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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gttgacttctcttattgactttactgcaaaattttatttctatatcactatttgttatcctagaattattttctcacaatagttcgtttatgatatgcagGGAATAGTGCTGCTAATCATCTTGATATCAGGACTCAAATGTATGATGGGAATTGATACCCCATCAAAGTTCGATGCTCCCCCGGAATCGTAAGCCCATT

Basic information

species Oryza sativa
transcript LOC_Os12g03060.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g03060.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G179737_T02 (Zea mays), 3'ss of exon 8
----------------------------------------gttgacttctc--ttattgactttactgcaaaatttta-tttctatatcactatt-tgttatcctagaattattttctcacaatagttcgtttatgatatgcagGGAATAGTGCTGCTAATCATCTTGATATCAGGACTCAAATGTATGATGGGAATTGATACCCCATCAAAGTTCGATGCTCCCCCGGAATCGTAAGCCCATT
                                         ||  ||| ||  || ||    | |    ||||  |    ||  ||  ||   || |||| |  |   |       |          |   |||     ||||||| |||||||| || |||||| |||||||||||||||  || |||||||| || ||||| || || | ||| || ||||||| ||| || | | | |   
gtgagttgctgctgtgcttgtgctccgttccattcatttcattaccttatcagttcttattctgaaaaaaaaacgtgggcttgcattgcatccttgtgttgtattctcacacgcaccctgggtctacttaattactgcgtgcagGGGATAGTGCTTCTCATCATCCTGATATCAGGACTCATGTGCATGATGGGCATCGATACTCCCTCGAGGTTTGAAGCTCCCCAGGAGTCTTGATCTCTCC

upper sequence: LOC_Os12g03060.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G179737_T03 (Zea mays), 3'ss of exon 7
----------------------------------------gttgacttctc--ttattgactttactgcaaaatttta-tttctatatcactatt-tgttatcctagaattattttctcacaatagttcgtttatgatatgcagGGAATAGTGCTGCTAATCATCTTGATATCAGGACTCAAATGTATGATGGGAATTGATACCCCATCAAAGTTCGATGCTCCCCCGGAATCGTAAGCCCATT
                                         ||  ||| ||  || ||    | |    ||||  |    ||  ||  ||   || |||| |  |   |       |          |   |||     ||||||| |||||||| || |||||| |||||||||||||||  || |||||||| || ||||| || || | ||| || ||||||| ||| || | |       
gtgagttgctgctgtgcttgtgctccgttccattcatttcattaccttatcagttcttattctgaaaaaaaaacgtgggcttgcattgcatccttgtgttgtattctcacacgcaccctgggtctacttaattactgcgtgcagGGGATAGTGCTTCTCATCATCCTGATATCAGGACTCATGTGCATGATGGGCATCGATACTCCCTCGAGGTTTGAAGCTCCCCAGGAGTCTTGA-------

upper sequence: LOC_Os12g03060.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G017941_T01 (Zea mays), 3'ss of exon 8
----------------------------------------------------gttgacttctcttattgactttactgcaaaattt-tatttctatatcactatttgtt--atcctagaattattttctcacaatagttcgtttatgatatgcagGGAATAGTGCTGCTAATCATCTTGATATCAGGACTCAAATGTATGATGGGAATTGATACCCCATCAAAGTTCGATGCTCCCCCGGAATCGTAAGCCCATT
                                                    || | |||   |    |    |   |  ||||   | || |  | ||| | |   ||  ||||| |  || | |||||||    | | || ||  || |||||||||||||||| || ||||||||||||||||| ||||  |||||||||||||| ||||| || || ||||| || ||||||| ||| || | | | |  |
gtaagtcgtttacctgtgctctgtttcattgctcgttggttctattctgaacgtgggcttgcatgcaggggggtggggggaaatccatgttacgttgtcagtgtgccttgtatccttgtgttgtattctcac----gcttgtctactatgtgcagGGAATAGTGCTCCTTATCATCTTGATATCAGGGCTCATGTGTATGATGGGAATCGATACTCCCTCCAAGTTTGAAGCTCCCCAGGAGTCTTGATCTCCCT

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|58694491|gb|CK083178.1|CK083178
EST:     GTGATGGGGAGTGCTTAGTAAAATCAACTCTGCTAGAAGGAAGCTTTGTT                         GGAATAGTGCTGCTAATCATCTTGATATCAGGACTCAAATGTATGATGGGA
genomic: GTGATGGGGAGTGCTTAGTAAAATCAACTCTGCTAGAAGGAAGCTTTGTTgtaagttgtc ... tgatatgcagGGAATAGTGCTGCTAATCATCTTGATATCAGGACTCAAATGTATGATGGGA
EST: gi|33653555|gb|CF276169.1|CF276169
EST:     GTGATGGGGAGTGCTTAGTAAAATCAACTCTGCTAGAAGGAAGCTTTGTT                         GGAATAGTGCTGCTAATCATCTTGATATCAGGACTCAAATGTATGATGGGA
genomic: GTGATGGGGAGTGCTTAGTAAAATCAACTCTGCTAGAAGGAAGCTTTGTTgtaagttgtc ... tgatatgcagGGAATAGTGCTGCTAATCATCTTGATATCAGGACTCAAATGTATGATGGGA
EST: gi|163926921|gb|EG715146.1|EG715146
EST:     GTGATGGGGAGTGCTTAGTAAAATCAACTCTGCTAGAAGGAAGCTTTGTT                         GGAATAGTGCTGCTAATCATCTTGATATCAGGACTCAAATGTATGATGGGA
genomic: GTGATGGGGAGTGCTTAGTAAAATCAACTCTGCTAGAAGGAAGCTTTGTTgtaagttgtc ... tgatatgcagGGAATAGTGCTGCTAATCATCTTGATATCAGGACTCAAATGTATGATGGGA
EST: gi|33681633|gb|CF309872.1|CF309872
EST:     GTGATGGGGAGTGCTTAGTAAAATCAACTCTGCTAGAAGGAAGCTTTGTT                         GGAATAGTGCTGCTAATCATCTTGATATCAGGACTCAAATGTATGATGGGA
genomic: GTGATGGGGAGTGCTTAGTAAAATCAACTCTGCTAGAAGGAAGCTTTGTTgtaagttgtc ... tgatatgcagGGAATAGTGCTGCTAATCATCTTGATATCAGGACTCAAATGTATGATGGGA
EST: gi|89178438|gb|CI015143.1|CI015143
EST:     GTGATGGGGAGTGCTTAGTAAAATCAACTCTGCTAGAAGGAAGCTTTGTT                         GGAATAGTGCTGCTAATCATCTTGATATCAGGACTCAAATGTATGATGGGA
genomic: GTGATGGGGAGTGCTTAGTAAAATCAACTCTGCTAGAAGGAAGCTTTGTTgtaagttgtc ... tgatatgcagGGAATAGTGCTGCTAATCATCTTGATATCAGGACTCAAATGTATGATGGGA
EST: gi|86598271|gb|CI354888.1|CI354888
EST:     GTGATGGGGAGTGCTTAGTAAAATCAACTCTGCTAGAAGGAAGCTTTGTT                         GGAATAGTGCTGCTAATCATCTTGATATCAGGACTCAAATGTATGATGGGA
genomic: GTGATGGGGAGTGCTTAGTAAAATCAACTCTGCTAGAAGGAAGCTTTGTTgtaagttgtc ... tgatatgcagGGAATAGTGCTGCTAATCATCTTGATATCAGGACTCAAATGTATGATGGGA
EST: gi|86834645|gb|CI340762.1|CI340762
EST:     GTGATGGGGAGTGCTTAGTAAAATCAACTCTGCTAGAAGGAAGCTTTGTT                         GGAATAGTGCTGCTAATCATCTTGATATCAGGACTCAAATGTATGATGGGA
genomic: GTGATGGGGAGTGCTTAGTAAAATCAACTCTGCTAGAAGGAAGCTTTGTTgtaagttgtc ... tgatatgcagGGAATAGTGCTGCTAATCATCTTGATATCAGGACTCAAATGTATGATGGGA
EST: gi|88278361|gb|CI399361.1|CI399361
EST:     TAGAAGGAAGCTTTGTT                         GGAATAGTGCTGCTAATCATCTTGATATCAGGACTCAAATGTATGATGGGA
genomic: TAGAAGGAAGCTTTGTTgtaagttgtc ... tgatatgcagGGAATAGTGCTGCTAATCATCTTGATATCAGGACTCAAATGTATGATGGGA
EST: gi|58674334|gb|CK063020.1|CK063020
EST:     GTGATGGGGAGTGCTTAGTAAAATCAACTCTGCTAGAAGGAAGCTTTGTT                         GGAATAGTGCTGCTAATCATCTTGATATCAGGACTCAAATGTATGATGGGA
genomic: GTGATGGGGAGTGCTTAGTAAAATCAACTCTGCTAGAAGGAAGCTTTGTTgtaagttgtc ... tgatatgcagGGAATAGTGCTGCTAATCATCTTGATATCAGGACTCAAATGTATGATGGGA
EST: gi|88446415|gb|CI563245.1|CI563245
EST:     TTAGTAAAATCAACTCTGCTAGAAGGAAGCTTTGTT                         GGAATAGTGCTGCTAATCATCTTGATATCAGGACTCAAATGTATGATGGGA
genomic: TTAGTAAAATCAACTCTGCTAGAAGGAAGCTTTGTTgtaagttgtc ... tgatatgcagGGAATAGTGCTGCTAATCATCTTGATATCAGGACTCAAATGTATGATGGGA
EST: gi|29687248|gb|CB683523.1|CB683523
EST:     GTGATGGGGAGTGCTTAGTAAAATCAACTTTGCTAGAAGGAAGCTTTGTT                         GGAATAGTGCTGCTAATCATCTTGATATCAGGACTCAAATGTATGATGGGA
genomic: GTGATGGGGAGTGCTTAGTAAAATCAACTCTGCTAGAAGGAAGCTTTGTTgtaagttgtc ... tgatatgcagGGAATAGTGCTGCTAATCATCTTGATATCAGGACTCAAATGTATGATGGGA
EST: gi|88278276|gb|CI399276.1|CI399276
EST:     GCTAGAAGGAAGCTTTGTT                         GGAATAGTGCTGCTAATCATCTTGATATCAGGACTCAAATGTATGATGGGA
genomic: GCTAGAAGGAAGCTTTGTTgtaagttgtc ... tgatatgcagGGAATAGTGCTGCTAATCATCTTGATATCAGGACTCAAATGTATGATGGGA
EST: gi|86831384|gb|CI299442.1|CI299442
EST:     GTGATGGGGAGTGCTTAGTACAATCAACTCTGCTAGAAGGAAGCTTTGTT                         GGAATAGTGCTGCTAATCATCTTGATA
genomic: GTGATGGGGAGTGCTTAGTAAAATCAACTCTGCTAGAAGGAAGCTTTGTTgtaagttgtc ... tgatatgcagGGAATAGTGCTGCTAATCATCTTGATA
EST: gi|88239235|gb|CI240397.1|CI240397
EST:     GTGATGGGGAGTGCTTAGTAAAATCAACTCTGCTAGAAGGAAGCTTTGTT                         GGAATAGTGCTGCTAATCATCTTGATATCAGGACTCAAATGTATGATGGGA
genomic: GTGATGGGGAGTGCTTAGTAAAATCAACTCTGCTAGAAGGAAGCTTTGTTgtaagttgtc ... tgatatgcagGGAATAGTGCTGCTAATCATCTTGATATCAGGACTCAAATGTATGATGGGA
EST: gi|38475562|gb|CF959695.1|CF959695
EST:     GTGATGGGGAGTGCTTAGTAAAATCAACTCTGCTAGAAGGAAGCTGTGTT                         GGAATAGTGCTGCTAATCATCTTGATATCAGGACTCAAATGTATGATGGGA
genomic: GTGATGGGGAGTGCTTAGTAAAATCAACTCTGCTAGAAGGAAGCTTTGTTgtaagttgtc ... tgatatgcagGGAATAGTGCTGCTAATCATCTTGATATCAGGACTCAAATGTATGATGGGA
EST: gi|88582726|gb|CI700154.1|CI700154
EST:     GTGATGGGGAGTGCTTAGTAAAATCAACTCTGCTACAAGGAAGCTTTGTT                         GGAATAGTGCTGCTAATCATCTTGATATCAGGACTCAAATGTATGATGGGA
genomic: GTGATGGGGAGTGCTTAGTAAAATCAACTCTGCTAGAAGGAAGCTTTGTTgtaagttgtc ... tgatatgcagGGAATAGTGCTGCTAATCATCTTGATATCAGGACTCAAATGTATGATGGGA
EST: gi|33805224|gb|CF328489.1|CF328489
EST:     GTGATGGGGAGTGCTTAGTAAAATCAACTCTGCTAGAAGGAAGCTTTGTT                         GGAATAGTGCTGCTAATCATCTTGATATCAGGACTCAAAAGTATGATGGGA
genomic: GTGATGGGGAGTGCTTAGTAAAATCAACTCTGCTAGAAGGAAGCTTTGTTgtaagttgtc ... tgatatgcagGGAATAGTGCTGCTAATCATCTTGATATCAGGACTCAAATGTATGATGGGA
EST: gi|88277877|gb|CI398679.1|CI398679
EST:     GGAAGCTTTGTT                         GGAATAGTGCTGCTAATCATCTTGATATCAGGACTCAAATNTATGATGGGA
genomic: GGAAGCTTTGTTgtaagttgtc ... tgatatgcagGGAATAGTGCTGCTAATCATCTTGATATCAGGACTCAAATGTATGATGGGA
EST: gi|87028733|gb|CI349452.1|CI349452
EST:     TGATGGGGAGTGCTTAGTAAAATCAACTCTGCTAGAAGGAAGCTTTGTT                         GGAATAGTGCTGCTAATCATCTTGATATCAGGACTCAAATGTATGATGGGA
genomic: TGATGGGGAGTGCTTAGTAAAATCAACTCTGCTAGAAGGAAGCTTTGTTgtaagttgtc ... tgatatgcagGGAATAGTGCTGCTAATCATCTTGATATCAGGACTCAAATGTATGATGGGA
EST: gi|88906025|gb|CI089611.1|CI089611
EST:     GTGATGGGGAGTGCTTAGTAAAATCAACTCTGCTAGAAGGAAGCTTTGTT                         GGAATAGTGCTGCTAATCATCTTGATATCAGGACTCAAATGTATGATGGGA
genomic: GTGATGGGGAGTGCTTAGTAAAATCAACTCTGCTAGAAGGAAGCTTTGTTgtaagttgtc ... tgatatgcagGGAATAGTGCTGCTAATCATCTTGATATCAGGACTCAAATGTATGATGGGA
EST: gi|88416649|gb|CI543550.1|CI543550
EST:     TGCTAGAAGGAAGCTTTGTT                         GGAATAGTGCTGCTAATCATCTTGATATCAGGACTCAAATGTATGATGGGA
genomic: TGCTAGAAGGAAGCTTTGTTgtaagttgtc ... tgatatgcagGGAATAGTGCTGCTAATCATCTTGATATCAGGACTCAAATGTATGATGGGA
EST: gi|88413203|gb|CI523764.1|CI523764
EST:     AGGAAGCTTTGTT                         GGAATAGTGCTGCTAATCATCTTGATATCAGGACTCAAATGTATGATGGGA
genomic: AGGAAGCTTTGTTgtaagttgtc ... tgatatgcagGGAATAGTGCTGCTAATCATCTTGATATCAGGACTCAAATGTATGATGGGA
EST: gi|86418859|gb|CI053660.1|CI053660
EST:     GTGATGGGGAGTGCTTAGTAAAATCAACTCTGCTAGAAGGAAGCTTTGTT                         GGAATAGTGCTGCTAATCATCTTGATATCAGGACTCAAATGTATGATGGGA
genomic: GTGATGGGGAGTGCTTAGTAAAATCAACTCTGCTAGAAGGAAGCTTTGTTgtaagttgtc ... tgatatgcagGGAATAGTGCTGCTAATCATCTTGATATCAGGACTCAAATGTATGATGGGA
EST: gi|29657294|gb|CB653569.1|CB653569
EST:     GTGATGGGGAGTGCTTAGTAAAATCAACTCTGCTAGAAGGAAGCTTTGTT                         GGAATAGTGCTGCTAATCATCTTGATATCAGGACTCAAATGTATGATGGGA
genomic: GTGATGGGGAGTGCTTAGTAAAATCAACTCTGCTAGAAGGAAGCTTTGTTgtaagttgtc ... tgatatgcagGGAATAGTGCTGCTAATCATCTTGATATCAGGACTCAAATGTATGATGGGA
EST: gi|29618675|gb|CB623687.1|CB623687
EST:     GTGATGGGGAGTGCTTAGTAAAATCAACTCTGCTAGAAGGAAGCTTTGTT                         GGAATAGTGCTGCTAATCATCTTGATATCAGGACTCAAATGTATGATGGGA
genomic: GTGATGGGGAGTGCTTAGTAAAATCAACTCTGCTAGAAGGAAGCTTTGTTgtaagttgtc ... tgatatgcagGGAATAGTGCTGCTAATCATCTTGATATCAGGACTCAAATGTATGATGGGA
EST: gi|88291767|gb|CI539938.1|CI539938
EST:     GGGAGTGCTTAGTAAAATCAACTCTGCTAGAAGGAAGCTTTGTT                         GGAATAGTGCTGCTAATCATCTTGATATCAGGACTCAAATGTATGATGGGA
genomic: GGGAGTGCTTAGTAAAATCAACTCTGCTAGAAGGAAGCTTTGTTgtaagttgtc ... tgatatgcagGGAATAGTGCTGCTAATCATCTTGATATCAGGACTCAAATGTATGATGGGA
EST: gi|88995219|gb|CI036794.1|CI036794
EST:     GTGATGGGGAGTGCTTAGTAAAATCNACTCTGCTAGAAGGAAGCTTTGTT                         GGAATAGTGCTGCTAATCATCTTGATATCAGGACTCAAATGTATGATGGGA
genomic: GTGATGGGGAGTGCTTAGTAAAATCAACTCTGCTAGAAGGAAGCTTTGTTgtaagttgtc ... tgatatgcagGGAATAGTGCTGCTAATCATCTTGATATCAGGACTCAAATGTATGATGGGA
EST: gi|38471525|gb|CF955656.1|CF955656
EST:     GTGATGGGGAGTGCTTAGTAAAATCAACTCTGCTAGAAGGAAGCTTTGTT                         GGAATAGTGCTGCTAATCATCTTGATATCAGGACTCAAATGTATGATGGGA
genomic: GTGATGGGGAGTGCTTAGTAAAATCAACTCTGCTAGAAGGAAGCTTTGTTgtaagttgtc ... tgatatgcagGGAATAGTGCTGCTAATCATCTTGATATCAGGACTCAAATGTATGATGGGA
EST: gi|88384390|gb|CI551316.1|CI551316
EST:     GTGATGGGGAGTGCTTAGTAAAATCAACTCTGCTAGAAGGAAGCTTTGTT                         GGAATAGTGCTGCTAATCATCTTGATATCAGGACTCAAATGTATGATGGGA
genomic: GTGATGGGGAGTGCTTAGTAAAATCAACTCTGCTAGAAGGAAGCTTTGTTgtaagttgtc ... tgatatgcagGGAATAGTGCTGCTAATCATCTTGATATCAGGACTCAAATGTATGATGGGA

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: 35 (upstream exon), 70 (downstream exon)
Score: 10

CAGGTACCTCGCAGAGAAGACTAATACTACTAAACCCGGCCGTGGAAAATGTGATGGGGAGTGCTTAGTAAAATCAACTCTGCTAGAAGGAAGCTTTGTTgtaagttgtc ... tgatatgcagGGAATAGTGCTGCTAATCATCTTGATATCAGGACTCAAATGTATGATGGGAATTGATACCCCATCAAAGTTCGATGCTCCCCCGGAATCGTAAGCCCATT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cactatttgttatcctagaattattttctcacaatagttcgtttatgatatgcagGGAATAGTGCTGCTAATCATCTTGATATCAGGACTCAAATGTATGATGGGAATTGATACCCCATCAAAGTTCGATGCTCCCCCGGAATCGTAAGCCCATT
                         ttctcac  putative branch site (score: 10)
               tagaattattttct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttgacttctcttattgactttactgcaaaattttatttctatatcactatttgttatcctagaattattttctcacaatagttcgtttatgatatgcagGGAATAGTGCTGCTAATCATCTTGATATCAGGACTCAAATGTATGATGGGAATTGATACCCCATCAAAGTTCGATGCTCCCCCGGAATCGTAAGCCCATT

- - - - - - - - - - -tactgca