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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_Os12g03060.2
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|29657294|gb|CB653569.1|CB653569
EST:     AATGTGATGGGGAGTGCTTAGTAAAATCAACTCTGCTAGAAGGAAGCTTT                         GTTGGAATAGTGCTGCTAATCATCTTGATATCAGGACTCAAATGTATGATG
genomic: AATGTGATGGGGAGTGCTTAGTAAAATCAACTCTGCTAGAAGGAAGCTTTgttgtaagtt ... tgatatgcagG--G-AATAGTGCTGCTAATCATCTTGATATCAGGACTCAAATGTATGATG
EST: gi|88239235|gb|CI240397.1|CI240397
EST:     AATGTGATGGGGAGTGCTTAGTAAAATCAACTCTGCTAGAAGGAAGCTTTGTT                       
genomic: AATGTGATGGGGAGTGCTTAGTAAAATCAACTCTGCTAGAAGGAAGC--T-TTgttgtaagtt ... tgatatgc
EST: gi|33653555|gb|CF276169.1|CF276169
EST:     AATGTGATGGGGAGTGCTTAGTAAAATCAACTCTGCTAGAAGGAAGCTTTGTT                       
genomic: AATGTGATGGGGAGTGCTTAGTAAAATCAACTCTGCTAGAAGGAAGC--T-TTgttgtaagtt ... tgatatgc
EST: gi|29687248|gb|CB683523.1|CB683523
EST:     AATGTGATGGGGAGTGCTTAGTAAAATCAACTTTGCTAGAAGGAAGCTTT                         GTTGGAATAGTGCTGCTAATCATCTTGATATCAGGACTCAAATGTATGATG
genomic: AATGTGATGGGGAGTGCTTAGTAAAATCAACTCTGCTAGAAGGAAGCTTTgttgtaagtt ... tgatatgcagG--G-AATAGTGCTGCTAATCATCTTGATATCAGGACTCAAATGTATGATG
EST: gi|88416649|gb|CI543550.1|CI543550
EST:     TGCTAGAAGGAAGCTTTGTT                       
genomic: TGCTAGAAGGAAGC--T-TTgttgtaagtt ... tgatatgc
EST: gi|163926921|gb|EG715146.1|EG715146
EST:     AATGTGATGGGGAGTGCTTAGTAAAATCAACTCTGCTAGAAGGAAGCTTT                         GTTGGAATAGTGCTGCTAATCATCTTGATATCAGGACTCAAATGTATGATG
genomic: AATGTGATGGGGAGTGCTTAGTAAAATCAACTCTGCTAGAAGGAAGCTTTgttgtaagtt ... tgatatgcagG--G-AATAGTGCTGCTAATCATCTTGATATCAGGACTCAAATGTATGATG
EST: gi|88906025|gb|CI089611.1|CI089611
EST:     AATGTGATGGGGAGTGCTTAGTAAAATCAACTCTGCTAGAAGGAAGCTTTGTT                       
genomic: AATGTGATGGGGAGTGCTTAGTAAAATCAACTCTGCTAGAAGGAAGC--T-TTgttgtaagtt ... tgatatgc
EST: gi|88384390|gb|CI551316.1|CI551316
EST:     AATGTGATGGGGAGTGCTTAGTAAAATCAACTCTGCTAGAAGGAAGCTTTGTT                       
genomic: AATGTGATGGGGAGTGCTTAGTAAAATCAACTCTGCTAGAAGGAAGC--T-TTgttgtaagtt ... tgatatgc
EST: gi|38478567|gb|CF962700.1|CF962700
EST:     AATGTGATGGGGAGTGCTTAGTAAAATCAACTCTGCTAGAAGGAAGCTTT                         GGAATAGTGCTGCTAATCATCTTGATATCAGGACTCACATGTATGATGGGA
genomic: AATGTGATGGGGAGTGCTTAGTAAAATCAACTCTGCTAGAAGGAAGCTTTgttgtaagtt ... tgatatgcagGGAATAGTGCTGCTAATCATCTTGATATCAGGACTCAAATGTATGATGGGA
EST: gi|86598271|gb|CI354888.1|CI354888
EST:     AATGTGATGGGGAGTGCTTAGTAAAATCAACTCTGCTAGAAGGAAGCTTTGTT                       
genomic: AATGTGATGGGGAGTGCTTAGTAAAATCAACTCTGCTAGAAGGAAGC--T-TTgttgtaagtt ... tgatatgc
EST: gi|87028733|gb|CI349452.1|CI349452
EST:     TGATGGGGAGTGCTTAGTAAAATCAACTCTGCTAGAAGGAAGCTTTGTT                       
genomic: TGATGGGGAGTGCTTAGTAAAATCAACTCTGCTAGAAGGAAGC--T-TTgttgtaagtt ... tgatatgc
EST: gi|33805224|gb|CF328489.1|CF328489
EST:     AATGTGATGGGGAGTGCTTAGTAAAATCAACTCTGCTAGAAGGAAGCTTTGTT                       
genomic: AATGTGATGGGGAGTGCTTAGTAAAATCAACTCTGCTAGAAGGAAGC--T-TTgttgtaagtt ... tgatatgc
EST: gi|38471525|gb|CF955656.1|CF955656
EST:     AATGTGATGGGGAGTGCTTAGTAAAATCAACTCTGCTAGAAGGAAGCTTT                         GTTGGAATAGTGCTGCTAATCATCTTGATATCAGGACTCAAATGTATGATG
genomic: AATGTGATGGGGAGTGCTTAGTAAAATCAACTCTGCTAGAAGGAAGCTTTgttgtaagtt ... tgatatgcagG--G-AATAGTGCTGCTAATCATCTTGATATCAGGACTCAAATGTATGATG
EST: gi|29618675|gb|CB623687.1|CB623687
EST:     AATGTGATGGGGAGTGCTTAGTAAAATCAACTCTGCTAGAAGGAAGCTTT                         GTTGGAATAGTGCTGCTAATCATCTTGATATCAGGACTCAAATGTATGATG
genomic: AATGTGATGGGGAGTGCTTAGTAAAATCAACTCTGCTAGAAGGAAGCTTTgttgtaagtt ... tgatatgcagG--G-AATAGTGCTGCTAATCATCTTGATATCAGGACTCAAATGTATGATG
EST: gi|88446415|gb|CI563245.1|CI563245
EST:     TTAGTAAAATCAACTCTGCTAGAAGGAAGCTTTGTT                       
genomic: TTAGTAAAATCAACTCTGCTAGAAGGAAGC--T-TTgttgtaagtt ... tgatatgc
EST: gi|58694491|gb|CK083178.1|CK083178
EST:     AATGTGATGGGGAGTGCTTAGTAAAATCAACTCTGCTAGAAGGAAGCTTTGTT                       
genomic: AATGTGATGGGGAGTGCTTAGTAAAATCAACTCTGCTAGAAGGAAGC--T-TTgttgtaagtt ... tgatatgc
EST: gi|86834645|gb|CI340762.1|CI340762
EST:     AATGTGATGGGGAGTGCTTAGTAAAATCAACTCTGCTAGAAGGAAGCTTTGTT                       
genomic: AATGTGATGGGGAGTGCTTAGTAAAATCAACTCTGCTAGAAGGAAGC--T-TTgttgtaagtt ... tgatatgc
EST: gi|58674334|gb|CK063020.1|CK063020
EST:     AATGTGATGGGGAGTGCTTAGTAAAATCAACTCTGCTAGAAGGAAGCTTT                         GTTGGAATAGTGCTGCTAATCATCTTGATATCAGGACTCAAATGTATGATG
genomic: AATGTGATGGGGAGTGCTTAGTAAAATCAACTCTGCTAGAAGGAAGCTTTgttgtaagtt ... tgatatgcagG--G-AATAGTGCTGCTAATCATCTTGATATCAGGACTCAAATGTATGATG
EST: gi|86831384|gb|CI299442.1|CI299442
EST:     AATGTGATGGGGAGTGCTTAGTACAATCAACTCTGCTAGAAGGAAGCTTT                         GTTGGAATAGTGCTGCTAATCATCTTGATA
genomic: AATGTGATGGGGAGTGCTTAGTAAAATCAACTCTGCTAGAAGGAAGCTTTgttgtaagtt ... tgatatgcagG--G-AATAGTGCTGCTAATCATCTTGATA
EST: gi|88278361|gb|CI399361.1|CI399361
EST:     TAGAAGGAAGCTTTGTT                       
genomic: TAGAAGGAAGC--T-TTgttgtaagtt ... tgatatgc
EST: gi|88291767|gb|CI539938.1|CI539938
EST:     GGGAGTGCTTAGTAAAATCAACTCTGCTAGAAGGAAGCTTTGTT                       
genomic: GGGAGTGCTTAGTAAAATCAACTCTGCTAGAAGGAAGC--T-TTgttgtaagtt ... tgatatgc
EST: gi|88995219|gb|CI036794.1|CI036794
EST:     AATGTGATGGGGAGTGCTTAGTAAAATCNACTCTGCTAGAAGGAAGCTTTGTT                       
genomic: AATGTGATGGGGAGTGCTTAGTAAAATCAACTCTGCTAGAAGGAAGC--T-TTgttgtaagtt ... tgatatgc
EST: gi|38475562|gb|CF959695.1|CF959695
EST:     GTGATGGGGAGTGCTTAGTAAAATCAACTCTGCTAGAAGGAAGCTGTGTT                         GGAATAGTGCTGCTAATCATCTTGATATCAGGACTCAAATGTATGATGGG
genomic: GTGATGGGGAGTGCTTAGTAAAATCAACTCTGCTAGAAGGAAGC--T-TTgttgtaagtt ... tgatatgcagGGAATAGTGCTGCTAATCATCTTGATATCAGGACTCAAATGTATGATGGG
EST: gi|88278276|gb|CI399276.1|CI399276
EST:     GCTAGAAGGAAGCTTTGTT                       
genomic: GCTAGAAGGAAGC--T-TTgttgtaagtt ... tgatatgc
EST: gi|89178438|gb|CI015143.1|CI015143
EST:     AATGTGATGGGGAGTGCTTAGTAAAATCAACTCTGCTAGAAGGAAGCTTTGTT                       
genomic: AATGTGATGGGGAGTGCTTAGTAAAATCAACTCTGCTAGAAGGAAGC--T-TTgttgtaagtt ... tgatatgc
EST: gi|33681633|gb|CF309872.1|CF309872
EST:     AATGTGATGGGGAGTGCTTAGTAAAATCAACTCTGCTAGAAGGAAGCTTT                         GTTGGAATAGTGCTGCTAATCATCTTGATATCAGGACTCAAATGTATGATG
genomic: AATGTGATGGGGAGTGCTTAGTAAAATCAACTCTGCTAGAAGGAAGCTTTgttgtaagtt ... tgatatgcagG--G-AATAGTGCTGCTAATCATCTTGATATCAGGACTCAAATGTATGATG
EST: gi|86418859|gb|CI053660.1|CI053660
EST:     AATGTGATGGGGAGTGCTTAGTAAAATCAACTCTGCTAGAAGGAAGCTTTGTT                       
genomic: AATGTGATGGGGAGTGCTTAGTAAAATCAACTCTGCTAGAAGGAAGC--T-TTgttgtaagtt ... tgatatgc


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cactatttgttatcctagaattattttctcacaatagttcgtttatgatatgcagGGAATAGTGCTGCTAATCATCTTGATATCAGGACTCAAATGTATGATGGGAATTGATACCCCATCAAAGTTCGATGCTCCCCCGGAATCGTAAGCCCATT
                         ttctcac  putative branch site (score: 2)
               tagaattattttct  TA-rich tract