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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAAGAACTTGTCAATGAAGACTTGGAATGCCTCGTTCTTGCTAGCGATGGACTTTGGGATGTCGTGGAAAATGAGgtaataaaccaccaagcacattatctcaacctgaaaacgattcgaatttctcaatgaaaccactgctgcttatgtagcattgaacaaagcatcactttattgtcttctctgtctgatctgggtatacatttttaatgattgctaaattctctgataattctgtttaccaaaatag

Basic information

species Oryza sativa
transcript LOC_Os02g15594.1
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g15594.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G073788_T01 (Zea mays), 5'ss of exon 7
GAAGAACTTGTCAATGAAGACTTGGAATGCCTCGTTCTTGCTAGCGATGGACTTTGGGATGTCGTGGAAAATGAGgtaataaaccaccaagcacattatctcaacctgaaaacgattcgaatttctcaatgaaaccactgctgcttatgtagcattgaac-aaagcatcactttattgtcttctctgtctgatctgggtatacatttttaatgattgctaaattctctgataattctgtttaccaaaatag-----------------------------
|||||||  |||| ||  |   |||||||||| ||||||||||| ||||| ||||||||||| ||||||||||||||||||| ||  | | ||  | |      ||| | | |     |      |  | | ||          || | ||  |||| |  |||||||||||| | || |||  |||| || | ||||  |||||| ||     |||  |       |||||  |    |||   ||  |                              
GAAGAACAGGTCAGTGGTGGGCTGGAATGCCTGGTTCTTGCTAGTGATGGGCTTTGGGATGTTGTGGAAAATGAGgtaataacccttcca-caattcagtcattcctcagagcaggcagttgccttttacgtaa--------atttgtata--attgtatgaaagcatcacttcactgcctttactgtttgctttggggctacattcttgtgctttg--aggcatattgatatcttcacttaattaataacaatgttgttgatgcttttatgaaaaaaag

upper sequence: LOC_Os02g15594.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G442404_T01 (Zea mays), 5'ss of exon 7
GAAGAACTTGTCAATGAAGACTTGGAATGCCTCGTTCTTGCTAGCGATGGACTTTGGGATGTCGTGGAAAATGAGgtaataaaccaccaagcacattatctcaacctgaaaacgattcgaatttctcaatgaaaccactgctgcttatgtagcattgaaca-aagcatcactttattgtcttctctgtctgatctgggtatacatttttaatgattgctaaattctctgataattctgtttaccaaaatag
|||||||   ||| ||| ||  |||||||||| ||||| ||||| || || ||||||||||| |||||||||||||||||||     |     || ||| |||  |     |   ||| || |   || |         | |   | ||||  |||| |   || |||||| | | || |||  |                                                                  
GAAGAACAGTTCAGTGATGAGCTGGAATGCCTGGTTCTCGCTAGTGACGGGCTTTGGGATGTTGTGGAAAATGAGgtaataacttttc-----cactat-tcagtc-----attcttcaaagtaggcagttgctttttaggtaaatttgtataattgtatggaaacatcacctcactgccttaacc-----------------------------------------------------------------
















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|86428595|gb|CI075276.1|CI075276
EST:     AATGCCTCGTTCTTGCTAGCGATGGACTTTGGGATGTCGTGGAAAATGAG                         GAAGCTGTTTCCCTTGCGAAAACAGAAGACCTGCCTGAGTCGGTGGCTAGG
genomic: AATGCCTCGTTCTTGCTAGCGATGGACTTTGGGATGTCGTGGAAAATGAGgtaataaacc ... accaaaatagGAAGCTGTTTCCCTTGCGAAAACAGAAGACCTGCCTGAGTCGGTGGCTAGG
EST: gi|89198338|gb|CI007398.1|CI007398
EST:     AATGCCTCGTTCTTGCTAGCGATGGACTTTGGGATGTCGTGGAAAATGAG                         GAAGCTGTTTCCCTTGCGAAAACAGAAGACCTGCCTGAGTCGGTGGCTAGG
genomic: AATGCCTCGTTCTTGCTAGCGATGGACTTTGGGATGTCGTGGAAAATGAGgtaataaacc ... accaaaatagGAAGCTGTTTCCCTTGCGAAAACAGAAGACCTGCCTGAGTCGGTGGCTAGG
EST: gi|29639155|gb|CB644164.1|CB644164
EST:     AATGCCTCGTTCTTGCTAGCGATGGACTTTGGGATGTCGTGGAAAATGAG                         GAAGCTGTTTCCCTTGCGAAAACAGAAGACCTGCCTGAGTCGGTGGCTAGG
genomic: AATGCCTCGTTCTTGCTAGCGATGGACTTTGGGATGTCGTGGAAAATGAGgtaataaacc ... accaaaatagGAAGCTGTTTCCCTTGCGAAAACAGAAGACCTGCCTGAGTCGGTGGCTAGG
EST: gi|25797747|gb|CA753700.1|CA753700
EST:     AATGCCTCGTTCTTGCTAGCGATGGACTTTGGGATGTCGTGGAAAATGAG                         GAAGCTGTTTCCCTTGCGAAAACAGAAGACCTGCCTGAGTCGGTGGCTAGG
genomic: AATGCCTCGTTCTTGCTAGCGATGGACTTTGGGATGTCGTGGAAAATGAGgtaataaacc ... accaaaatagGAAGCTGTTTCCCTTGCGAAAACAGAAGACCTGCCTGAGTCGGTGGCTAGG
EST: gi|87010644|gb|CI278346.1|CI278346
EST:     AATGCCTCGTTCTTGCTAGCGATGGACTTTGGGATGTCGTGGAAAATGAG                         GAAGCTGTTTCCCTTGCGAAAACAGAAGACCTGCCTGAGTCGGTGGCTAGG
genomic: AATGCCTCGTTCTTGCTAGCGATGGACTTTGGGATGTCGTGGAAAATGAGgtaataaacc ... accaaaatagGAAGCTGTTTCCCTTGCGAAAACAGAAGACCTGCCTGAGTCGGTGGCTAGG
EST: gi|86600759|gb|CI356516.1|CI356516
EST:     AATGCCTCGTTCTTGCTAGCGATGGACTTTGGGATGTCGTGGAAAATGAG                         GAAGCTGTTTCCCTTGCGAAAACAGAAGACCTGCCTGAGTCGGTGGCTAGG
genomic: AATGCCTCGTTCTTGCTAGCGATGGACTTTGGGATGTCGTGGAAAATGAGgtaataaacc ... accaaaatagGAAGCTGTTTCCCTTGCGAAAACAGAAGACCTGCCTGAGTCGGTGGCTAGG
EST: gi|325493254|gb|JG457778.1|JG457778
EST:     AATGCCTCGTTCTTGCTAGCGATGGACTTTGGGATGTCGTGGAAAATGAG                         GAAGCTGTTTCCCTTGCGAAAACAGAAGAACTGGCTGAGTCGGTGGCTAGG
genomic: AATGCCTCGTTCTTGCTAGCGATGGACTTTGGGATGTCGTGGAAAATGAGgtaataaacc ... accaaaatagGAAGCTGTTTCCCTTGCGAAAACAGAAGACCTGCCTGAGTCGGTGGCTAGG
EST: gi|86842757|gb|CI341870.1|CI341870
EST:     AATCCCTCGTTCTTGCTAGCGATGGACTTTGGGATGTCGTGGAAAATGAG                         GAACCTGTTTCCCTTGCGAAAACAGAAGACCTGCCTGAGTCGGTGGCTAGG
genomic: AATGCCTCGTTCTTGCTAGCGATGGACTTTGGGATGTCGTGGAAAATGAGgtaataaacc ... accaaaatagGAAGCTGTTTCCCTTGCGAAAACAGAAGACCTGCCTGAGTCGGTGGCTAGG
EST: gi|88286197|gb|CI522497.1|CI522497
EST:     TGCTAGCGATNGACTTTGGGATGTCGTGGAAAATGAG                         GAAGCTGTTTCCCTTGCGAAAACAGAAGACCTGCCTGAGTCGGTGGCTAGG
genomic: TGCTAGCGATGGACTTTGGGATGTCGTGGAAAATGAGgtaataaacc ... accaaaatagGAAGCTGTTTCCCTTGCGAAAACAGAAGACCTGCCTGAGTCGGTGGCTAGG
EST: gi|86878147|gb|CI340674.1|CI340674
EST:     AGCGATGGACTTTGGGATGTCGTGGAAAATGA-                         GAAGCTGTTTCCCTTGCGAAAACAGAAGACCTGCCTGAGTCGGTGGCTAGG
genomic: AGCGATGGACTTTGGGATGTCGTGGAAAATGAGgtaataaacc ... accaaaatagGAAGCTGTTTCCCTTGCGAAAACAGAAGACCTGCCTGAGTCGGTGGCTAGG
EST: gi|88250968|gb|CI349198.1|CI349198
EST:     AATGCCTCGTTCTTGCTAGCGATGGACTTTGGGATGTCGTGGAAAATGAG                         GAAGCTGTTTCCCTTGCGAAAACAGAAGACCTGCCTGAGTCGGTGGCTAGG
genomic: AATGCCTCGTTCTTGCTAGCGATGGACTTTGGGATGTCGTGGAAAATGAGgtaataaacc ... accaaaatagGAAGCTGTTTCCCTTGCGAAAACAGAAGACCTGCCTGAGTCGGTGGCTAGG
EST: gi|86539934|gb|CI180140.1|CI180140
EST:     AATGCCTCGTTCTTGCTAGCGATGGACTTTGGGATGTCGTGGAAAATGAG                         GAAGCTGTTTCCCTTGCGAAAACAGAAGACCTGCCTGAGTCGGTGGCTAGG
genomic: AATGCCTCGTTCTTGCTAGCGATGGACTTTGGGATGTCGTGGAAAATGAGgtaataaacc ... accaaaatagGAAGCTGTTTCCCTTGCGAAAACAGAAGACCTGCCTGAGTCGGTGGCTAGG
EST: gi|88846462|gb|CI373230.1|CI373230
EST:     AATGCCTCGTTCTTGGTAGCGATGGACTGTGGGATGTCGTGGAAAATGAG                         GAAGCTGTTTCCCTTGCGAAAACAGAAAACCTGCCTGAGTCGGTGGCTAGG
genomic: AATGCCTCGTTCTTGCTAGCGATGGACTTTGGGATGTCGTGGAAAATGAGgtaataaacc ... accaaaatagGAAGCTGTTTCCCTTGCGAAAACAGAAGACCTGCCTGAGTCGGTGGCTAGG

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: 68 (upstream exon), 75 (downstream exon)
Score: 31

GAAGAACTTGTCAATGAAGACTTGGAATGCCTCGTTCTTGCTAGCGATGGACTTTGGGATGTCGTGGAAAATGAGgtaataaacc ... accaaaatagGAAGCTGTTTCCCTTGCGAAAACAGAAGACCTGCCTGAGTCGGTGGCTAGGAAACTCACGGAAATAGCCTATTCTCGAGGCAGCGCTGACAACATTACAT




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Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAAGAACTTGTCAATGAAGACTTGGAATGCCTCGTTCTTGCTAGCGATGGACTTTGGGATGTCGTGGAAAATGAGgtaataaaccaccaagcacattatctcaacctgaaaacgattcgaatttctcaatgaaaccactgctgcttatgtagcattgaacaaagcatcactttattgtcttctctgtctgatctgggtatacatttttaatgattgctaaattctctgataattctgtttaccaaaatag

- - - - - - - - - - - - - - - - - - - - - -  GATGGA