Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGGTTTTGAACTGGAATATCTCAATATTGGCGGTGGCCTGGGCATAGATTATCACCACACGGATGCAGTCTTGCCTACACCTATGGACCTCATCAACACTgtgagctcaatatccatgttatatttccgattctcatcttcgtaggcacattatttatttaaatagatcacttcctactttggatttttgcactgttaaaatttggcatatggcgtgattcttatatgtgcccctgtgattttttgtag

Basic information

species Oryza sativa
transcript LOC_Os02g24354.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g24354.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G020446_T01 (Zea mays), 5'ss of exon 4
AGGTTTTGAACTGGAATATCTCAATATTGGCGGTGGCCTGGGCATAGATTATCACCACACGGATGCAGTCTTGCCTACACCTATGGACCTCATCAACACTgtgagctcaatatccatgttatatttccgattctcatcttcgtaggcacat-tatttatttaaatagatcacttcctactttggatttttgcactgttaaaatttggcatatg----gcgtgattc-ttatatgtgcccctgtgatttt-ttgtag
||||||| |  |||| || || ||||| || |||||  |||| |||||||| || || || ||||||||||| |||||||||||||| |||||||||||||| ||||||| || | |   || |||| || ||  ||||| | |||| ||  |   | |||||| | | || ||    | ||       ||   | |  ||| ||||| ||||    || |||||| | ||   ||  |   | ||||| ||| ||
AGGTTTTAAGTTGGAGTACCTGAATATCGGAGGTGGTTTGGGAATAGATTACCATCATACCGATGCAGTCTTACCTACACCTATGGATCTCATCAACACTgtaagctcaacattcttaccatgtttctgactcatatctttgcaggcgcacatgcatctttaaa-ataccagtttt--ccttaa-----tgtgatatggaaagttggcttatgctgagcttgattcatcatgcttgttctatttattttgttgcag

upper sequence: LOC_Os02g24354.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G090722_T02 (Zea mays), 5'ss of exon 4
AGGTTTTGAACTGGAATATCTCAATATTGGCGGTGGCCTGGGCATAGATTATCACCACACGGATGCAGTCTTGCCTACACCTATGGACCTCATCAACACTgtgagctcaatatccatgttatatttccgattctcatcttcgtaggcacat-tatttatttaaatagatcacttcctactttggatttttgcactgttaaaatttggcat-atggcgtgattcttatatgtgcccctgt--gattttttgtag
||||||| |  |||| || || |||||||| |||||  |||| |||||||| || || || ||||||||||| |||||||||||||| |||||||||||||| ||||||  || | |   || |||| |||||  ||||| | |||||||  |   | |||||| | | || |||    | | |   |  |    ||||   | ||  || ||||| |||||| |    |||   || |    ||| ||| ||
AGGTTTTAAGTTGGAGTACCTGAATATTGGAGGTGGTTTGGGAATAGATTACCATCATACCGATGCAGTCTTACCTACACCTATGGATCTCATCAACACTgtaagctcagcattcttaccatgtttctgattcatatctttgcaggcacacatgcatctttaaa-atagcagttctccttattgtgatacggtaagttagcttatgcaattatggcttgattcatcatggtggttctatttattttgttgcag
















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|56158558|gb|AU095738.2|AU095738
EST:     ATCACCACACGGATGCAGTCTTGCCTACACCTATGGACCTCATCAACACT                         GTGCGAGAATTAGTTCTGTCACGAGATCTTACACTCATCATTGAACCTGGG
genomic: ATCACCACACGGATGCAGTCTTGCCTACACCTATGGACCTCATCAACACTgtgagctcaa ... ttttttgtagGTGCGAGAATTAGTTCTGTCACGAGATCTTACACTCATCATTGAACCTGGG
EST: gi|66923878|gb|CX110726.1|CX110726
EST:     ATCACCACACGGATGCAGTCTTGCCTACACCTATGGACCTCATCAACACT                         GTGCGAGAATTAGTTCTGTCACGAGATCTTACACTCATCATTGAACCTGGG
genomic: ATCACCACACGGATGCAGTCTTGCCTACACCTATGGACCTCATCAACACTgtgagctcaa ... ttttttgtagGTGCGAGAATTAGTTCTGTCACGAGATCTTACACTCATCATTGAACCTGGG
EST: gi|29617055|gb|CB622067.1|CB622067
EST:     ATCACCACACGGATGCAGTCTTGCCTACACCTATGGACCTCATCAACACT                         GTGCGAGAATTAGTTCTGTCACGAGATCTTACACTCATCATTGAACCTGGG
genomic: ATCACCACACGGATGCAGTCTTGCCTACACCTATGGACCTCATCAACACTgtgagctcaa ... ttttttgtagGTGCGAGAATTAGTTCTGTCACGAGATCTTACACTCATCATTGAACCTGGG
EST: gi|218504209|gb|FG952211.1|FG952211
EST:     ATCACCACACGGATGCAGTCTTGCCTACACCTATGGACCTCATCAACACT                         GTGCGAGAATTAGTTCTGTCACGAGATCTTACACTCATCATTGAACCTGGG
genomic: ATCACCACACGGATGCAGTCTTGCCTACACCTATGGACCTCATCAACACTgtgagctcaa ... ttttttgtagGTGCGAGAATTAGTTCTGTCACGAGATCTTACACTCATCATTGAACCTGGG
EST: gi|300215949|gb|HO088575.1|HO088575
EST:     ATCACCACACGGATGCAGTCTTGCCTACACCTATGGACCTCATCAACACT                         GTGCGAGAATTAGTTCTGTCACGAGATCTTACACTCATCATTGAACCTGGG
genomic: ATCACCACACGGATGCAGTCTTGCCTACACCTATGGACCTCATCAACACTgtgagctcaa ... ttttttgtagGTGCGAGAATTAGTTCTGTCACGAGATCTTACACTCATCATTGAACCTGGG
EST: gi|86504611|gb|CI147244.1|CI147244
EST:     ATCACCACACGGATGCAGTCTTGCCTACACCTATGGACCTCATCAACACT                         GTGCGAGAATTAGTTCTGTCACGAGATCTTACACTCATCATTGAACCTGGG
genomic: ATCACCACACGGATGCAGTCTTGCCTACACCTATGGACCTCATCAACACTgtgagctcaa ... ttttttgtagGTGCGAGAATTAGTTCTGTCACGAGATCTTACACTCATCATTGAACCTGGG
EST: gi|29678833|gb|CB675108.1|CB675108
EST:     ATCACCACACGGATGCAGTCTTGCCTACACCTATGGACCTCATCAACACT                         GTGCGAGAATTAGTTCTGTCACGAGATCTTACACTCATCATTGAACCTGGG
genomic: ATCACCACACGGATGCAGTCTTGCCTACACCTATGGACCTCATCAACACTgtgagctcaa ... ttttttgtagGTGCGAGAATTAGTTCTGTCACGAGATCTTACACTCATCATTGAACCTGGG
EST: gi|29646003|gb|CB651010.1|CB651010
EST:     ATCACCACACGGATGCAGTCTTGCCTACACCTATGGACCTCATCAACACT                         GTGCGAGAATTAGTTCTGTCACGAGATCTTACACTCATCATTGAACCTGGG
genomic: ATCACCACACGGATGCAGTCTTGCCTACACCTATGGACCTCATCAACACTgtgagctcaa ... ttttttgtagGTGCGAGAATTAGTTCTGTCACGAGATCTTACACTCATCATTGAACCTGGG
EST: gi|218503477|gb|FG956525.1|FG956525
EST:     ATCACCACACGGATGCAGTCTTGCCTACACCTATGGACCTCATCAACACT                         GTGCGAGAATTAGTTCTGTCACGAGATCTTACACTCATCATTGAACCTGGG
genomic: ATCACCACACGGATGCAGTCTTGCCTACACCTATGGACCTCATCAACACTgtgagctcaa ... ttttttgtagGTGCGAGAATTAGTTCTGTCACGAGATCTTACACTCATCATTGAACCTGGG
EST: gi|86497107|gb|CI139740.1|CI139740
EST:     ATCACCACACGGATGCAGTCTTGCCTACACCTATGGACCTCATCAACACT                         GTGCGAGAATTAGTTCTGTCACGAGATCTTACACTCATCATTGAACCTGGG
genomic: ATCACCACACGGATGCAGTCTTGCCTACACCTATGGACCTCATCAACACTgtgagctcaa ... ttttttgtagGTGCGAGAATTAGTTCTGTCACGAGATCTTACACTCATCATTGAACCTGGG
EST: gi|29615943|gb|CB620955.1|CB620955
EST:     ATCACCACACGGATGCAGTCTTGCNTACACCTATGGACCTCATCAACACT                         GTGCGAGAATTAGTTCTGTCACGAGATCTTACACTCATCATTGAACCTGGG
genomic: ATCACCACACGGATGCAGTCTTGCCTACACCTATGGACCTCATCAACACTgtgagctcaa ... ttttttgtagGTGCGAGAATTAGTTCTGTCACGAGATCTTACACTCATCATTGAACCTGGG

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: 75 (upstream exon), 75 (downstream exon)
Score: 92

AGGTTTTGAACTGGAATATCTCAATATTGGCGGTGGCCTGGGCATAGATTATCACCACACGGATGCAGTCTTGCCTACACCTATGGACCTCATCAACACTgtgagctcaa ... ttttttgtagGTGCGAGAATTAGTTCTGTCACGAGATCTTACACTCATCATTGAACCTGGGAGATCCCTCATAGCTAACACTTGCTGCTTCGTCAATAGGGTCACTGGTG




<











<


<