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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCAGAAAGTGGTGAAGAGAGTTTAGAGAGAGAATCAGTTTATTCTTTGAAGTGTCATATATCTCATGATGTAAACCACCTTCATGAAGGACTTAAGCATgtaagttatgttaccattattaaactcataatttctattttatatcgagtagctcattgctgattctgacaggatagttttttatgtgtacattatttttatactatgcttgcataaaacctcagaatttgtatgagaaggcccatgtaattattcttgtattctttcctgcag

Basic information

species Oryza sativa
transcript LOC_Os01g36930.1
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g36930.1 (Oryza sativa), 5'ss of exon 10
lower sequence: GRMZM2G017086_T03 (Zea mays), 5'ss of exon 10
TGCAGAAAGTGGTGAAGAGAGTTTAGAGAGAGAATCAGTTTATTCTTTGAAGTGTCATATATCTCATGATGTAAACCACCTTCATGAAGGACTTAAGCATgtaagttatgttaccattattaaactcataatttctattttatatcgagtagctcattgctgattctgacaggatagttttttatgtgtacattatttttatactatgcttgcataaaacctcagaatttgtatgagaaggcccatgtaattattcttgtattctttcctgcag
||||||||||||||| |||||  | |||| ||||||||| |||||  | ||||||||||||||||| ||||| ||||| |||||||| ||| |||||||||||||| |||||     |      | |||     |||| || ||||             |  | | | | || ||  ||||| | || || ||   |   |    |   ||| | ||                                                         
TGCAGAAAGTGGTGAGGAGAGCATGGAGACAGAATCAGTATATTCCCTTAAGTGTCATATATCTCAAGATGTGAACCATCTTCATGAGGGAATTAAGCATgtaagtaatgttg----tgccgctcccatg----ctatgttgtatc-------------ccaagttttatagcatgttttttcaggtatatatatctgaaacttcaaatttgtaaaagtga-----------------------------------------------------

upper sequence: LOC_Os01g36930.1 (Oryza sativa), 5'ss of exon 10
lower sequence: GRMZM2G028733_T02 (Zea mays), 5'ss of exon 11
TGCAGAAAGTGGTGAAGAGAGTTTAGAGAGAGAATCAGTTTATTCTTTGAAGTGTCATATATCTCATGATGTAAACCACCTTCATGAAGGACTTAAGCATgtaagttatgttaccattattaaactcata-atttctattttata---tcgagtagctcattgctgattctgacaggatagttttttatgtgtacattatttttatactatgcttgcataaaacctcagaatttgtatgagaaggcccatgtaattattcttgtattctttcctgcag
||||||||||||||| |||||  | |||| ||||| |||||||||  | ||||||||||||||||| ||||| ||||| |||||||| ||| ||||||||||||||| | | || | | ||    ||    || | ||| | | |   || | | | | |  |   | |  ||||   ||||||||   |   | || |  |                                                                            
TGCAGAAAGTGGTGAGGAGAGCATGGAGACAGAATTAGTTTATTCCCTTAAGTGTCATATATCTCAAGATGTGAACCATCTTCATGAGGGAATTAAGCATgtaagttctataacaagtttttttttctggtatatatatctgaaaacttcaaattggtaaaagtgaagttagacaatctagttttt---gcagaaataacctg---------------------------------------------------------------------------

upper sequence: LOC_Os01g36930.1 (Oryza sativa), 5'ss of exon 10
lower sequence: AT1G51710.1 (Arabidopsis thaliana), 5'ss of exon 9
TGCAGAAAGTGGTGAAGAGAGTTTAGAGAGAGAATCAGTTTATTCTTTGAAGTGTCATATATCTCATGATGTAAACCACCTTCATGAAGGACTTAAGCATgtaagttatgttaccattattaaactcataatttctattttatatcgagtagctcattgct--gattctgacaggatagttttttatgtgtacattattt-ttatactatgcttgcataaaacctcagaatttgtatgagaaggcccatgtaattattcttgtattctttcctgcag
|  ||||||||| ||||| || | ||||| |||||| || |||||| | || ||||||||||| ||||| || |||||| | ||||||||| | || ||||| ||  |  ||   || |||  | | |||   | | |||   ||     |||   || ||  ||| |  | |  ||||            |||   |||  |||| | |||||     |||  |     |||  ||||   |   ||    ||| |||| ||     || ||| ||
TCAAGAAAGTGGCGAAGAAAGCTCAGAGACAGAATCTGTATATTCTCTAAAATGTCATATATCACATGAAGTGAACCACTTGCATGAAGGATTAAAACATgtgagcaacttt--tataattcca-ttatagactttgtttctgatttttcagcatgtttctcggatacaaaaaaaatag-----------gacagcgtttgctatattctgcttattataaattttttttttttgatgaacggcttca----atttttctggt-----ttactgaag

upper sequence: LOC_Os01g36930.1 (Oryza sativa), 5'ss of exon 10
lower sequence: Vv09s0002g02500.t01 (Vitis vinifera), 5'ss of exon 10
TGCAGAAAGTGGTGAAGAGAGTTTAGAGAGAGAATCAGTTTATTCTTTGAAGTGTCATATATCTCATGATGTAAACCACCTTCATGAAGGACTTAAGCATgtaagttatgttaccattattaaactcataatttctattttatatcgagtagctcattgct--gattctgacaggatagtttttta---tgtgtacattatttttatactatgcttgcataaaacctcagaatttgtatgagaaggcccatgtaattattcttgtattctttcctgcag
 | |||||||||||||||||| | |||||  ||||||||||||||  | || || || ||||| || || || |||||  | ||||||||||| || || ||||||  | ||  ||  | |||    |   | ||  | |||    ||  | |||||| ||    || |   |  ||| ||| |||   |   | || ||  |||                                                                          
CGAAGAAAGTGGTGAAGAGAGCTCAGAGACTGAATCAGTTTATTCACTTAAATGCCACATATCACACGAGGTGAACCATTTGCATGAAGGACTAAAACACgtaagt-gttttcacagaactaataggaagctatcagtctta----gaagatctcattcctttagttttcttataatactttattagcatacatgcaataccttt--------------------------------------------------------------------------

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|163920010|gb|EG709816.1|EG709816
EST:     AGTGTCATATATCTCATGATGTAAACCACCTTCATGAAGGACTTAAGCAT                         GGTTTGAAGTCAGAACTTGAGAAGGCTTCACCTTCACTGGGTCGCACTGCT
genomic: AGTGTCATATATCTCATGATGTAAACCACCTTCATGAAGGACTTAAGCATgtaagttatg ... tttcctgcagGGTTTGAAGTCAGAACTTGAGAAGGCTTCACCTTCACTGGGTCGCACTGCT
EST: gi|29615418|gb|CB620430.1|CB620430
EST:     AGTGTCATATATCTCATGATGTAAACCACCTTCATGAAGGACTTAAGCAT                         GGTTTGAAGTCAGAACTTGAGAAAGCTTCACCTTCACTGGGTCGCACTGCT
genomic: AGTGTCATATATCTCATGATGTAAACCACCTTCATGAAGGACTTAAGCATgtaagttatg ... tttcctgcagGGTTTGAAGTCAGAACTTGAGAAGGCTTCACCTTCACTGGGTCGCACTGCT
EST: gi|58601182|gb|CK011710.1|CK011710
EST:     AGTGTCATATATCTCATGATGTAAACCACCTTCATGAAGGACTTAAGCAT                         GGTTTGAAGTCA-A-CTTGAGAAGGCTTCACCTTCACTGGGTCGCACTGCT
genomic: AGTGTCATATATCTCATGATGTAAACCACCTTCATGAAGGACTTAAGCATgtaagttatg ... tttcctgcagGGTTTGAAGTCAGAACTTGAGAAGGCTTCACCTTCACTGGGTCGCACTGCT
EST: gi|218489926|gb|FG960730.1|FG960730
EST:     AGTGTCATATATCTCATGATGTAAACCACCTTCATGAAGGACTTAAGCAT                         GGTTTGAAGTCAGAACTTGAGAAGGCTTCACCTTCACTGGGTCGCACTGCT
genomic: AGTGTCATATATCTCATGATGTAAACCACCTTCATGAAGGACTTAAGCATgtaagttatg ... tttcctgcagGGTTTGAAGTCAGAACTTGAGAAGGCTTCACCTTCACTGGGTCGCACTGCT
EST: gi|29615343|gb|CB620355.1|CB620355
EST:     AGTGTCATATATCTCATGATGTAAACCACCTTCATGAAGGACTTAAGCAT                         GGTTTGAAGTC
genomic: AGTGTCATATATCTCATGATGTAAACCACCTTCATGAAGGACTTAAGCATgtaagttatg ... tttcctgcagGGTTTGAAGTC
EST: gi|66916241|gb|CX103089.1|CX103089
EST:     AGTGTCATATATCTCATGATGTAAACCACCTTCATGAAGGACTTAAGCAT                         GGTTTGAAGTCAGAACTTGAGAAGGCTTCACCTTCACTGGGTCGCACTGCT
genomic: AGTGTCATATATCTCATGATGTAAACCACCTTCATGAAGGACTTAAGCATgtaagttatg ... tttcctgcagGGTTTGAAGTCAGAACTTGAGAAGGCTTCACCTTCACTGGGTCGCACTGCT

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: 54 (upstream exon), 65 (downstream exon)
Score: 63

TGCAGAAAGTGGTGAAGAGAGTTTAGAGAGAGAATCAGTTTATTCTTTGAAGTGTCATATATCTCATGATGTAAACCACCTTCATGAAGGACTTAAGCATgtaagttatg ... tttcctgcagGGTTTGAAGTCAGAACTTGAGAAGGCTTCACCTTCACTGGGTCGCACTGCTCTTTATACAAGAGAGTCAAGAATAAATGAGTTGCCTAG




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