATATGGTTCGCCGAACAAGGCCAATAGCTACAGT
genomic: CTGCCATTGCTGAAGCTAAGACGATTAAAGACAAGCCAACCATGATCAAGgtatacgagt ... tttctcttagGTGACGACCACAATCGGATATGGTTCGCCGAACAAGGCCAATAGCTACAGT
EST: gi|169043722|gb|FE453466.1|FE453466
EST:     CTGCCATTGCTGAAGCTAAGACGATTAAAGACAAGCCAACCATGATCAAG                         GTGACGACCACAATCGGATATGGTTCGCCGAACAAGGCCAATAGCTACAGT
genomic: CTGCCATTGCTGAAGCTAAGACGATTAAAGACAAGCCAACCATGATCAAGgtatacgagt ... tttctcttagGTGACGACCACAATCGGATATGGTTCGCCGAACAAGGCCAATAGCTACAGT
EST: gi|169024172|gb|FE432511.1|FE432511
EST:     CTGCCATTGCTGAAGCTAAGACGATTAAAGACAAGCCAACCATGATCAAG                         GTGACGACCACAATCGGATATGGTTCGCCGAACAAGGCCAATAGCTACAGT
genomic: CTGCCATTGCTGAAGCTAAGACGATTAAAGACAAGCCAACCATGATCAAGgtatacgagt ... tttctcttagGTGACGACCACAATCGGATATGGTTCGCCGAACAAGGCCAATAGCTACAGT
EST: gi|169088444|gb|FE495490.1|FE495490
EST:     CTGCCATTGCTGAAGCTAAGACGATTAAAGACAAGCCAACCATGATCAAG                         GTGACGACCACAATCGGATATGGTTCGCCGAACAAGGCCAATAGCTACAGT
genomic: CTGCCATTGCTGAAGCTAAGACGATTAAAGACAAGCCAACCATGATCAAGgtatacgagt ... tttctcttagGTGACGACCACAATCGGATATGGTTCGCCGAACAAGGCCAATAGCTACAGT
EST: gi|169049426|gb|FE458285.1|FE458285
EST:     CTGCCATTGCTGAAGCTAAGACGATTAAAGACAAGCCAACCATGATCAAG                         GTGACGACCACAATCGGATATGGTTCGCCGAACAAGGCCAATAGCTACAGT
genomic: CTGCCATTGCTGAAGCTAAGACGATTAAAGACAAGCCAACCATGATCAAGgtatacgagt ... tttctcttagGTGACGACCACAATCGGATATGGTTCGCCGAACAAGGCCAATAGCTACAGT
EST: gi|169081962|gb|FE487471.1|FE487471
EST:     CTGCCATTGCTGAAGCTAAGACGATTAAAGACAAGCCAACCATGATCAAG                         GTGACGACCACAATCGGATATGGTTCGCCGAACAAGGCCAATAGCTACAGT
genomic: CTGCCATTGCTGAAGCTAAGACGATTAAAGACAAGCCAACCATGATCAAGgtatacgagt ... tttctcttagGTGACGACCACAATCGGATATGGTTCGCCGAACAAGGCCAATAGCTACAGT
EST: gi|169022715|gb|FE428403.1|FE428403
EST:     CTGCCATTGCTGAAGCTAAGACGATTAAAGACAAGCCAACCATGATCAAG                         GTGACGACCACAATCGGATATGGTTCGCCGAACAAGGCCAATAGCTACAGT
genomic: CTGCCATTGCTGAAGCTAAGACGATTAAAGACAAGCCAACCATGATCAAGgtatacgagt ... tttctcttagGTGACGACCACAATCGGATATGGTTCGCCGAACAAGGCCAATAGCTACAGT
EST: gi|169019106|gb|FE426771.1|FE426771
EST:     CTGCCATTGCTGAAGCTAAGACGATTAAAGACAAGCCAACCATGATCAAG                         GTGACGACCACAATCGGATATGGTTCGCCGAACAAGGCCAATAGCTACAGT
genomic: CTGCCATTGCTGAAGCTAAGACGATTAAAGACAAGCCAACCATGATCAAGgtatacgagt ... tttctcttagGTGACGACCACAATCGGATATGGTTCGCCGAACAAGGCCAATAGCTACAGT

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), 35 (downstream exon)
Score: 230

GCACACAATCTGGGTAAAGAACGGAAACACTGGCTATGATGAGATTAGAGCTGCCATTGCTGAAGCTAAGACGATTAAAGACAAGCCAACCATGATCAAGgtatacgagt ... tttctcttagGTGACGACCACAATCGGATATGGTTCGCCGAACAAGGCCAATAGCTACAGTGTCCACGGCAGTGCACTAGGCTCGAAGGAAGTTGATGCTACGAGAAAGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtatacgagtcattattgttatgatttgtcattgccttctattttttctcttagGTGACGACCACAATCGGATATGGTTCGCCGAACAAGGCCAATAGCTACAGTGTCCACGGCAGTGCACTAGGCTCGAAGGAAGTTGATGCTACGAGAAAGA
                         tttgtcattgccttct  CT-rich tract
            attattgttatgattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatacgagtcattattgttatgatttgtcattgccttctattttttctcttagGTGACGACCACAATCGGATATGGTTCGCCGAACAAGGCCAATAGCTACAGTGTCCACGGCAGTGCACTAGGCTCGAAGGAAGTTGATGCTACGAGAAAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA