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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGACATTGGACAATTCCATCCCGATGGTTGCTTAGAAATTGTAGACCGGAAGAAGGACATTGTTAAGCTTCAACATGGCGAATACGTATCGCTGGGCAAGgtatgatgctatctacacttggacaagagaagtgatttcgtttttacttttggcag

Basic information

species Selaginella moellendorffii
transcript EFJ26722
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ26722 (Selaginella moellendorffii), 5'ss of exon 9
lower sequence: LOC_Os11g06880.1 (Oryza sativa), 5'ss of exon 5
TGACATTGGACAATTCCATCCCGATGGTTGCTTAGAAATTGTAGACCGGAAGAAGGACATTGTTAAGCTTCAACATGGCGAATACGTATCGCTGGGCAAGgtatgatg-----ctatctacacttggacaagaga-----agtgatttcgtttttacttttggcag-------
|||||||||||  || ||||| ||||||||| | |||||| | ||||| ||||||||||| || |||||||||||||| ||||| |||||  | || |||||| | |      |  | | ||     |  || |      ||  |||    | | ||| ||   |        
TGACATTGGACGTTTGCATCCAGATGGTTGCCTTGAAATTATTGACCGTAAGAAGGACATAGTCAAGCTTCAACATGGTGAATATGTATCTTTAGGAAAGgtaagctaagcttccttttccagccaaattagcggcagtcagctattgtaatctaactattataaaaccacag

upper sequence: EFJ26722 (Selaginella moellendorffii), 5'ss of exon 9
lower sequence: GRMZM2G118286_T01 (Zea mays), 5'ss of exon 10
TGACATTGGACAATTCCATCCCGATGGTTGCTTAGAAATTGTAGACCGGAAGAAGGACATTGTTAAGCTTCAACATGGCGAATACGTATCGCTGGGCAAGgtatgatgctatct-acacttggacaagagaagtgatttcgtttttacttttggcag----------
 ||||| ||||  |||||||| ||||| ||| | |||||  | ||||| ||||| || || || |||||||||||||||||||| ||||| || || ||||||||      ||| |  || |  |||  |     ||| |  |  |    |||  ||          
AGACATCGGACGGTTCCATCCAGATGGCTGCCTTGAAATCATTGACCGTAAGAAAGATATCGTGAAGCTTCAACATGGCGAATATGTATCTCTCGGGAAGgtatgcaatattcttattctggtccaactggctgaattgcactgcttaacttgttaggtgatgacag

upper sequence: EFJ26722 (Selaginella moellendorffii), 5'ss of exon 9
lower sequence: AT2G04350.2 (Arabidopsis thaliana), 5'ss of exon 10
TGACATTGGACAATTCCATCCCGATGGTTGCTTAGAAATTGTAGACCGGAAGAAGGACATTGTTAAGCTTCAACATGGCGAATACGTATCGCTGGGCAAGgtatg---atgctatctacacttggacaagagaa--gtgatttcgtttttacttttggcag---------------------------------
 || |||||   |||||| || ||||| ||  | ||| |  | ||  | ||||| || |||||||| ||||||||||| ||||||||||| || || ||||| ||   ||   |  || | |      |||| |  ||| | |    |  | | |   ||                                  
AGATATTGGGAGATTCCACCCTGATGGATGTCTCGAAGTCATCGATAGAAAGAAAGATATTGTTAAACTTCAACATGGGGAATACGTATCCCTTGGAAAGgtttgcctatagaacttaaattctacatagaggatggtggtatatgataaaatctcatcatgctctttcattgcctggatcacacaattcacag

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|169062087|gb|FE469679.1|FE469679
EST:     AGAAGGACATTGTTAAGCTTCAACATGGCGAATACGTATCGCTGGGCAAG                         GTCGAGGCAGCATTATCGGTTAGCCCGATGGTGGACAGCATCATGGTGCAT
genomic: AGAAGGACATTGTTAAGCTTCAACATGGCGAATACGTATCGCTGGGCAAGgtatgatgct ... cttttggcagGTCGAGGCAGCATTATCGGTTAGCCCGATGGTGGACAGCATCATGGTGCAT
EST: gi|169098530|gb|FE498534.1|FE498534
EST:     AGAAGGACATTGTTAAGCTTCAACATGGCGAATACGTATCGCTGGGCAAG                         GTCGAGGCAGCATTATCGGTTAGCCCGATGGTGGACAGCATCATGGTGCAT
genomic: AGAAGGACATTGTTAAGCTTCAACATGGCGAATACGTATCGCTGGGCAAGgtatgatgct ... cttttggcagGTCGAGGCAGCATTATCGGTTAGCCCGATGGTGGACAGCATCATGGTGCAT
EST: gi|169102589|gb|FE508568.1|FE508568
EST:     AGAAGGACATTGTTAAGCTTCAACATGGCGAATACGTATCGCTGGGCAAG                         GTCGAGGCAGCATTATCGGTTAGCCCGATGGTGGACAGCATCATGGTGCAT
genomic: AGAAGGACATTGTTAAGCTTCAACATGGCGAATACGTATCGCTGGGCAAGgtatgatgct ... cttttggcagGTCGAGGCAGCATTATCGGTTAGCCCGATGGTGGACAGCATCATGGTGCAT
EST: gi|169020953|gb|FE429340.1|FE429340
EST:     AGAAGGACATTGTTAAGCTTCAACATGGCGAATACGTATCGCTGGGCAAG                         GTCGAGGCAGCATTATCGGTTAGCCCGATGGTGGACAGCATCATGGTGCAT
genomic: AGAAGGACATTGTTAAGCTTCAACATGGCGAATACGTATCGCTGGGCAAGgtatgatgct ... cttttggcagGTCGAGGCAGCATTATCGGTTAGCCCGATGGTGGACAGCATCATGGTGCAT
EST: gi|169062086|gb|FE469678.1|FE469678
EST:     AGAAGGACATTGTTAAGCTTCAACATGGCGAATACGTATCGCTGGGCAAG                         GTCGAGGCAGCATTATCGGTTAGCCCGATGGTGGACAGCATCATGGTGCAT
genomic: AGAAGGACATTGTTAAGCTTCAACATGGCGAATACGTATCGCTGGGCAAGgtatgatgct ... cttttggcagGTCGAGGCAGCATTATCGGTTAGCCCGATGGTGGACAGCATCATGGTGCAT
EST: gi|169081832|gb|FE487445.1|FE487445
EST:     AGAAGGACATTGTTAAGCTTCAACATGGCGAATACGTATCGCTGGGCAAG                         GTCGAGGCAGCATTATCGGTTAGCCCGATGGTGGACAGCATCATGGTGCAT
genomic: AGAAGGACATTGTTAAGCTTCAACATGGCGAATACGTATCGCTGGGCAAGgtatgatgct ... cttttggcagGTCGAGGCAGCATTATCGGTTAGCCCGATGGTGGACAGCATCATGGTGCAT
EST: gi|169088887|gb|FE492865.1|FE492865
EST:     AGAAGGACATTGTTAAGCTTCAACATGGCGAATACGTATCGCTGGGCAAG                         GTCGAGGCAGCATTATCGGTTAGCCCGATGGTGGACAGCATCATGGTGCAT
genomic: AGAAGGACATTGTTAAGCTTCAACATGGCGAATACGTATCGCTGGGCAAGgtatgatgct ... cttttggcagGTCGAGGCAGCATTATCGGTTAGCCCGATGGTGGACAGCATCATGGTGCAT
EST: gi|169098740|gb|FE500252.1|FE500252
EST:     AGAAGGACATTGTTAAGCTTCAACATGGCGAATACGTATCGCTGGGCAAG                         GTCGAGGCAGCATTATCGGTTAGCCCGATGGTGGACAGCATCATGGTGCAT
genomic: AGAAGGACATTGTTAAGCTTCAACATGGCGAATACGTATCGCTGGGCAAGgtatgatgct ... cttttggcagGTCGAGGCAGCATTATCGGTTAGCCCGATGGTGGACAGCATCATGGTGCAT
EST: gi|169113590|gb|FE514501.1|FE514501
EST:     AGAAGGACATTGTTTAGCTTCAACATGGCGAATACGTATCGCTGGGCAAG                         GTCGAGGCAGCATTATCGGTTAGCCCGATGGTGGACAGCATCATGGTGCAT
genomic: AGAAGGACATTGTTAAGCTTCAACATGGCGAATACGTATCGCTGGGCAAGgtatgatgct ... cttttggcagGTCGAGGCAGCATTATCGGTTAGCCCGATGGTGGACAGCATCATGGTGCAT
EST: gi|169054875|gb|FE463479.1|FE463479
EST:     AGAAGGACATTGTTAAGCTTCAACATGGCGAATACGTATCGCTGGGCAAG                         GTCGAGGCAGCATTATCGGTTAGCCCGATGGTGGACAGCATCATGGTGCAT
genomic: AGAAGGACATTGTTAAGCTTCAACATGGCGAATACGTATCGCTGGGCAAGgtatgatgct ... cttttggcagGTCGAGGCAGCATTATCGGTTAGCCCGATGGTGGACAGCATCATGGTGCAT

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), 35 (downstream exon)
Score: 38

TGACATTGGACAATTCCATCCCGATGGTTGCTTAGAAATTGTAGACCGGAAGAAGGACATTGTTAAGCTTCAACATGGCGAATACGTATCGCTGGGCAAGgtatgatgct ... cttttggcagGTCGAGGCAGCATTATCGGTTAGCCCGATGGTGGACAGCATCATGGTGCATGCTGATCCTTTCCACAGCTACTGCGTTGCGCTGGTTGTACCATCGCAGA




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