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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTCCTACTCGCAGAGCCTCACTAAGAGGCCCATGAAGGGAATGCTCACGGGACCCGTGACAATTTTGAACTGGTCCTTCGTCAGAAATGACCAGCCGAGgtgagcttttgtctttctcatcgacatctttgctaactggtcttacgtttcattcattcaccacag

Basic information

species Selaginella moellendorffii
transcript EFJ28889
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ28889 (Selaginella moellendorffii), 5'ss of exon 9
lower sequence: LOC_Os12g42884.3 (Oryza sativa), 5'ss of exon 11
CTTCCTACTCGCAGAGCCTCACTAAGAGGCCCATGAAGGGAATGCTCACGGGACCCGTGACAATTTTGAACTGGTCCTTCGTCAGAAATGACCAGCCGAGgtgagcttttgtctttctcatcgacatctttgctaactggtcttacgtttcattcattcaccacag-----------------------
|        |||||||| | ||     | ||||||||||||||| | || || ||||| |||||  | |||||||| || ||||| ||||||||||||||||  |    |||  ||      |  ||  |   ||    |  || || || |    |        |                       
CCAAGATGGCGCAGAGCATGACCTCTCGCCCCATGAAGGGAATGTTGACTGGTCCCGTCACAATCCTTAACTGGTCTTTTGTCAGGAATGACCAGCCGAGgtccgtgcctgttgttgatgatgcaatgctaattattcagg-ttgcgattgagctttctgttgaggctgacattttcacacttgctcag

upper sequence: EFJ28889 (Selaginella moellendorffii), 5'ss of exon 9
lower sequence: LOC_Os12g42876.1 (Oryza sativa), 5'ss of exon 10
CTTCCTACTCGCAGAGCCTCACTAAGAGGCCCATGAAGGGAATGCTCACGGGACCCGTGACAATTTTGAACTGGTCCTTCGTCAGAAATGACCAGCCGAGgtgagcttttgtctttctcatcgacatctttgctaa-ctggtcttacgttt-cattcattcaccacag----------------------
|    |   |||||||| | ||     | ||||||||||||||| | || || ||||| |||||  | |||||||| || ||||| |||||||||||||||| ||    |||  ||   |  |  ||||    |   |||||  |   |   ||||| ||    |                         
CCAAGTTGGCGCAGAGCATGACCTCTCGCCCCATGAAGGGAATGTTGACTGGTCCCGTCACAATCCTTAACTGGTCTTTTGTCAGGAATGACCAGCCGAGgtcagtgcctgttgttgataatgtaatctaatttgttctggttgtgaatgagcattcttttctgagtctgacattcatacgctggctcag

upper sequence: EFJ28889 (Selaginella moellendorffii), 5'ss of exon 9
lower sequence: GRMZM2G149751_T03 (Zea mays), 5'ss of exon 11
CTTCCTACTCGCAGAGCCTCACTAAGAGGCCCATGAAGGGAATGCTCACGGGACCCGTGACAATTTTGAACTGGTCCTTCGTCAGAAATGACCAGCCGAGgtgagcttttgtctttctcatcgac--atctttgctaactggtcttacgtttcattcattcaccacag-----------------------------
|        | |||||| | ||     | || |||||||| ||||| || || || || |||||  | ||||||||||||||| | |||||||||||||||| ||    |         |  |    || | || |     |     |||||  ||| | |      |                             
CGAAGACGGCACAGAGCATGACGTCTCGCCCAATGAAGGGGATGCTGACTGGCCCAGTCACAATCCTCAACTGGTCCTTCGTCCGGAATGACCAGCCGAGgtcagtaactagagcaagaacggtttgatttctggtgctcagagcaccgttttcttcttccgtttttggtactgacgttgctcctcccatcttccag

upper sequence: EFJ28889 (Selaginella moellendorffii), 5'ss of exon 9
lower sequence: GLYMA13G15140.1 (Glycine max), 5'ss of exon 10
CTTCCTACTCGCAGAGCCTCACTAAGAGGCCCATGAAGGGAATGCTCACGGGACCCGTGACAATTTTGAACTGGTCCTTCGTCAGAAATGACCAGCCGAGgtgag----------cttttgtctttctcatcgacatctttgctaactggtcttacgt-ttcattcattcaccacag------------
||||     | || ||  | || ||  | || |||||||||||||| || || || || || ||| ||||||||||||| || ||| |||||||||| ||||  |           || || ||  ||    |   |   || |   |  |  |   | |   |||||| | ||               
CTTCAACTGCTCAAAGTTTGACCAAACGACCAATGAAGGGAATGCTTACTGGCCCTGTTACTATTCTGAACTGGTCCTTTGTTAGAGATGACCAGCCAAGgtatgaaaataattctttatggctaccttgcaggtttgaatgatcgtttttgctggatatctgttcatttaacattatcttgttattag

upper sequence: EFJ28889 (Selaginella moellendorffii), 5'ss of exon 9
lower sequence: Vv06s0009g01080.t01 (Vitis vinifera), 5'ss of exon 10
CTTCCTACTCGCAGAGCCTCACTAAGAGGCCCATGAAGGGAATGCTCACGGGACCCGTGACAATTTTGAACTGGTCCTTCGTCAGAAATGACCAGCCGAGgtgag---cttttgtctttctcatcgacatct-ttgctaactggtcttacgtttcattcattcaccacag-------------------
| ||     | |||||| | |||||| | || |||||||||||||| || ||||| || || ||  |||||||||| || ||||||||||||||||| |||| ||    |   | |   |  ||| |  ||  | | |  ||    ||  |||  | | ||| |    |                    
CCTCAATGGCTCAGAGCATGACTAAGCGCCCAATGAAGGGAATGCTAACTGGACCTGTTACCATCCTGAACTGGTCTTTTGTCAGAAATGACCAGCCCAGgtaagaaaatcaagccaaccaaatctatctcagtcgatttctacgattttgttataatgattgaatctaatgcttttacctgatcttag

upper sequence: EFJ28889 (Selaginella moellendorffii), 5'ss of exon 9
lower sequence: Vv08s0056g01570.t01 (Vitis vinifera), 5'ss of exon 10
CTTCCTACTCGCAGAGCCTCACTAAGAGGCCCATGAAGGGAATGCTCACGGGACCCGTGACAATTTTGAACTGGTCCTTCGTCAGAAATGACCAGCCGAGgtgagcttttgtctttctcatcgacatctttgctaactggtcttacgtttcattc--attcaccacag-----------------------------
|  ||    | |||||| | |||    | || |||||||||||||| || || || || || ||| ||||||||||||||||  ||||||||||||| ||||     ||       |||||  | | |      |    |   ||  | ||  |   | | |  | ||                             
CCACCATGGCTCAGAGCATGACTGCTCGCCCAATGAAGGGAATGCTTACTGGCCCTGTTACTATTCTGAACTGGTCCTTCGTGCGAAATGACCAGCCCAGgta----ttaagaaaactcataaaaagcggcttaagaaagatgtatatctctctgaaactaataatagtttgcatgatttatatggcttcttttcag

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|169057671|gb|FE463722.1|FE463722
EST:     AAATGACCAGCCGAG                         AGAGAAAACCACGTACCAGATTGCCTTGTCCATCAAAGAGGAGGTCGAAGA
genomic: AAATGACCAGCCGAGgtgagctttt ... ttcaccacagAGAGAAAACCACGTACCAGATTGCCTTGTCCATCAAAGAGGAGGTCGAAGA
EST: gi|169060119|gb|FE468105.1|FE468105
EST:     GGACCCGTGACAATTTTGAACTGGTCCTTCGTCAGAAATGACCAGCCGAG                         AGAGAAAACCACGTACCAGATTGCCTTGTCCATCAAAGAGGAGGTCGAAGA
genomic: GGACCCGTGACAATTTTGAACTGGTCCTTCGTCAGAAATGACCAGCCGAGgtgagctttt ... ttcaccacagAGAGAAAACCACGTACCAGATTGCCTTGTCCATCAAAGAGGAGGTCGAAGA
EST: gi|169109743|gb|FE511814.1|FE511814
EST:     CTGGTCCTTCGTCAGAAATGACCAGCCGAG                         AGAGAAAACCACGTACCAGATTGCCTTGTCCATCAAAGAGGAGGTCGAAGA
genomic: CTGGTCCTTCGTCAGAAATGACCAGCCGAGgtgagctttt ... ttcaccacagAGAGAAAACCACGTACCAGATTGCCTTGTCCATCAAAGAGGAGGTCGAAGA
EST: gi|169057672|gb|FE463723.1|FE463723
EST:     GGACCCGTGACAATTTTGAACTGGTCCTTCGTCAGAAATGACCAGCCGAG                         AGAGAAAACCACGTACCAGATTGCCTTGTCCATCANAGAGGAGGTCGAAGA
genomic: GGACCCGTGACAATTTTGAACTGGTCCTTCGTCAGAAATGACCAGCCGAGgtgagctttt ... ttcaccacagAGAGAAAACCACGTACCAGATTGCCTTGTCCATCAAAGAGGAGGTCGAAGA
EST: gi|169101347|gb|FE502516.1|FE502516
EST:     GGACCCGTGACAATTTTGAACTGGTCCTTCGTCAGAAATGACCAGCCGAG                         AGAGAAAACCACGTACCAGATTGCCTTGTCCATCAAAGAGGAGGTCGAAGA
genomic: GGACCCGTGACAATTTTGAACTGGTCCTTCGTCAGAAATGACCAGCCGAGgtgagctttt ... ttcaccacagAGAGAAAACCACGTACCAGATTGCCTTGTCCATCAAAGAGGAGGTCGAAGA
EST: gi|169103370|gb|FE507542.1|FE507542
EST:     GGACCCGTGACAATTTTGAACTGGTCCTTCGTCAGAAATGACCAGCCGAG                         AGAGAAAACCACGTACCAGATTGCCTTGTCCATCAAAGAGGAGGTCGAAGA
genomic: GGACCCGTGACAATTTTGAACTGGTCCTTCGTCAGAAATGACCAGCCGAGgtgagctttt ... ttcaccacagAGAGAAAACCACGTACCAGATTGCCTTGTCCATCAAAGAGGAGGTCGAAGA
EST: gi|169030928|gb|FE440328.1|FE440328
EST:     GAAATGACCAGCCGAG                         AGAGAAAACCACGTACCAGATTGCCTTGTCCATCAAAGAGGAGGTCGAAGA
genomic: GAAATGACCAGCCGAGgtgagctttt ... ttcaccacagAGAGAAAACCACGTACCAGATTGCCTTGTCCATCAAAGAGGAGGTCGAAGA
EST: gi|169061438|gb|FE469537.1|FE469537
EST:     GGACCCGTGACAATTTTGAACTGGTCCTTCGTCAGAAATGACCAGCCGAG                         AGAGAAAACCACGTACCAGATTGCCTTGTCCATCAAAGAGGAGGTCGAAGA
genomic: GGACCCGTGACAATTTTGAACTGGTCCTTCGTCAGAAATGACCAGCCGAGgtgagctttt ... ttcaccacagAGAGAAAACCACGTACCAGATTGCCTTGTCCATCAAAGAGGAGGTCGAAGA
EST: gi|169032657|gb|FE436930.1|FE436930
EST:     GGACCCGTGACAATTTTGAACTGGTCCTTCGTCAGAAATGACCAGCCGAG                         AGAGAAAACCACGTACCAGATTGCCTTGTCCATCAAAGAGGAGGTCGAAGA
genomic: GGACCCGTGACAATTTTGAACTGGTCCTTCGTCAGAAATGACCAGCCGAGgtgagctttt ... ttcaccacagAGAGAAAACCACGTACCAGATTGCCTTGTCCATCAAAGAGGAGGTCGAAGA
EST: gi|169022654|gb|FE429707.1|FE429707
EST:     GGACCCGTGACAATTTTGAACTGGTCCTTCGTCAGAAATGACCAGCCGAG                         AGAGAAAACCACGTACCAGATTGCCTTGTCCATCAAAGAGGAGGTCGAAGA
genomic: GGACCCGTGACAATTTTGAACTGGTCCTTCGTCAGAAATGACCAGCCGAGgtgagctttt ... ttcaccacagAGAGAAAACCACGTACCAGATTGCCTTGTCCATCAAAGAGGAGGTCGAAGA
EST: gi|169022653|gb|FE429706.1|FE429706
EST:     GGACCCGTGACAATTTTGAACTGGTCCTTCGTCAGAAATGACCAGCCGAG                         AGAGAAAACCACGTACCAGATTGCCTTGTCCATCAAAGAGGAGGTCGAAGA
genomic: GGACCCGTGACAATTTTGAACTGGTCCTTCGTCAGAAATGACCAGCCGAGgtgagctttt ... ttcaccacagAGAGAAAACCACGTACCAGATTGCCTTGTCCATCAAAGAGGAGGTCGAAGA
EST: gi|169027728|gb|FE434865.1|FE434865
EST:     ACCCGTGACAATTTTGAACTGGTCCTTCGTCAGAAATGACCAGCCGAG                         AGAGAAAACCACGTACCAGATTGCCTTGTCCATCAAAGAGGAGGTCGAAGA
genomic: ACCCGTGACAATTTTGAACTGGTCCTTCGTCAGAAATGACCAGCCGAGgtgagctttt ... ttcaccacagAGAGAAAACCACGTACCAGATTGCCTTGTCCATCAAAGAGGAGGTCGAAGA
EST: gi|169053882|gb|FE460973.1|FE460973
EST:     GGACCCGTGACAATTTTGAACTGGTCCTTCGTCAGAAATGACCAGCCGAG                         AGAGAAAACCACGTACCAGATTGCCTTGTCCATCAAAGAGGAGGTCGAAGA
genomic: GGACCCGTGACAATTTTGAACTGGTCCTTCGTCAGAAATGACCAGCCGAGgtgagctttt ... ttcaccacagAGAGAAAACCACGTACCAGATTGCCTTGTCCATCAAAGAGGAGGTCGAAGA
EST: gi|169101346|gb|FE502515.1|FE502515
EST:     GGACCCGTGACAATTTTGAACTGGTCCTTCGTCAGAAATGACCAGCCGAG                         AGAGAAAACCACGTACCAGATTGCCTTGTCCATCAAAGAGGAGGTCGAAGA
genomic: GGACCCGTGACAATTTTGAACTGGTCCTTCGTCAGAAATGACCAGCCGAGgtgagctttt ... ttcaccacagAGAGAAAACCACGTACCAGATTGCCTTGTCCATCAAAGAGGAGGTCGAAGA

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: 139

CTTCCTACTCGCAGAGCCTCACTAAGAGGCCCATGAAGGGAATGCTCACGGGACCCGTGACAATTTTGAACTGGTCCTTCGTCAGAAATGACCAGCCGAGgtgagctttt ... ttcaccacagAGAGAAAACCACGTACCAGATTGCCTTGTCCATCAAAGAGGAGGTCGAAGACCTTGAGAAAGCTGGCATCCAT




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