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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTATTCACTGGGCTACTGTCGGCCCGAGAAAATTCTCAACAGTGCCGAGAACTTGGGGGAAGTTCTTCGTGGGGATCGGATCGAGAACTCTGTTTATTCTgtaagcatgtttccgctgataatatttgtttctaaaagtttttgcttcgcag

Basic information

species Selaginella moellendorffii
transcript EFJ33415
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ33415 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: LOC_Os06g37160.1 (Oryza sativa), 5'ss of exon 2
CTATTCACTGGGCTACTGTCGGCCCGAGAAAATTCTCAACAGTGCCGAGAACTTGGGGGAAGTTCTTCGTGGGGATCGGATCGAGAACTCTGTTTATTCTgtaagcatgtt--tccgctgataatatttgtttc--taaaagtttttgct--tcgcag------------------------------------------------------------------------------------
|||||  || | ||||||    || |||  ||||   || ||||| |||||||| |||||||| |||||||||||||| || || |||||||| |||  ||||||  | ||  |   || ||     | |||||   | ||| |  ||||  | | ||                                                                                    
CTATTTTCTAGACTACTGCAAACCTGAGGCAATTAAGAATAGTGCTGAGAACTTAGGGGAAGTCCTTCGTGGGGATCGCATTGAAAACTCTGTCTATAATgtaaggctattacttttctaattgctctagtttcaacacaagatgatgctgcttgtagggctagggagcagtggagctttgccacttactatgcaaaactgtttgttcattagctatagtttaactttttcaactcttgtag

upper sequence: EFJ33415 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: LOC_Os08g17370.1 (Oryza sativa), 5'ss of exon 2
-CTATTCACTGGGCTACTGTCGGCCCGAGAAAATTCTCAACAGTGCCGAGAACTTGGGGGAAGTTCTTCGTGGGGATCGGATCGAGAACTCT---------GTTTATTCTgtaagcatgtttccgctgataatatttgtttctaaaagttttt-gcttcgcag---------------------
   ||  |    |   | |    ||       ||  || |||||||  | ||  | || |||||||||||||| ||||| ||||||||||||         |||| ||     | |  |||| |  |||| || | |   | ||   ||  |  | ||   |                      
GACATCAATCAAGACCCAGCTTCCCTACTCTTATG-TCGACAGTGCTCAAAATCTCGGTGAAGTTCTTCGTGGTGATCGAATCGAGAACTCTCCATACACGgtttgttactctatcgcgttttctttgattatttcttgatatattggtcctaaggttaatattttaacttctattctttccag

upper sequence: EFJ33415 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: PP1S140_64V6.1 (Physcomitrella patens), 5'ss of exon 2
CTATTCACTGGGCTACTGTCGGCCCGA---GAAAATTCTCAACAGTGCCGAGAACTTGGGGGAAGTTCTTCGTGGGGATCGGATCGAGAACTCTGTTTATTCTgtaagcatgtttccgctgataatatttgtttctaaaagtttttgcttcgcag------------------------------------------------
    || || | ||||||   |||          ||| | |||||||||||||||||||| || |||||||| || ||||| || ||||||||   |||   |||| | |   |       | | | || ||    | || | ||| |  |   |                                                
---CTCGCTTGACTACTGCAAGCCAAGTTCAGGGATTGTGAACAGTGCCGAGAACTTGGGAGAGGTTCTTCGAGGTGATCGCATTGAGAACTCACCTTACGTTgtacgtaatctctgagccaaagtcttggtgcacataattcttttcagcaatgttagtataccccttgagttgaaggctttatattgtacgttatacatct

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|169018854|gb|FE427039.1|FE427039
EST:     ACTTGGGGGAAGTTCTTCGTGGGGATCGGATCGAGAACTCTGTTTATTCT                         TTTTCCATGAGGGAAGACAGGTCGTGCATTGTTGCTTGCAAAGGCGAAAAG
genomic: ACTTGGGGGAAGTTCTTCGTGGGGATCGGATCGAGAACTCTGTTTATTCTgtaagcatgt ... tgcttcgcagTTTTCCATGAAGGAAGACAAGTCGTGCATTGTTGCTTGCAAAGGCGAAAAG
EST: gi|169075702|gb|FE481776.1|FE481776
EST:     ACTTGGGGGAAGTTCTTCGTGGGGATCGGATCGAGAACTCTGTTTATTCT                         TTTTCCATGAAGGAAGACAAGTCGTGCATTGTTGCTTGCAAAGGCGAAAAG
genomic: ACTTGGGGGAAGTTCTTCGTGGGGATCGGATCGAGAACTCTGTTTATTCTgtaagcatgt ... tgcttcgcagTTTTCCATGAAGGAAGACAAGTCGTGCATTGTTGCTTGCAAAGGCGAAAAG
EST: gi|169115215|gb|FE516970.1|FE516970
EST:     ACTTGGGGGAAGTTCTTCGTGGGGATCGGATCGAGAACTCTGTTTATTCT                         TTTTCCATGAAGGAAGACAAGTCGTGCATTGTTGCTTGCAAAGGCGAAAAG
genomic: ACTTGGGGGAAGTTCTTCGTGGGGATCGGATCGAGAACTCTGTTTATTCTgtaagcatgt ... tgcttcgcagTTTTCCATGAAGGAAGACAAGTCGTGCATTGTTGCTTGCAAAGGCGAAAAG
EST: gi|169024527|gb|FE436285.1|FE436285
EST:     ATCGAGAACTCTGTTTATTCT                         TTTTCCATGAAGGAAGACAAGTCGTGCATTGTTGCTTGCAAAGGCGAAAAG
genomic: ATCGAGAACTCTGTTTATTCTgtaagcatgt ... tgcttcgcagTTTTCCATGAAGGAAGACAAGTCGTGCATTGTTGCTTGCAAAGGCGAAAAG
EST: gi|169025118|gb|FE434705.1|FE434705
EST:     ACTTGGGGGAAGTTCTTCGTGGGGATCGGATCGAGAACTCTGTTTATTCT                         TTTTCCATGAGGGAAGACAGGTCGTGCATTGTTGCTTGCAAAGGCGAAAAG
genomic: ACTTGGGGGAAGTTCTTCGTGGGGATCGGATCGAGAACTCTGTTTATTCTgtaagcatgt ... tgcttcgcagTTTTCCATGAAGGAAGACAAGTCGTGCATTGTTGCTTGCAAAGGCGAAAAG
EST: gi|169041649|gb|FE448232.1|FE448232
EST:     ACTTGGGGGAAGTTCTTCGTGGGGATCGGATCGAGAACTCTGTTTATTCT                         TTTTCCATGAGGGAAGACAGGTCGTGCATTGTTGCTTGCAAAGGCGAAAAG
genomic: ACTTGGGGGAAGTTCTTCGTGGGGATCGGATCGAGAACTCTGTTTATTCTgtaagcatgt ... tgcttcgcagTTTTCCATGAAGGAAGACAAGTCGTGCATTGTTGCTTGCAAAGGCGAAAAG
EST: gi|169031680|gb|FE437481.1|FE437481
EST:     ACTTGGGGGAAGTTCTTCGTGGGGATCGGATCGAGAACTCTGTTTATTCT                         TTTTCCATGAGGGAAGACAGGTCGTGCATTGTTGCTTGCAAAGGCGAAAAG
genomic: ACTTGGGGGAAGTTCTTCGTGGGGATCGGATCGAGAACTCTGTTTATTCTgtaagcatgt ... tgcttcgcagTTTTCCATGAAGGAAGACAAGTCGTGCATTGTTGCTTGCAAAGGCGAAAAG
EST: gi|169029116|gb|FE439374.1|FE439374
EST:     ATCGGATCGAGAACTCTGTTTATTCT                         TTTTCCATGAGGGAAGACAGGTCGTGCATTGTTGCTTGCAAAGGCGAAAAG
genomic: ATCGGATCGAGAACTCTGTTTATTCTgtaagcatgt ... tgcttcgcagTTTTCCATGAAGGAAGACAAGTCGTGCATTGTTGCTTGCAAAGGCGAAAAG
EST: gi|169081742|gb|FE488200.1|FE488200
EST:     CGGATCGAGAACTCTGTTTATTCT                         TTTTCCATGAAGGAAGACAAGTCGTGCATTGTTGCTTGCAAAGGCGAAAAG
genomic: CGGATCGAGAACTCTGTTTATTCTgtaagcatgt ... tgcttcgcagTTTTCCATGAAGGAAGACAAGTCGTGCATTGTTGCTTGCAAAGGCGAAAAG

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: 30 (upstream exon), 34 (downstream exon)
Score: 21

CTATTCACTGGGCTACTGTCGGCCCGAGAAAATTCTCAACAGTGCCGAGAACTTGGGGGAAGTTCTTCGTGGGGATCGGATCGAGAACTCTGTTTATTCTgtaagcatgt ... tgcttcgcagTTTTCCATGAAGGAAGACAAGTCGTGCATTGTTGCTTGCAAAGGCGAAAAGCTGTCCGAAAAGAGTGCCAAGAATTTCAAAGAGAAGATTGACGAGGATT




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