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

...tagttcctgaaacagtttagttgcaactgtactaattttcttgaagttatgttactttgctttaacaagttaataaaaatggttttaatgtcatttacagATGGGTTTAATGGTTAACCCTCCTAAGCCTGGAGATATCTCTTATCTGAAGTTTTCTGCTGAAAG

Basic information

species Oryza sativa
transcript LOC_Os07g01760.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g01760.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM5G840582_T01 (Zea mays), 3'ss of exon 9
--------------------------------------------------------tagttcctgaaacagtttag--ttg---caactgtactaatt-ttcttgaagttatgttactttgctttaacaagttaataaaaatggtt--ttaa---tgtcatttacagATGGGTTTAATGGTTAACCCTCCTAAGCCTGGAGATATCTCTTATCTGAAGTTTTCTGCTGAAAG
                                                        |   |  || ||||   ||   |||   || ||  || |||| ||||| ||| | |||| |||||||||| |||  ||   |   | |||  ||||   || | ||||||||||||  | ||||||||||||||||| |||||||||||||| || | ||||||  |||| |||||
gtaagcgaaacacggctcaatgttttattcttttgctcttccactgaacccggtactctgttttggaacaacatatgtttggaccacctacaccaattgttcttaaagctttgtttctttgctttaccaaactacagagcgtagttgcttaagtctgccttttacagATGGGAGTGATGGTTAACCCTCCTAAACCTGGAGATATCTCATACCCGAAGTTCACTGCCGAAAG

upper sequence: LOC_Os07g01760.1 (Oryza sativa), 3'ss of exon 8
lower sequence: AT1G23310.2 (Arabidopsis thaliana), 3'ss of exon 10
tagttcctgaaacagtttagttgcaactgtactaattttcttgaagttatgttactttgctttaaca-agttaataaaaatggttttaatgtcatt--------tacagATGGGTTTAATGGTTAACCCTCCTAAGCCTGGAGATATCTCTTATCTGAAGTTTTCTGCTGAAAG
                           |     ||   |||| |||| ||||   ||| ||||   | |  | ||    ||| | |    || |||        | ||||||||||| |||||||| ||||| ||||||||||| || || |||    ||||  |   ||||||
--------------------------gtaagtcaaaggtcttaaagtaatgtggatttacttttctagaaatcattggtatgttctgcgagtgattattacctgtgcagATGGGTTTGATGGTTAATCCTCCAAAGCCTGGAGACATTTCATATGACCAGTTCGCCCGTGAAAG

upper sequence: LOC_Os07g01760.1 (Oryza sativa), 3'ss of exon 8
lower sequence: AT1G70580.2 (Arabidopsis thaliana), 3'ss of exon 10
tagttcctgaaacagtttagttgcaactgtactaattttcttgaagttatgttactttgctttaacaagttaataaaaatggttttaatgtcatt-tacagATGGGTTTAATGGTTAACCCTCCTAAGCCTGGAGATATCTCTTATCTGAAGTTTTCTGCTGAAAG
                | || |  | |  | || | ||||||      | |||    |   | ||  |  | |           | | |||  || |  |||||||||||||||||| ||| || ||||||||||| || || |||    | ||   |  ||| ||
---------------gtaagct--agcccttcttagtttcttag---caagttctggttactgaatgatctcactgctgaaacctgattgtttttgtgtagATGGGTTTAATGGTTAGCCCACCAAAGCCTGGAGACATTTCATATGACCAATTCGTTCGTGAGAG

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|58658560|gb|CK047240.1|CK047240
EST:     ACAAGGTTGCATCAATCGCACTCAGTCCAAATGTTCCTGGGCAGATCTTT                         ATGGGTTTAATGGTTAACCCTCCTAAGCCTGGAGATATCTCTTATCTGAAG
genomic: ACAAGGTTGCATCAATCGCACTCAGTCCAAATGTTCCTGGGCAGATCTTTgtaagtcaaa ... tcatttacagATGGGTTTAATGGTTAACCCTCCTAAGCCTGGAGATATCTCTTATCTGAAG
EST: gi|29671704|gb|CB667979.1|CB667979
EST:     ACAAGGTTGCATCAATCGCACTCAGTCCAAATGTTCCTGGGCAGATCTTT                         ATGGGTTTAATGGTTAACCCTCCTAAGCCTGGAGATATCTCTTATCTGAAG
genomic: ACAAGGTTGCATCAATCGCACTCAGTCCAAATGTTCCTGGGCAGATCTTTgtaagtcaaa ... tcatttacagATGGGTTTAATGGTTAACCCTCCTAAGCCTGGAGATATCTCTTATCTGAAG
EST: gi|33381539|gb|CF196882.1|CF196882
EST:     ACAAGGTTGCATCAATCGCACTCAGTCCAAATGTTCCTGGGCAGATCTTT                         ATGGGTTTAATGGTTAACCCTCCTAAGCCTGGAGATATCTCTTATCTGAAG
genomic: ACAAGGTTGCATCAATCGCACTCAGTCCAAATGTTCCTGGGCAGATCTTTgtaagtcaaa ... tcatttacagATGGGTTTAATGGTTAACCCTCCTAAGCCTGGAGATATCTCTTATCTGAAG
EST: gi|33381769|gb|CF197112.1|CF197112
EST:     ACAAGGTTGCATCAATCGCACTCAGTCCNNNTGTTCCTGGGCAGATCTTT                         ATGGGTTTAAT
genomic: ACAAGGTTGCATCAATCGCACTCAGTCCAAATGTTCCTGGGCAGATCTTTgtaagtcaaa ... tcatttacagATGGGTTTAAT
EST: gi|29645692|gb|CB650699.1|CB650699
EST:     ACAAGGTTGCATCAATCGCACTCAGTCCAAATGTTCCTGGGCAGATCTTT                         ATGGGTTTAATGGTTAACCCTCCTAAGCCTGGAGATATCTCTTATCTGAAG
genomic: ACAAGGTTGCATCAATCGCACTCAGTCCAAATGTTCCTGGGCAGATCTTTgtaagtcaaa ... tcatttacagATGGGTTTAATGGTTAACCCTCCTAAGCCTGGAGATATCTCTTATCTGAAG
EST: gi|58688608|gb|CK077295.1|CK077295
EST:     CAAGGTTGCAGTCAATCGCACTCAGTCCAAATGTTCCTGGGCAGATCTTT                         ATGGGTTTAATGGTTAACCCTCCTAAGCCTGGAGATATCTCTTATCTGAAG
genomic: CAAGGTTGCA-TCAATCGCACTCAGTCCAAATGTTCCTGGGCAGATCTTTgtaagtcaaa ... tcatttacagATGGGTTTAATGGTTAACCCTCCTAAGCCTGGAGATATCTCTTATCTGAAG
EST: gi|13420573|gb|AU174663.1|AU174663
EST:     ACAAGGTTGCATCAATCGCACTCAGTCCAAATGTTCCTGGGCAGATCTTT                         ATGGGTTTAATGGTTAACCCTCCTAAGCCTGGAGATATCTCTTATCTGAAG
genomic: ACAAGGTTGCATCAATCGCACTCAGTCCAAATGTTCCTGGGCAGATCTTTgtaagtcaaa ... tcatttacagATGGGTTTAATGGTTAACCCTCCTAAGCCTGGAGATATCTCTTATCTGAAG
EST: gi|29615822|gb|CB620834.1|CB620834
EST:     ACAAGGTTGCATCAATCGCACTCAGTCCAAATGTTCCTGGGCAGATCTTT                         ATGGGTTTAATGGTTAACCCTCCTAAGCCTGGAGATATCTCTTATCTGAAG
genomic: ACAAGGTTGCATCAATCGCACTCAGTCCAAATGTTCCTGGGCAGATCTTTgtaagtcaaa ... tcatttacagATGGGTTTAATGGTTAACCCTCCTAAGCCTGGAGATATCTCTTATCTGAAG
EST: gi|33381622|gb|CF196965.1|CF196965
EST:     ACAAGGTTGCATCAATCGCACTCAGTCCAAATGTTCCTGGGCAGATCTTT                         ATGGGTTTAATGGTTAACCCTCCTA
genomic: ACAAGGTTGCATCAATCGCACTCAGTCCAAATGTTCCTGGGCAGATCTTTgtaagtcaaa ... tcatttacagATGGGTTTAATGGTTAACCCTCCTA
EST: gi|33801487|gb|CF326616.1|CF326616
EST:     ACAAGGTTGCATCAATCGCACTCAGTCCAAATGTTCCTGGGCAGATCTTT                         ATGGGTTTAATGGTTAACCCTCCTAAGCCTGGAGATATCTCTTATCTGAAG
genomic: ACAAGGTTGCATCAATCGCACTCAGTCCAAATGTTCCTGGGCAGATCTTTgtaagtcaaa ... tcatttacagATGGGTTTAATGGTTAACCCTCCTAAGCCTGGAGATATCTCTTATCTGAAG
EST: gi|58588206|gb|CF986514.1|CF986514
EST:     ACAAGGTTGCATCAATCGCACTCAGTCCAAATGTTCCTGGGCAGATCTTT                         ATGGGTTTAATGGT
genomic: ACAAGGTTGCATCAATCGCACTCAGTCCAAATGTTCCTGGGCAGATCTTTgtaagtcaaa ... tcatttacagATGGGTTTAATGGT
EST: gi|33381971|gb|CF197314.1|CF197314
EST:     ACAAGGTTGCATCAATCGCACTCAGTCCAAATGTTCCTGGGCAGATCTTT                         ATGGGTTTAATGGTTAACCCTCCTAAGCCTGGAGATATCTCTTATCTGAAG
genomic: ACAAGGTTGCATCAATCGCACTCAGTCCAAATGTTCCTGGGCAGATCTTTgtaagtcaaa ... tcatttacagATGGGTTTAATGGTTAACCCTCCTAAGCCTGGAGATATCTCTTATCTGAAG
EST: gi|33675257|gb|CF303496.1|CF303496
EST:     ACAAGGTTGCATCAATCGCACTCAGTCCAAATGTTCCTGGGCAGATCTTT                         ATGGGTTTAATGGTTAACCCTCCTAAGCCTGGAGATATCTCTTATCTGAAG
genomic: ACAAGGTTGCATCAATCGCACTCAGTCCAAATGTTCCTGGGCAGATCTTTgtaagtcaaa ... tcatttacagATGGGTTTAATGGTTAACCCTCCTAAGCCTGGAGATATCTCTTATCTGAAG
EST: gi|5667553|gb|AU077813.1|AU077813
EST:     ACAAGGTTGCATCAATCGCACTCAGTCCAAATGTTCCTGGGCAGATCTTT                         ATGGGTTTAATGGTTAACCCTTCTAAGCCTGGAGATATCTCTTATCTGAAG
genomic: ACAAGGTTGCATCAATCGCACTCAGTCCAAATGTTCCTGGGCAGATCTTTgtaagtcaaa ... tcatttacagATGGGTTTAATGGTTAACCCTCCTAAGCCTGGAGATATCTCTTATCTGAAG
EST: gi|313079823|gb|HO213262.1|HO213262
EST:     ACAAGGTTGCATCAATCGCACTCAGTCCAAATGTTCCTGGGCAGATCTTT                         ATGGGTTTAATGGTTAACCCTCCTAAGCCTGGAGATATCTCTTATCTGAAG
genomic: ACAAGGTTGCATCAATCGCACTCAGTCCAAATGTTCCTGGGCAGATCTTTgtaagtcaaa ... tcatttacagATGGGTTTAATGGTTAACCCTCCTAAGCCTGGAGATATCTCTTATCTGAAG
EST: gi|701822|gb|D48113.1|D48113
EST:     ACAAGGTTGCATCAATCGCACTCAGTCCAAATGTTCCTGGGCAGATCTTT                         ATGGGGTTAATGGTTAACCCTCCTAAGCCTGGGGNTATCCCTTATCTGAGG
genomic: ACAAGGTTGCATCAATCGCACTCAGTCCAAATGTTCCTGGGCAGATCTTTgtaagtcaaa ... tcatttacagATGGGTTTAATGGTTAACCCTCCTAAGCCTGGAGATATCTCTTATCTGAAG
EST: gi|33381462|gb|CF196805.1|CF196805
EST:     ACAAGGTTGCATCAATCGCACTCAGTCCAAATGTTCCTGGGCAGATCTTT                         ATGGGTTTAATGGTTAACCCTCCTAAGCCTGGAGATATCTCTTATCTGAAG
genomic: ACAAGGTTGCATCAATCGCACTCAGTCCAAATGTTCCTGGGCAGATCTTTgtaagtcaaa ... tcatttacagATGGGTTTAATGGTTAACCCTCCTAAGCCTGGAGATATCTCTTATCTGAAG
EST: gi|11442608|gb|BF430511.1|BF430511
EST:     ACAAGGTTGCATCAATCGCACTCAGTCCAAATGTTCCTGGGCAGATCTTT                         ATGGGTTTAATGGTTAACCCTCCTAAGCCTGGAGATATCTCTTATCTGAAG
genomic: ACAAGGTTGCATCAATCGCACTCAGTCCAAATGTTCCTGGGCAGATCTTTgtaagtcaaa ... tcatttacagATGGGTTTAATGGTTAACCCTCCTAAGCCTGGAGATATCTCTTATCTGAAG
EST: gi|29689279|gb|CB685554.1|CB685554
EST:     ACAAGGTTGCATCAATCGCACTCAGTCCAAATGTTCCTGGGCAGATCTTT                         ATGGGTTTAATGGTTAACCCTCCTAAGCCTGGAAATATCTCTTATCT
genomic: ACAAGGTTGCATCAATCGCACTCAGTCCAAATGTTCCTGGGCAGATCTTTgtaagtcaaa ... tcatttacagATGGGTTTAATGGTTAACCCTCCTAAGCCTGGAGATATCTCTTATCT
EST: gi|38479882|gb|CF963971.1|CF963971
EST:     ACAAGGTTGCATCAATCGCACTCAGTCCAAATGTTCCTGGGCAGATCTTT                         ATGGGTTTAATGGTTAACCCTCCTAAGCCTGGAGATATCTCTTATCTGAAG
genomic: ACAAGGTTGCATCAATCGCACTCAGTCCAAATGTTCCTGGGCAGATCTTTgtaagtcaaa ... tcatttacagATGGGTTTAATGGTTAACCCTCCTAAGCCTGGAGATATCTCTTATCTGAAG

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: 370

ACAGTAGACGAGATCTACAAGGTTGCATCAATCGCACTCAGTCCAAATGTTCCTGGGCAGATCTTTgtaagtcaaa ... tcatttacagATGGGTTTAATGGTTAACCCTCCTAAGCCTGGAGATATCTCTTATCTGAAGTTTTCTGCTGAAAG




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttatgttactttgctttaacaagttaataaaaatggttttaatgtcatttacagATGGGTTTAATGGTTAACCCTCCTAAGCCTGGAGATATCTCTTATCTGAAGTTTTCTGCTGAAAG
                                     ttttaat  putative branch site (score: 370)
               tttaacaagttaataa  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tagttcctgaaacagtttagttgcaactgtactaattttcttgaagttatgttactttgctttaacaagttaataaaaatggttttaatgtcatttacagATGGGTTTAATGGTTAACCCTCCTAAGCCTGGAGATATCTCTTATCTGAAGTTTTCTGCTGAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- gttcctg
- - - - - - - - - agttgca
- - - - - - - - - - - - - - - - - - tttcttg
- - - - - - - - - - - - - - - - - - - - - - - ttatgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aataaaa