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'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGCTTACAGTGATTCCCGAGGTATCCCTGGTATTAGGAAGGAAGTCGCCGAGTTCATCGAGAGGCGTGATGGTTATCCAAGgtcagaatgatcaagagtactcatgacaagtctcaactggtggtgttcttttacatcatagctttcttgggccatattctcacacctgtatcctatacctattgcag

Basic information

species Oryza sativa
transcript LOC_Os07g01760.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g01760.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM5G840582_T01 (Zea mays), 5'ss of exon 4
------------------GTGCTTACAGTGATTCCCGAGGTATCCCTGGTATTAGGAAGGAAGTCGCCGAGTTCATCGAGAGGCGTGATGGTTATCCAAGgtcagaatgatcaagagtactcatgacaagtctcaactggtggtgttcttttacatcatagctttcttgggccatattctcacacctgtatcctatacctattgcag
                  |||| ||||||||| |||| |||||||| || || ||||||||||| || || |||||| | | ||||||||| ||||| ||||  || |              ||||||    |  |||| ||   || | ||||          |  |  |||||   || || | | ||| || | | |  |||||
TGGCGCCGGGAGGTCTAGGTGCGTACAGTGATGCCCGTGGTATCCCCGGAATCAGGAAGGAAGTTGCTGACTTCATCCACAAGCGTGATGGATATCCGAGgttggattcg------------atgaca----tttactgctgaaattttcttac----------ttgtaagccatg--ctaacgcttctatgctctgcttgctgcag

upper sequence: LOC_Os07g01760.1 (Oryza sativa), 5'ss of exon 3
lower sequence: Vv00s0225g00130.t01 (Vitis vinifera), 5'ss of exon 5
GTGCTTACAGTGATTCCCGAGGTATCCCTGGTATTAGGAAGGAAGTCGCCGAGTTCATCGAGAGGCGTGATGGTTATCCAAGgtcagaatgatcaagagtactcatgacaagtctcaactggtggtgttcttttacatcatagctttcttgggccatattctca-cacctgta--tcctatacctattgcag
||||||| ||||| || |||||| | ||||| || ||||||||||| || |||||||| | |||||||||||| |||||||||| | |||| | ||   ||  | | ||   | |||| |  |     |  | || |   | | | |   |  | | |||   | |   | |   || |  ||| ||  |||
GTGCTTATAGTGACTCTCGAGGTCTTCCTGGAATAAGGAAGGAAGTGGCAGAGTTCATTGGGAGGCGTGATGGGTATCCAAGgtgataatgctaaa---tatccttaac---tttcaattaat-----tggtctaaacattggttctaaagttctaaattgaaagcggttattgctctttgaccaataacag
















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|29615657|gb|CB620669.1|CB620669
EST:     ATTAGGAAGGAAGTCGCCGAGTTCATCGAGAGGCGTGATGGTTATCCAAG                         TGATCCAGAACTTATTTACCTCACAGATGGTGCCAGCAAAGGTGTGATGCA
genomic: ATTAGGAAGGAAGTCGCCGAGTTCATCGAGAGGCGTGATGGTTATCCAAGgtcagaatga ... cctattgcagTGATCCAGAACTTATTTACCTCACAGATGGTGCCAGCAAAGGTGTGATGCA
EST: gi|29671704|gb|CB667979.1|CB667979
EST:     GAGAGGAGTGATGGTTATCCAAG                         TGATCCAGAACTTATTTACCTCACAGATGGTGCCAGCAAAGGTGTGATGCA
genomic: GAGAGGCGTGATGGTTATCCAAGgtcagaatga ... cctattgcagTGATCCAGAACTTATTTACCTCACAGATGGTGCCAGCAAAGGTGTGATGCA
EST: gi|58611970|gb|CK039682.1|CK039682
EST:     ATTAGGAAGGAAGTCGCCGAGTTCATCGAGAGGCGTGATGGTTATCCAAG                         TGATCCAGAACTTATTTACCTCACAGATGGTGCCAGCAAAGGTGTGATGCA
genomic: ATTAGGAAGGAAGTCGCCGAGTTCATCGAGAGGCGTGATGGTTATCCAAGgtcagaatga ... cctattgcagTGATCCAGAACTTATTTACCTCACAGATGGTGCCAGCAAAGGTGTGATGCA
EST: gi|29614592|gb|CB619605.1|CB619605
EST:     ATTAGGAAGGAAGTCGCCGAGTTCATCGAGAGGCGTGATGGTTATCCAAG                         TGATCCAGAACTTATTTACCTCACAGATGGTGCCAGCAAAGGTGTGATGCA
genomic: ATTAGGAAGGAAGTCGCCGAGTTCATCGAGAGGCGTGATGGTTATCCAAGgtcagaatga ... cctattgcagTGATCCAGAACTTATTTACCTCACAGATGGTGCCAGCAAAGGTGTGATGCA
EST: gi|29684690|gb|CB680965.1|CB680965
EST:     ATTAGGAAGGAAGGCGCCGAGTTCATCGAGAGGCGTGATGGTTATCCAAG                         TGATCCAGAACTTATTTACCTCACAGATGGTGCCAGCAAAGGTGTGATGCA
genomic: ATTAGGAAGGAAGTCGCCGAGTTCATCGAGAGGCGTGATGGTTATCCAAGgtcagaatga ... cctattgcagTGATCCAGAACTTATTTACCTCACAGATGGTGCCAGCAAAGGTGTGATGCA
EST: gi|58589507|gb|CF987815.1|CF987815
EST:     ATTAGGAAGGAAGTCGCCGAGTTCATCGAGAGGCGTGATGGTTATCCAAG                         TGATCCAGAACTTATTTACCTCACAGATGGTGCCAGCAAAGGTGTGATGCA
genomic: ATTAGGAAGGAAGTCGCCGAGTTCATCGAGAGGCGTGATGGTTATCCAAGgtcagaatga ... cctattgcagTGATCCAGAACTTATTTACCTCACAGATGGTGCCAGCAAAGGTGTGATGCA
EST: gi|29616796|gb|CB621808.1|CB621808
EST:     ATTAGGAAGGAAGTCGCCGAGTTCATCGAGAGGCGTGATGGTTATCCAAG                         TGATCCAGAACTTATTTACCTCACAGATGGTGCCAGCAAAGGTGTGATGCA
genomic: ATTAGGAAGGAAGTCGCCGAGTTCATCGAGAGGCGTGATGGTTATCCAAGgtcagaatga ... cctattgcagTGATCCAGAACTTATTTACCTCACAGATGGTGCCAGCAAAGGTGTGATGCA
EST: gi|33381143|gb|CF196486.1|CF196486
EST:     ATTAGGAAGGAAGTCGCCGAGTTCATCGAGAGGCGTGATGGTTATCCAAG                         TGATCCAGAACTTATTTACCTCACAGATGGTGCCAGCAAAGGTGTGATGCA
genomic: ATTAGGAAGGAAGTCGCCGAGTTCATCGAGAGGCGTGATGGTTATCCAAGgtcagaatga ... cctattgcagTGATCCAGAACTTATTTACCTCACAGATGGTGCCAGCAAAGGTGTGATGCA
EST: gi|58607278|gb|CK035311.1|CK035311
EST:     TTAGGAAGGAAGTCGCCGAGTTCATCGAGAGTGCGTGATGGTTATCCAAG                         TGATCCAGAACTTATTTACCTCACAGATGGTGCCAGCAAAGTGTGTGATGC
genomic: TTAGGAAGGAAGTCGCCGAGTTCATCGAGAG-GCGTGATGGTTATCCAAGgtcagaatga ... cctattgcagTGATCCAGAACTTATTTACCTCACAGATGGTGCCAGCAAAG-GTGTGATGC
EST: gi|13420574|gb|AU174664.1|AU174664
EST:     ATTAGGAAGGAAGTCGCCGAGTTCATCGAGAGGCGTGATGGTTATCCAAG                         TGATCCAGAACTTATTTACCTCACAGATGGTGCCAGCAAAGGTGTGATGCA
genomic: ATTAGGAAGGAAGTCGCCGAGTTCATCGAGAGGCGTGATGGTTATCCAAGgtcagaatga ... cctattgcagTGATCCAGAACTTATTTACCTCACAGATGGTGCCAGCAAAGGTGTGATGCA
EST: gi|29615352|gb|CB620364.1|CB620364
EST:     ATTAGGAAGGAAGTCGCCGAGTTCATCGAGAGGCGTGATGGTTATCCAAG                         TGATCCAGAACTTATTTACCTCACAGATGGTGCCAGCAAAGGTGTGATGCA
genomic: ATTAGGAAGGAAGTCGCCGAGTTCATCGAGAGGCGTGATGGTTATCCAAGgtcagaatga ... cctattgcagTGATCCAGAACTTATTTACCTCACAGATGGTGCCAGCAAAGGTGTGATGCA
EST: gi|29615840|gb|CB620852.1|CB620852
EST:     ATTAGGAAGGAAGTCGCCGAGTTCATCGAGAGGCGTGATGGTTATCCAAG                         TGATCCAGAACTTATTTACCTCACAGATGGTGCCAGCAAAGGTGTGATGCA
genomic: ATTAGGAAGGAAGTCGCCGAGTTCATCGAGAGGCGTGATGGTTATCCAAGgtcagaatga ... cctattgcagTGATCCAGAACTTATTTACCTCACAGATGGTGCCAGCAAAGGTGTGATGCA
EST: gi|87005459|gb|CI285681.1|CI285681
EST:     ATTAGGAAGGAAGTCGCCGAGTTCATCGAGAGGCGTGATGGTTATCCAAG                         TGATCCAGAACTTATTTACCTCACAGATGGTGCCAGCAAAGGTGTGATGCA
genomic: ATTAGGAAGGAAGTCGCCGAGTTCATCGAGAGGCGTGATGGTTATCCAAGgtcagaatga ... cctattgcagTGATCCAGAACTTATTTACCTCACAGATGGTGCCAGCAAAGGTGTGATGCA
EST: gi|58693367|gb|CK082054.1|CK082054
EST:     ATTAGGAAGGAAGTCGCCGAGTTCATCGAGAGGCGTGATGGTTATCCAAG                         TGATCCAGAACTTATTTACCTCACAGATGGTGCCAGCAAAGGTGTGATGCA
genomic: ATTAGGAAGGAAGTCGCCGAGTTCATCGAGAGGCGTGATGGTTATCCAAGgtcagaatga ... cctattgcagTGATCCAGAACTTATTTACCTCACAGATGGTGCCAGCAAAGGTGTGATGCA
EST: gi|29676307|gb|CB672582.1|CB672582
EST:     ATTAGGAAGGAAGTCGCCGAGTTCATCGAGAGGCGTGATGGTTATCCAAG                         TGATCCAGAACTTATTTACCTCACAGATGGTGCCAGCAAAGGTGTGATGCA
genomic: ATTAGGAAGGAAGTCGCCGAGTTCATCGAGAGGCGTGATGGTTATCCAAGgtcagaatga ... cctattgcagTGATCCAGAACTTATTTACCTCACAGATGGTGCCAGCAAAGGTGTGATGCA
EST: gi|33381689|gb|CF197032.1|CF197032
EST:     ATTAGGAAGGAAGTCGCCGAGTTCATCGAGAGGCGTGATGGTTATCCAAG                         TGATCCAGAACTTATTTACCTCACAGATGGTGCCAGCAAAGGTGTGATGCA
genomic: ATTAGGAAGGAAGTCGCCGAGTTCATCGAGAGGCGTGATGGTTATCCAAGgtcagaatga ... cctattgcagTGATCCAGAACTTATTTACCTCACAGATGGTGCCAGCAAAGGTGTGATGCA
EST: gi|29616434|gb|CB621446.1|CB621446
EST:     ATTAGGAAGGAAGTCGCCGAGTTCATCGAGAGGCGTGATGGTTATCCAAG                         TGATCCAGAACTTATTTACCTCACAGATGGTGCCAGCAAAGGTGTGATGCA
genomic: ATTAGGAAGGAAGTCGCCGAGTTCATCGAGAGGCGTGATGGTTATCCAAGgtcagaatga ... cctattgcagTGATCCAGAACTTATTTACCTCACAGATGGTGCCAGCAAAGGTGTGATGCA
EST: gi|29614424|gb|CB619437.1|CB619437
EST:     ATTAGGAAGGAAGTCGCCGAGTTCATCGAGAGGCGTGATGGTTATCCAAG                         TGATCCAGAACTTATTTACCTCACAGATGGTGCCAGCAAAGGTGTGATGCA
genomic: ATTAGGAAGGAAGTCGCCGAGTTCATCGAGAGGCGTGATGGTTATCCAAGgtcagaatga ... cctattgcagTGATCCAGAACTTATTTACCTCACAGATGGTGCCAGCAAAGGTGTGATGCA
EST: gi|29636374|gb|CB641383.1|CB641383
EST:     ATTAGGAAGGAAGTCGCCGAGTTCATCGAGAGGCGTGATGGTTATCCAAG                         TGATCCAGAACTTATTTACCTCACAGATGGTGCCAGCAAAGGTGTGATGCA
genomic: ATTAGGAAGGAAGTCGCCGAGTTCATCGAGAGGCGTGATGGTTATCCAAGgtcagaatga ... cctattgcagTGATCCAGAACTTATTTACCTCACAGATGGTGCCAGCAAAGGTGTGATGCA
EST: gi|58693563|gb|CK082250.1|CK082250
EST:     ATTAGGAAGGAAGTCGCCGAGTTCATCGAGAGGCGTGATGGTTATCCAAG                         TGATCCAGAACTTATTTACCTCACAGATGGTGCCAGCAAAGGTGTGATGCA
genomic: ATTAGGAAGGAAGTCGCCGAGTTCATCGAGAGGCGTGATGGTTATCCAAGgtcagaatga ... cctattgcagTGATCCAGAACTTATTTACCTCACAGATGGTGCCAGCAAAGGTGTGATGCA
EST: gi|58687854|gb|CK076541.1|CK076541
EST:     ATTAGGAAGGAAGTCGCCGAGTTCATCGAGAGGCGTGATGGTTATCCAAG                         TGATCCAGAACTTATTTACCTCACAGATGGTGCCAGCAAAGGTGTGATGCA
genomic: ATTAGGAAGGAAGTCGCCGAGTTCATCGAGAGGCGTGATGGTTATCCAAGgtcagaatga ... cctattgcagTGATCCAGAACTTATTTACCTCACAGATGGTGCCAGCAAAGGTGTGATGCA
EST: gi|58694270|gb|CK082957.1|CK082957
EST:     ATTAGGAAGGAAGTCGCCGAGTTCATCGAGAGGCGTGATGGTTATCCAAG                         TGATCCAGAACTTATTTACCTCACAGATGGTGCCAGCAAAGGTGTGATGCA
genomic: ATTAGGAAGGAAGTCGCCGAGTTCATCGAGAGGCGTGATGGTTATCCAAGgtcagaatga ... cctattgcagTGATCCAGAACTTATTTACCTCACAGATGGTGCCAGCAAAGGTGTGATGCA
EST: gi|29614163|gb|CB619176.1|CB619176
EST:     ATTAGGAAGGAAGTCGCCGAGTTCATCGAGAGGCGTGATGGTTATCCAAG                         TGATCCAGAACTTATTTACCTCACAGATGGTGCCAGCAAAGGTGTGATGCA
genomic: ATTAGGAAGGAAGTCGCCGAGTTCATCGAGAGGCGTGATGGTTATCCAAGgtcagaatga ... cctattgcagTGATCCAGAACTTATTTACCTCACAGATGGTGCCAGCAAAGGTGTGATGCA
EST: gi|38477834|gb|CF961967.1|CF961967
EST:     ATTAGGAAGGAAGTCGCCGAGTTCATCGAGAGGCGTGATGGTTATCCAAG                         TGATCCAGAACTTATTTACCTCACAGATGGTGCCAGCAAAGGTGTGATGCA
genomic: ATTAGGAAGGAAGTCGCCGAGTTCATCGAGAGGCGTGATGGTTATCCAAGgtcagaatga ... cctattgcagTGATCCAGAACTTATTTACCTCACAGATGGTGCCAGCAAAGGTGTGATGCA
EST: gi|58593995|gb|CF992303.1|CF992303
EST:     ATTAGGAAGGAAGTCGCCGAGTTCATCGAGAGGCGTGATGGTTATCCAAG                         TGATCCAGAACTTATTTACCTCACAGATGGTGCCAGCAAAGGTGTGATGCA
genomic: ATTAGGAAGGAAGTCGCCGAGTTCATCGAGAGGCGTGATGGTTATCCAAGgtcagaatga ... cctattgcagTGATCCAGAACTTATTTACCTCACAGATGGTGCCAGCAAAGGTGTGATGCA
EST: gi|29689279|gb|CB685554.1|CB685554
EST:     ATTAGGAAGGAAGTCGCCGAGTTCATCGAGAGGCGTGATGGTTATCCAAG                         TGATCCAGAACTTATTTACCTCACAGATGGTGCCAGCAAAGGTGTGATGCA
genomic: ATTAGGAAGGAAGTCGCCGAGTTCATCGAGAGGCGTGATGGTTATCCAAGgtcagaatga ... cctattgcagTGATCCAGAACTTATTTACCTCACAGATGGTGCCAGCAAAGGTGTGATGCA

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), 66 (downstream exon)
Score: 243

GTGCTTACAGTGATTCCCGAGGTATCCCTGGTATTAGGAAGGAAGTCGCCGAGTTCATCGAGAGGCGTGATGGTTATCCAAGgtcagaatga ... cctattgcagTGATCCAGAACTTATTTACCTCACAGATGGTGCCAGCAAAGGTGTGATGCAAATGCTGAATACCATTATCAGAAATGAGAGAGATGGG




<











<


<









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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGCTTACAGTGATTCCCGAGGTATCCCTGGTATTAGGAAGGAAGTCGCCGAGTTCATCGAGAGGCGTGATGGTTATCCAAGgtcagaatgatcaagagtactcatgacaagtctcaactggtggtgttcttttacatcatagctttcttgggccatattctcacacctgtatcctatacctattgcag

- - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG