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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTCTCGTCACCCGGGGGCTACCGCTGCGTATCGTGATGATTGGAACTCTCACTGGAGCGCAGTGGGTAATCTACGACGCCTTCAAAGTCTTCGTTGGACTgtaagtttcttgctatttctctccttgtgggaagttctcaaatctcctctctcgtgctcttccatcccag

Basic information

species Selaginella moellendorffii
transcript EFJ31007
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ34706 (Selaginella moellendorffii), 5'ss of exon 5
lower sequence: LOC_Os04g37600.1 (Oryza sativa), 5'ss of exon 5
CTCTCGTCACCCGGGGGCTACCGCTGCGTATCGTGATGATTGGAACTCTCACTGGAGCGCAGTGGGTAATCTACGACGCCTTCAAAGTCTTCGTTGGACTgtaagt-----ttcttgctatttctctcct-tgtgg-----gaagttctcaaatctc-------ctctctcgtgctcttccatcccag
 |||  | || || || || ||  |||||||||||||||| || |||||||||||||||||||||| | |||| ||||| ||||||||  | ||||||||||||||     |  ||| |  ||||  ||| ||        ||  ||  | ||  ||        |   | |   | |||  | | ||
GTCTATTTACGCGTGGACTCCCTTTGCGTATCGTGATGATCGGTACTCTCACTGGAGCGCAGTGGGGACTCTATGACGCTTTCAAAGTGATGGTTGGACTgtaagtgttcctctttgttgattctggcctctgccaacattgatattgaccaacttcaggaagatttatttggtttgttctcttctag

upper sequence: EFJ34706 (Selaginella moellendorffii), 5'ss of exon 5
lower sequence: GLYMA19G27380.1 (Glycine max), 5'ss of exon 5
CTCTCGTCACCCGGGGGCTACCGCTGCGTATCGTGATGATTGGAACTCTCACTGGAGCGCAGTGGGTAATCTACGACGCCTTCAAAGTCTTCGTTGGACTgtaagtttcttgctatttctctccttgtgggaagttctcaaatctcctctctcgtgctcttccatcccag-----------------------
 |||| | || || || || || || || || || |||||||||||||| |||||||| || |||| ||| || || || |||||||||||||| ||| |||||||||    | ||| ||   |         ||||     | || |  ||    |     | | | |                        
GTCTCTTTACGCGTGGTCTCCCCCTCCGAATTGTTATGATTGGAACTCTTACTGGAGCCCAATGGGGAATATATGATGCATTCAAAGTCTTCGTCGGATTgtaagtttac-acaattgctagtcaatgatagggttccattctttcattccttcatcatggacgtgctaatgagattttttcccccttcccag

upper sequence: EFJ34706 (Selaginella moellendorffii), 5'ss of exon 5
lower sequence: AT3G48850.1 (Arabidopsis thaliana), 5'ss of exon 4
CTCTCGTCACCCGGGGGCTACCGCTGCGTATCGTGATGATTGGAACTCTCACTGGAGCGCAGTGGGTAATCTACGACGCCTTCAAAGTCTTCGTTGGACTgtaagtttc--ttgctatttctc--tccttgtgggaa---gttctcaaatctcctctctc-gtgctcttccatcccag-----------
 | |  | ||||| || || || || || ||  | ||||| ||||| |||||||||||||||||||| ||||| || ||  ||||||| || | |||| |||||||||   |    | | |||  | | | |  |||    || | |||    |||  || ||   ||   ||   |            
GTATGTTAACCCGTGGCCTTCCTCTTCGCATTTTCATGATAGGAACACTCACTGGAGCGCAGTGGGTTATCTATGATGCTGTCAAAGTTTTAGCTGGATTgtaagttttcatcatcaatactcaattcatttaagaactaattatgaaagacactccatcagttaactataattttatcattttattag

upper sequence: EFJ34706 (Selaginella moellendorffii), 5'ss of exon 5
lower sequence: AT5G14040.1 (Arabidopsis thaliana), 5'ss of exon 5
CTCTCGTCACCCGGGGGCTACCGCTGCGTATCGTGATGATTGGAACTCTCACTGGAGCGCAGTGGGTAATCTACGACGCCTTCAAAGTCTTCGTTGGACTgtaagtttcttgctat-ttctctccttgtgggaagttc-tcaaatctcctctct-cgtgctcttccatcccag---------------
  ||  ||||  | ||||| || ||  | || |||||||| || ||  | |||||||| ||||||| | | ||||| ||||||||||| || ||||| ||||||||| ||  || | ||| ||   | | | |  ||  |   | || |    | |       || || |                  
GACTGTTCACAAGAGGGCTTCCTCTTAGAATTGTGATGATCGGGACGTTGACTGGAGCACAGTGGGGATTATACGATGCCTTCAAAGTGTTTGTTGGCCTgtaagttcctctctctcttcacttactttcgtaccttaattgtaccttcaaaatgcaaaactctcaattcttttgatttggtattcag

upper sequence: EFJ34706 (Selaginella moellendorffii), 5'ss of exon 5
lower sequence: Vv14s0068g01260.t01 (Vitis vinifera), 5'ss of exon 5
CTCTCGTCACCCGGGGGCTACCGCTGCGTATCGTGATGATTGGAACTCTCACTGGAGCGCAGTGGGTAATCTACGACGCCTTCAAAGTCTTCGTTGGACTgtaagtttct----tgctatttctc-tccttgtgggaagttctcaaatctcctctctcgt-gctcttccatcccag------------
 |||| ||||||||||||| || |||||||| || ||||||||||||||||| ||||| |||||||   | || || || |||||||| ||||| ||||||||||||  |    ||| | | ||  || |  |  |  ||| |    | |  ||| | || |||  | |                   
GTCTCTTCACCCGGGGGCTTCCCCTGCGTATTGTCATGATTGGAACTCTCACCGGAGCACAGTGGGGGCTATATGATGCTTTCAAAGTTTTCGTAGGACTgtaagttcttcctatgcaaatgctgatcttcatttggtgttttagttttttttctttagttgctaattcggtatgatcttatcttcag

upper sequence: EFJ34706 (Selaginella moellendorffii), 5'ss of exon 5
lower sequence: Vv17s0000g00400.t01 (Vitis vinifera), 5'ss of exon 5
CTCTCGTCACCCGGGGGCTACCGCTGCGTATCGTGATGATTGGAACTCTCACTGGAGCGCAGTGGGTAATCTACGACGCCTTCAAAGTCTTCGTTGGACTgtaagtttcttgctatttctctccttgtgggaagttctcaaatctcctctctcgtgctc--ttccatcccag------------------------------------------------------------------------------------------------
 |||| ||||||| || || || || ||||| || ||||||||||| || || ||||| || ||||  ||||||||  | |||||||| || ||||| ||||||||||||      | || || |||    || ||||    | |  |  |  || |    | | |||  |                                                                                                 
GTCTCTTCACCCGTGGTCTTCCTCTTCGTATAGTCATGATTGGAACCCTTACAGGAGCCCAATGGGGTATCTACGATACTTTCAAAGTTTTTGTTGGGCTgtaagtttctc----ctcctttcattgattaaaattcttctttgttttgccatgttcctggtactatctaacatgtttgaaggatctatttctgggtagttacattcactgtcctgttcccaattttatttgaataaaatgctaacaaggttttgttgctatccatag

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|169070433|gb|FE476798.1|FE476798
EST:     ACTGGAGCGCAGTGGGTAATCTACGACGCCTTCAAAGTCTTCGTTGGACT                         GCCGACCACTGGAGGAGTTTCGAAAGCTCCCGAGGAGCTAACCACGCCGCT
genomic: ACTGGAGCGCAGTGGGTAATCTACGACGCCTTCAAAGTCTTCGTTGGACTgtaagtttct ... tccatcccagGCCGACCACTGGAGGAGTTTCGAAAGCTCCCGAGGAGCTAACCACGCCGCT
EST: gi|169035239|gb|FE442604.1|FE442604
EST:     ACTGGAGCGCAGTGGGTAATCTACGACGCCTTCAAAGTCTTCGTTGGACT                         GCCGACCACTGGAGGAGTTTCGAAAGCTCCCGAGGAGCTAACCACGCCGCT
genomic: ACTGGAGCGCAGTGGGTAATCTACGACGCCTTCAAAGTCTTCGTTGGACTgtaagtttct ... tccatcccagGCCGACCACTGGAGGAGTTTCGAAAGCTCCCGAGGAGCTAACCACGCCGCT
EST: gi|169104740|gb|FE508988.1|FE508988
EST:     ACTGGAGCGCAGTGGGTAATCTACGACGCCTTCAAAGTCTTCGTTGGACT                         GCCGACCACTGGAGGAGTTTCGAAAGCTCCCGAGGAGCTAACCACGCCGCT
genomic: ACTGGAGCGCAGTGGGTAATCTACGACGCCTTCAAAGTCTTCGTTGGACTgtaagtttct ... tccatcccagGCCGACCACTGGAGGAGTTTCGAAAGCTCCCGAGGAGCTAACCACGCCGCT
EST: gi|169092867|gb|FE496331.1|FE496331
EST:     ACTGGAGCGCAGTGGGTAATTTACGACGCCTTCAAAGTCTTCGTTGGACT                         GCCGACCACTGGAGGAGTTTCGAAAGCTCCCGAGGAGCTAACCACGCCGCT
genomic: ACTGGAGCGCAGTGGGTAATCTACGACGCCTTCAAAGTCTTCGTTGGACTgtaagtttct ... tccatcccagGCCGACCACTGGAGGAGTTTCGAAAGCTCCCGAGGAGCTAACCACGCCGCT
EST: gi|169061542|gb|FE469329.1|FE469329
EST:     ACTGGAGCGCAGTGGGTAATTTACGACGCCTTCAAAGTCTTCGTTGGACT                         GCCGACCACTGGAGGAGTTTCGAAAGCTCCCGAGGAGCTAACCACGCCGCT
genomic: ACTGGAGCGCAGTGGGTAATCTACGACGCCTTCAAAGTCTTCGTTGGACTgtaagtttct ... tccatcccagGCCGACCACTGGAGGAGTTTCGAAAGCTCCCGAGGAGCTAACCACGCCGCT

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: 33 (upstream exon), 24 (downstream exon)
Score: 20

CTCTCGTCACCCGGGGGCTACCGCTGCGTATCGTGATGATTGGAACTCTCACTGGAGCGCAGTGGGTAATCTACGACGCCTTCAAAGTCTTCGTTGGACTgtaagtttct ... tccatcccagGCCGACCACTGGAGGAGTTTCGAAAGCTCCCGAGGAGCTAACCACGCCGCTACCACTTCCCACCGCCTAAAAGCATTCTTTTCATGGCGAGACGAAAGAA




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