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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGGTTGATCCATGTGACGATCTGACTGATGAAGATATCCGAACAGCCATTCAAAATGCCACTGGTCCAAAAAATGTTCTGTTTGTGCCCGAGgtacgctattcagtatcttgtttttcgttgtcattcggagtttttccag

Basic information

species Selaginella moellendorffii
transcript EFJ37641
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ37641 (Selaginella moellendorffii), 5'ss of exon 10
lower sequence: GRMZM2G129155_T01 (Zea mays), 5'ss of exon 10
GAGGTTGATCCATGTGACGATCTGACTGATGAAGATATCCGAACAGCCATTCAAAATGCCACTGGTCCAAAAAATGTTCTGTTTGTGCCCGAGgtacgctattcagtatcttgtttttcgt-tgtcattcggagtttttccag--------------------------------------------------
||||||||||| ||||| ||| | || |||||||||||||| |  || ||||||||||| |||||||| | || || ||||||||| || || ||| | |   |  |  ||  | || |||   | |||  |     |  ||                                                   
GAGGTTGATCCTTGTGAGGATGTTACAGATGAAGATATCCGCATGGCTATTCAAAATGCAACTGGTCCTAGAAGTGCTCTGTTTGTACCTGAAgtaagatgcacc-tgcctcttattgcgtgcattattgaggcacatagcaatcatcgttggaacttttagctgataattctttgctaacaatcacttaaag

upper sequence: EFJ37641 (Selaginella moellendorffii), 5'ss of exon 10
lower sequence: GLYMA07G30150.1 (Glycine max), 5'ss of exon 10
GAGGTTGATCCATGTGACGATCTGACTGATGAAGATATCCGAACAGCCATTCAAAATGCCACTGGTCCAAAAAATGTTCTGTTTGTGCCCGAGgtacg-ctattcagtatcttgtttttcgttgtcattcggagtttttccag------------------------------------------------------------------------------------
||||| ||||||||||| ||| |||||||||| ||||| || |||||||| || ||||||||||| || |||   |  |||||||| || || ||| | ||| ||    |||| ||   |     |    |   ||||   ||                                                                                    
GAGGTGGATCCATGTGAAGATTTGACTGATGATGATATTCGCACAGCCATACAGAATGCCACTGGACCTAAATCAGCACTGTTTGTTCCAGAAgtaggtctaatcgccctcttattgcacacacacccctgatattttcttagttgaaaccacattcttatcctaccaaatatgtaaattatttggccaactgaaaaaatacttatctattattttcatgttattag

upper sequence: EFJ37641 (Selaginella moellendorffii), 5'ss of exon 10
lower sequence: PP1S82_15V6.1 (Physcomitrella patens), 5'ss of exon 10
-------GAGGTTGATCCATGTGACGATCTGACTGATGAAGATATCCGAACAGCCATTCAAAATGCCACTGGTCCAAAAAATGTTCTGTTTGTGCCCGAGgtacgct---attcagtatcttgtttttcgttgtca----ttcggagtttttccag--------------------------------------------
       ||||||||||||||||| | | | || ||||| ||||| ||||| |||||||||||||| || || || |||||||| || |||||||| |||||||  |   |  | ||||     ||   || |          || ||  |  ||                                             
GGTACAGGAGGTTGATCCATGTGATGTTTTAACCGATGAGGATATTCGAACTGCCATTCAAAATGCAACAGGACCCAAAAATGTGCTCTTTGTGCCTGAGgtacaattcaaaacggtattacccttgcagtggctgaaatcctggtgtaatgtcaatctgaacagccgtagagctaagatcaattatttccttgggcaga

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|169045738|gb|FE453050.1|FE453050
EST:     CAGCCATTCAAAATGCCACTGGTCCAAAAAATGTTCTGTTTGTGCCCGAG                         GTTCCTTTTGAGGTACTCGTTCGTCGGCAGATAGCTCGCTTGCTAGAACCA
genomic: CAGCCATTCAAAATGCCACTGGTCCAAAAAATGTTCTGTTTGTGCCCGAGgtacgctatt ... gtttttccagGTTCCTTTTGAGGTACTCGTTCGTCGGCAGATAGCTCGCTTGCTAGAACCA
EST: gi|169096017|gb|FE500008.1|FE500008
EST:     CAGCCATTCAAAATGCCACTGGTCCAAAAAATGTTCTGTTTGTGCCCGAG                         GTTCCTTTTGAGGTACTCGTTCGTCGGCAGATAGCTCGCTTGCTAGAACCA
genomic: CAGCCATTCAAAATGCCACTGGTCCAAAAAATGTTCTGTTTGTGCCCGAGgtacgctatt ... gtttttccagGTTCCTTTTGAGGTACTCGTTCGTCGGCAGATAGCTCGCTTGCTAGAACCA

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: 29 (upstream exon), 32 (downstream exon)
Score: 3

GAGGTTGATCCATGTGACGATCTGACTGATGAAGATATCCGAACAGCCATTCAAAATGCCACTGGTCCAAAAAATGTTCTGTTTGTGCCCGAGgtacgctatt ... gtttttccagGTTCCTTTTGAGGTACTCGTTCGTCGGCAGATAGCTCGCTTGCTAGAACCAAGTTTGCAGTGTGCCAGATTTATCTACGACGAGCTTGTTAAG




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