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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGTGGGCTTGCACCTGGTGGATTCAACTTTGATGCCAAATTgttggttcccgctgacattgttttttttttttgtgtgtgtgtaaattggtctctgattcaactgaatttcaattgacttggaattctattatgtcaacag

Basic information

species Oryza sativa
transcript LOC_Os07g47290.1
intron # 17
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g47290.1 (Oryza sativa), 5'ss of exon 17
lower sequence: GRMZM2G081682_T02 (Zea mays), 5'ss of exon 16
-----------------------------------------------------------GGTGGGCTTGCACCTGGTGGATTCAACTTTGATGCCAAATTgttggttcccgctgacattgttttttttttttgtgtgtgtgtaaattggtctctgattcaactgaatttcaattgacttggaattctattatgtcaacag
                                                           ||||| |||||||||||||| ||||||||||||||||||||||  || ||   || |||   ||| || || ||||     | |||               | || | || ||   || ||| ||||| || ||  |||||
AGTTTGCCTATGTACTTCCTGGTTGCACTCATATAAGCTGCTGCATTTTTGTTTAACAGGGTGGACTTGCACCTGGTGGTTTCAACTTTGATGCCAAATTgtcagtaccttttgtcatatgtttcttgttctgtg-----gaaaa---------------attggaattgaaccaacatgggattcttttgtgataacag

upper sequence: LOC_Os07g47290.1 (Oryza sativa), 5'ss of exon 17
lower sequence: GRMZM2G427620_T01 (Zea mays), 5'ss of exon 9
--------------------------------------------------------------GGTGGGCTTGCACCTGGTG-GATTCAACTTTGATGCCAAATTgttggttcc-cgctgacattgttttttttttttgtgtgtgtgtaaattggt---ctctgattcaactgaatttcaattgacttggaa--ttctattatgtcaacag----------------------------------------------------
                                                              | |  |  ||    |||   ||  || || |    |    |  |    ||| |  || |  |||  ||     |||      | | |  || |    | |  || ||| |  |     |  || |||    ||| | | ||    ||                                                     
GTTGGGACACAGATCAGTTCATGACAGACATTGCAGAGGCTACTTTGGTTATGTCAAGTGTAGTTAAGAATgtgagtggcatgaaccagctctctccctttttactcaaatccacattgcctatgtacttcccagttgcactcatatgagctgctgcgtttttgtttaacagggtggacttgcacctggtggtttcaactttgatgccaaattgtcagtaccttttgtgtaggttgtaacatttctctatggcttcaatcag

upper sequence: LOC_Os07g47290.1 (Oryza sativa), 5'ss of exon 17
lower sequence: GRMZM2G081682_T01 (Zea mays), 5'ss of exon 17
GGTGGGCTTGCACCTGGTGGATTCAACTTTGATGCCAAATTgttggttcccgctgacattgttttttttttttgtgtgtgtgtaaattggtctctgattcaactgaatttcaattgacttggaattctattatgtcaacag
||||| |||||||||||||| ||||||||||||||||||||||  || ||   || |||   ||| || || ||||     | |||               | || | || ||   || ||| ||||| || ||  |||||
GGTGGACTTGCACCTGGTGGTTTCAACTTTGATGCCAAATTgtcagtaccttttgtcatatgtttcttgttctgtg-----gaaaa---------------attggaattgaaccaacatgggattcttttgtgataacag

upper sequence: LOC_Os07g47290.1 (Oryza sativa), 5'ss of exon 17
lower sequence: GRMZM2G005493_T01 (Zea mays), 5'ss of exon 17
GGTGGGCTTGCACCTGGTGGATTCAACTTTGATGCCAAATTgttggttcccgctgacattgttttttttttttgtgtgtgtgtaaattggtctctgattcaac-tgaatttcaattgacttggaattctattatgtcaacag
||||| |||||||||||||| ||||||||||| ||||||||||  || || | || ||||  ||| |  || ||||       |   || ||||||||| ||  || | || ||   || ||| |||||  | ||   ||||
GGTGGACTTGCACCTGGTGGCTTCAACTTTGACGCCAAATTgtcagtccctgatgtcatttgtttctcattctgtgaa---aaaggatgatctctgattaaaagtggagttaaaccaacatggtattcttctgtgatgacag

upper sequence: LOC_Os07g47290.1 (Oryza sativa), 5'ss of exon 17
lower sequence: GRMZM2G313536_T01 (Zea mays), 5'ss of exon 13
--------------------------------------------------------------GGTGGGCTTGCACCTGGTG-GATTCAACTTTGATGCCAAATTgttggttcc-cgctgacattgttttttttttttgtgtgtgtgtaaattggt---ctctgattcaactgaatttcaattgacttggaa--ttctattatgtcaacag----------------------
                                                              | |  |  ||    |||   ||  || || |    |    |  |    ||| |  || |  |||  ||     |||      | | |  || |    | |  || ||| |  |     |  || |||    ||| | | ||    ||                       
GTTGGGACACAGATCAGTTCATGACAGACATTGCAGAGGCTACTTTGGTTATGTCAAGTGTAGTTAAGAATgtgagtggcatgaaccagctctctccctttttactcaaatccacattgcctatgtacttcccagttgcactcatatgagctgctgcgtttttgtttaacagggtggacttgcacctggtggtttcaactttgatgccaaattgtcagtaccttttgtgtag

upper sequence: LOC_Os07g47290.1 (Oryza sativa), 5'ss of exon 17
lower sequence: GLYMA17G07380.1 (Glycine max), 5'ss of exon 17
GGTGGGCTTGCACCTGGTGGATTCAACTTTGATGCCAAATTgttggttcccgctgacattgttttttttttttgtgtgtgtgtaaattggtctctgattcaactgaatttcaattgacttgg-aattctattatgtcaacag
|| || |||||||| |||||||||||||| ||||| |||||||  || |      |      ||| | |  |||| |   |||   ||| | | |    |  || | ||||  |  |||| | |||  |||           
GGAGGACTTGCACCCGGTGGATTCAACTTCGATGCGAAATTgtcagtccttctctat----ctttatatacttgtattcctgt---ttgttttattccccccctcagtttctgt--acttagcaatgttatag---------

upper sequence: LOC_Os07g47290.1 (Oryza sativa), 5'ss of exon 17
lower sequence: Vv11s0052g01710.t01 (Vitis vinifera), 5'ss of exon 18
GGTGGGCTTGCACCTGGTGGATTCAACTTTGATGCCAAATTgttggttcccgctgacattgttt--------tttttttttgtg----tgtgtgtaaattggtct--ctgattcaactgaatttcaattgacttggaattctattatgtcaacag----------------------
|| ||||| || ||||| |||||||||||||||||||||||||  ||| |        ||||||         || ||||| |     ||| |||   || || |   || ||   |   | |||   || ||  | |   ||  ||   | |                        
GGAGGGCTGGCCCCTGGAGGATTCAACTTTGATGCCAAATTgtaagtttctttcttttttgtttatatggaccttatttttataatgttgtttgtttgtttgtttgtttgttttttcaatacttcttatgcctctggagattaccatactatcttcatttttttttatgaattttag

upper sequence: LOC_Os07g47290.1 (Oryza sativa), 5'ss of exon 17
lower sequence: EFJ07726 (Selaginella moellendorffii), 5'ss of exon 15
GGTGGGCTTGCACCTGGTGGATTCAACTTTGATGCCAAATTgttggttcccgctgacattgttttttttttttgtgtgtgtgtaaattggtctctgattcaactgaatttcaattgacttggaattctattatgtcaacag
|| || ||||| ||||||||||||||||| ||||||||| |||  ||       || |   ||  |     ||      |||   | | || | |  |     ||  |||||                             
GGAGGTCTTGCTCCTGGTGGATTCAACTTCGATGCCAAACTgtgcgtgtatttagaaaccattcctaccgatt-----cgtgctcacttgtgtgttgtgtg-ttgtttttcag----------------------------

upper sequence: LOC_Os07g47290.1 (Oryza sativa), 5'ss of exon 17
lower sequence: EFJ07670 (Selaginella moellendorffii), 5'ss of exon 15
GGTGGGCTTGCACCTGGTGGATTCAACTTTGATGCCAAATTgttggttcccgctgacattgttttttttttttgtgtgt-----gtgtaaattggtctctgattcaactgaatttcaattgacttggaattctattatgtcaacag
|| || ||||| ||||||||||||||||| ||||||||| |||  ||       || |   ||  |    ||  |         |||   | | || | || |     ||  |||||                             
GGAGGCCTTGCTCCTGGTGGATTCAACTTCGATGCCAAACTgtgcgtctatttagaaaccattcctaccattcctacaccattcgtgctcacttgtgtgtggtgtg-ttgtgtttcag----------------------------

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|86854458|gb|CI256580.1|CI256580
EST:     GGTGGGCTTGCACCTGGTGGATTCAACTTTGATGCCCAATT                         GAGGAGGGAGAGTACTGATGTTGAGGACATGTTTCTGGCTCATATATCGGG
genomic: GGTGGGCTTGCACCTGGTGGATTCAACTTTGATGCCAAATTgttggttccc ... atgtcaacagGAGGAGGGAGAGTACTGATGTTGAGGACATGTTTCTGGCTCATATATCGGG
EST: gi|33654092|gb|CF276706.1|CF276706
EST:     GGTGGGCTTGCACCTGGTGGATTCAACTTTGATGCCAAATT                         GAGGAGGGAGAGTACTGATGTTGAGGACATGTTTTTGGCTCATATATCGGG
genomic: GGTGGGCTTGCACCTGGTGGATTCAACTTTGATGCCAAATTgttggttccc ... atgtcaacagGAGGAGGGAGAGTACTGATGTTGAGGACATGTTTCTGGCTCATATATCGGG
EST: gi|88985909|gb|CI033238.1|CI033238
EST:     GGTGGGCTTGCACCTGGTGGATTCAACTTTGATGCCAAATT                         GAGGAGGGAGAGTACTGATGTTGAGGACATGTTTCTGGCTCATATATCGGG
genomic: GGTGGGCTTGCACCTGGTGGATTCAACTTTGATGCCAAATTgttggttccc ... atgtcaacagGAGGAGGGAGAGTACTGATGTTGAGGACATGTTTCTGGCTCATATATCGGG
EST: gi|29667757|gb|CB664032.1|CB664032
EST:     GGTGGGCTTGCACCTGGTGGATTCAACTTTGATGCCAAATT                         GAGGAGGGAGAGTACTGATGTTGAGGACATGTTTCTGGCTCATATATCGGG
genomic: GGTGGGCTTGCACCTGGTGGATTCAACTTTGATGCCAAATTgttggttccc ... atgtcaacagGAGGAGGGAGAGTACTGATGTTGAGGACATGTTTCTGGCTCATATATCGGG
EST: gi|29625367|gb|CB630378.1|CB630378
EST:     GGTGGGCTTGCACCTGGTGGATTCAACTTTGATGCCAAATT                         GAGGAGGGAGAGTACTGATGTTGAGGACATGTTTCTGGCTCATATATCGGG
genomic: GGTGGGCTTGCACCTGGTGGATTCAACTTTGATGCCAAATTgttggttccc ... atgtcaacagGAGGAGGGAGAGTACTGATGTTGAGGACATGTTTCTGGCTCATATATCGGG
EST: gi|38476165|gb|CF960298.1|CF960298
EST:     CTTTGATGCCAAATT                         GAGGAGGGAGAGTACTGATGTTGAGGACATGTTTCTGGCTCATATATCGGG
genomic: CTTTGATGCCAAATTgttggttccc ... atgtcaacagGAGGAGGGAGAGTACTGATGTTGAGGACATGTTTCTGGCTCATATATCGGG
EST: gi|29642115|gb|CB647122.1|CB647122
EST:     GGTGGGCTTGCACCTGGTGGATTCAACTTTGATGCCAAATT                         GAGGAGGGAGAGTACTGATGTTGAGGACATGTTTCTGGCTCATATATCGGG
genomic: GGTGGGCTTGCACCTGGTGGATTCAACTTTGATGCCAAATTgttggttccc ... atgtcaacagGAGGAGGGAGAGTACTGATGTTGAGGACATGTTTCTGGCTCATATATCGGG
EST: gi|88828748|gb|CI073618.1|CI073618
EST:     GATTCAACTTTGATGCCAAATT                         GAGGAGGGAGAGTACTGATGTTGAGGACATGTTTCTGGCTCATATATCGGG
genomic: GATTCAACTTTGATGCCAAATTgttggttccc ... atgtcaacagGAGGAGGGAGAGTACTGATGTTGAGGACATGTTTCTGGCTCATATATCGGG
EST: gi|29643120|gb|CB648127.1|CB648127
EST:     GGTGGGCTTGCACCTGGTGGATTCAACTTTGATGCCAAATT                         GAGGAGGGAGAGTACTGATGTTGAGGACATGTTTCTGGCTCATATATCGGG
genomic: GGTGGGCTTGCACCTGGTGGATTCAACTTTGATGCCAAATTgttggttccc ... atgtcaacagGAGGAGGGAGAGTACTGATGTTGAGGACATGTTTCTGGCTCATATATCGGG
EST: gi|44676968|gb|CR290402.1|CR290402
EST:     TAA-AATGGTGGGCCTGGCACGT-GTGGGATTCAACTTTGATGCCAATTT                         GAGGAGGGAGATTACTGATGTTGAGGACATGTTTCTGGCTCATATATCGGG
genomic: TAAGAATGGTGGG-CTTGCACCTGGT-GGATTCAACTTTGATGCCAAATTgttggttccc ... atgtcaacagGAGGAGGGAGAGTACTGATGTTGAGGACATGTTTCTGGCTCATATATCGGG
EST: gi|29688080|gb|CB684355.1|CB684355
EST:     GGTGGGCTTGCACCTGGTGGATTCAACTTTGATGCCAAATT                         GAGGAGGGAGAGTACTGATGTTGAGGACATGTTTCTGGCTCATATATCGGG
genomic: GGTGGGCTTGCACCTGGTGGATTCAACTTTGATGCCAAATTgttggttccc ... atgtcaacagGAGGAGGGAGAGTACTGATGTTGAGGACATGTTTCTGGCTCATATATCGGG
EST: gi|58031342|gb|CX728885.1|CX728885
EST:     GTGGATTCAACTTTGATGCCAAATT                         GAGGAGGGAGAGTACTGATGTTGAGGACATGTTTCTGGCTCATATATCGGG
genomic: GTGGATTCAACTTTGATGCCAAATTgttggttccc ... atgtcaacagGAGGAGGGAGAGTACTGATGTTGAGGACATGTTTCTGGCTCATATATCGGG
EST: gi|12622805|gb|AU173018.1|AU173018
EST:     GGTGGGCTTGCACCTGGTGGATTCAACTTTGATGCCAAATT                         GAGGAGGGAGAGTACTGATGTTGAGGACATGTTTCTGGCTCATATATCGGG
genomic: GGTGGGCTTGCACCTGGTGGATTCAACTTTGATGCCAAATTgttggttccc ... atgtcaacagGAGGAGGGAGAGTACTGATGTTGAGGACATGTTTCTGGCTCATATATCGGG
EST: gi|29661148|gb|CB657423.1|CB657423
EST:     GGTGGGCTTGCACCTGGTGGATTCAACTTTGATGCCAAATT                         GAGGAGGGAGAGTACTGATGTTGAGGACATGTTTTTGGCTCATATATCGGG
genomic: GGTGGGCTTGCACCTGGTGGATTCAACTTTGATGCCAAATTgttggttccc ... atgtcaacagGAGGAGGGAGAGTACTGATGTTGAGGACATGTTTCTGGCTCATATATCGGG
EST: gi|29657675|gb|CB653950.1|CB653950
EST:     GGTGGGCTTGCACCTGGTGGATTCAACTTTGATGCCAAATT                         GAGGAGGGAGAGTACTGATGTTGAGGACATGTTTCTGGCTCATATATCGGG
genomic: GGTGGGCTTGCACCTGGTGGATTCAACTTTGATGCCAAATTgttggttccc ... atgtcaacagGAGGAGGGAGAGTACTGATGTTGAGGACATGTTTCTGGCTCATATATCGGG
EST: gi|58031266|gb|CX728809.1|CX728809
EST:     GGTGGGCTTGCACCTGGTGGATTCAACTTTGATGCCAAATT                         GAGGAGGGAGAGTACTGATGTTGAGGACATGTTTCTGGCTCATATATCGGG
genomic: GGTGGGCTTGCACCTGGTGGATTCAACTTTGATGCCAAATTgttggttccc ... atgtcaacagGAGGAGGGAGAGTACTGATGTTGAGGACATGTTTCTGGCTCATATATCGGG
EST: gi|89194258|gb|CI116695.1|CI116695
EST:     GGTGGGCTTGCACCTGGTGGATTCAACTTTGATGCCAAATT                         GAGGAGGGAGAGTACTGATGTTGAGGACATGTTTCTGGCTCATATATCGGG
genomic: GGTGGGCTTGCACCTGGTGGATTCAACTTTGATGCCAAATTgttggttccc ... atgtcaacagGAGGAGGGAGAGTACTGATGTTGAGGACATGTTTCTGGCTCATATATCGGG
EST: gi|89172814|gb|CI022693.1|CI022693
EST:     GGTGGGCTTGCACCTGGTGGATTCAACTTTGATGCCAAATT                         GAGGAGGGAGAGTACTGATGTTGAGGACATGTTTCTGGCTCATATATCGGG
genomic: GGTGGGCTTGCACCTGGTGGATTCAACTTTGATGCCAAATTgttggttccc ... atgtcaacagGAGGAGGGAGAGTACTGATGTTGAGGACATGTTTCTGGCTCATATATCGGG
EST: gi|5004160|gb|AU069309.1|AU069309
EST:     GGTGGGCTTGCACCTGGTGGATTCAACTTTGATGCCAAATT                         GAGGAGGGAGAGTACTGATGTTGAGGACATGTTTCTGGCTCATATATCGGG
genomic: GGTGGGCTTGCACCTGGTGGATTCAACTTTGATGCCAAATTgttggttccc ... atgtcaacagGAGGAGGGAGAGTACTGATGTTGAGGACATGTTTCTGGCTCATATATCGGG
EST: gi|29665147|gb|CB661422.1|CB661422
EST:     GGTGGGCTTGCACCTGGTGGATTCAACTTTGATGCCAAATT                         GAGGAGGGAGAGTACTGATGTTGAGGACATGTTTCTGGCTCATATATCGGG
genomic: GGTGGGCTTGCACCTGGTGGATTCAACTTTGATGCCAAATTgttggttccc ... atgtcaacagGAGGAGGGAGAGTACTGATGTTGAGGACATGTTTCTGGCTCATATATCGGG
EST: gi|29620969|gb|CB625980.1|CB625980
EST:     GGTGGGCTTGCACCTGGTGGATTCAACTTTGATGCCAAATT                         GAGGAGGGAGAGTACTGATGTTGAGGACATGTTTCTGGCTCATATATCGGG
genomic: GGTGGGCTTGCACCTGGTGGATTCAACTTTGATGCCAAATTgttggttccc ... atgtcaacagGAGGAGGGAGAGTACTGATGTTGAGGACATGTTTCTGGCTCATATATCGGG
EST: gi|29688817|gb|CB685092.1|CB685092
EST:     GGTGGATTCAACCCTGATGCCAAATT                         GAGGAGGGAGAGTACTGATGTTGAGGACATGTTTCTGGCTCATATATCGGG
genomic: GGTGGATTCAACTTTGATGCCAAATTgttggttccc ... atgtcaacagGAGGAGGGAGAGTACTGATGTTGAGGACATGTTTCTGGCTCATATATCGGG
EST: gi|29644690|gb|CB649697.1|CB649697
EST:     GGTGGGCTTGCACCTGGTGGATTCAACTTTGATGCCAAATT                         GAGGAGGGAGAGTACTGATGTTGAGGACATGTTTCTGGCTCATATATCGGG
genomic: GGTGGGCTTGCACCTGGTGGATTCAACTTTGATGCCAAATTgttggttccc ... atgtcaacagGAGGAGGGAGAGTACTGATGTTGAGGACATGTTTCTGGCTCATATATCGGG
EST: gi|29637954|gb|CB642963.1|CB642963
EST:     GGTGGGCTTGCACCTGGTGGATTCAACTTTGATGCCAAATT                         GAGGAGGGAGAGTACTGATGTTGAGGACATGTTTCTGGCTCATATATCGGG
genomic: GGTGGGCTTGCACCTGGTGGATTCAACTTTGATGCCAAATTgttggttccc ... atgtcaacagGAGGAGGGAGAGTACTGATGTTGAGGACATGTTTCTGGCTCATATATCGGG

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: 65

GGTGGGCTTGCACCTGGTGGATTCAACTTTGATGCCAAATTgttggttccc ... atgtcaacagGAGGAGGGAGAGTACTGATGTTGAGGACATGTTTCTGGCTCATATATCGGGAATGGACACCCTAGCCCGCGGCCTTCGGAATGTTGTCAAGCTGATCGAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGTGGGCTTGCACCTGGTGGATTCAACTTTGATGCCAAATTgttggttcccgctgacattgttttttttttttgtgtgtgtgtaaattggtctctgattcaactgaatttcaattgacttggaattctattatgtcaacag

- - - - - - - TGGTGG
- - - - - - -  GGTGGA