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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattgatactgacagtatgcactagtgttgttttgcactacttccatactgtgttttagagcaattccatgaccatttcattcttccatggcttatattgcagGGTTTGCATCTGAACAGAATTCGATATCTGCTGATGTGCTGAAGAAAGCATATGAAGCTACAGAAGATGGGTTCTTCTCTGTTGTCACCAAGCAATGGCC

Basic information

species Oryza sativa
transcript LOC_Os06g50380.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g50380.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G069970_T02 (Zea mays), 3'ss of exon 2
------------------------gtaattgatactgacagtatgcactagtgttgt-tttgcact--acttccatactgtgttttag-agcaattccatgaccatttcattcttccatggcttatattgcagGGTTTGCATCTGAACAGAATTCGATATCTGCTGATGTGCTGAAGAAAGCATATGAAGCTACAGAAGATGGGTTCTTCTCTGTTGTCACCAAGCAATGGCC
                           | |   | |      ||    ||||  | | | || | |   ||| ||   ||   || || ||  || |  ||| || | ||||||| |||||||| ||||  ||||||||||||||| |||||| | || ||||||||||| |||||||| || |||||||||||||||||||| ||||| |||||||| ||||| ||||||||
gtaacttgctaacctttaaatctgagcagtagcattattcccatttcttagtactatatctggatttggctttcagtttgcacttaaggagtgatccagtgatcaatccattctttcatggcttgtatt-tagGGTTTGCATCTGAGCAGAATACAATGTCTGCTGATGTACTGAAGAAGGCGTATGAAGCTACAGAAGATGGATTCTTTTCTGTTGTTACCAAACAATGGCC

upper sequence: LOC_Os06g50380.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G151254_T02 (Zea mays), 3'ss of exon 2
-----------gtaattgatactg-acagtatgcactagtgttgtttt---gcactacttccatactgtgttttaga---gcaattccatgaccat-ttcattcttccatggcttatattgcagGGTTTGCATCTGAACAGAATTCGATATCTGCTGATGTGCTGAAGAAAGCATATGAAGCTACAGAAGATGGGTTCTTCTCTGTTGTCACCAAGCAATGGCC
               || |  |||  ||||| |||||| |   ||||    ||||||  ||   | |  | |||      |||  |  | ||     | |||| || |||||||| ||||  ||| ||||||||||| |||||| | || ||||||||||| |||||||| ||||||||||||||||||||||| ||||||||  |||| ||||| ||||||||
gtaacttgctaacctttaaatctgtgcagta-gcactattcccgtttcttagcactatatctgcatttggctttcagtttgcacataaaggagatcatccattttttcatggcttgtatt-tagGATTTGCATCTGAGCAGAATGCAATGTCTGCTGATGTACTGAAGAAGGCATATGAAGCTACAGAAGATGGATTCTTCTCCATTGTTACCAAACAATGGCC
















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|58673876|gb|CK062562.1|CK062562
EST:     CCCAGAGACGGCTTGCTATATCAACGATCACCTATTCCACCATCTGAAAA                         GGTTTGCATCTGAACAGAATTCGATGTCTGCTGATGTGCTGAAGAAAGCAT
genomic: CCCAGAGACGGCTTGCTATATCAACGATCACCTATTCCACCATCTGAAAAgtaattgata ... tatattgcagGGTTTGCATCTGAACAGAATTCGATATCTGCTGATGTGCTGAAGAAAGCAT
EST: gi|58676764|gb|CK065451.1|CK065451
EST:     CCCAGAGACGGCTTGCTATATCAACGATCACCTATTCCACCATCTGAAAA                         GGTTTGCATCTGAACAGAATTCGATGTCTGCTGATGTGCTGAAGAAAGCAT
genomic: CCCAGAGACGGCTTGCTATATCAACGATCACCTATTCCACCATCTGAAAAgtaattgata ... tatattgcagGGTTTGCATCTGAACAGAATTCGATATCTGCTGATGTGCTGAAGAAAGCAT
EST: gi|58662521|gb|CK051207.1|CK051207
EST:     CCCAGAGACGGCTTGCTATATCAACGATCACCTCTTCCACCATCTGAAAA                         GGTTTGCATCTGAACAGAATTCGATGTCTGCTGATGTGCTGAAGAAAGCAT
genomic: CCCAGAGACGGCTTGCTATATCAACGATCACCTATTCCACCATCTGAAAAgtaattgata ... tatattgcagGGTTTGCATCTGAACAGAATTCGATATCTGCTGATGTGCTGAAGAAAGCAT
EST: gi|29646160|gb|CB651167.1|CB651167
EST:     CCCAGAGACGGCTTGCTATATCAACGATCACCTATTCCACCATCTGAAAA                         GGTTTGCATCTGAACAGAATTCGATATCTGCTGATGTGCTGAAGAAAGCAT
genomic: CCCAGAGACGGCTTGCTATATCAACGATCACCTATTCCACCATCTGAAAAgtaattgata ... tatattgcagGGTTTGCATCTGAACAGAATTCGATATCTGCTGATGTGCTGAAGAAAGCAT
EST: gi|58653120|gb|CK041800.1|CK041800
EST:     CCCAGAGACGGCTTGCTATATCAACGATCACCTATTCCACCATCTGAAAA                         GGTTTGCATCTGAACAGAATTCGATGTCTGCTGATGTGCTGAAGAAAGCAT
genomic: CCCAGAGACGGCTTGCTATATCAACGATCACCTATTCCACCATCTGAAAAgtaattgata ... tatattgcagGGTTTGCATCTGAACAGAATTCGATATCTGCTGATGTGCTGAAGAAAGCAT
EST: gi|88298570|gb|CI563565.1|CI563565
EST:     CCAAAAGACGGCTTGCTATATCAACGATCACCTATTCCACCATCTGAAAA                         NGTTTGCATCTGAAACAGAATTCGATATCTGCTGATGTGCTGAAANAAAGC
genomic: CCAGA-GACGGCTTGCTATATCAACGATCACCTATTCCACCATCTGAAAAgtaattgata ... tatattgcagGGTTTGCATCTGAA-CAGAATTCGATATCTGCTGATGTGCTGAAG-AAAGC
EST: gi|58663964|gb|CK052650.1|CK052650
EST:     CCCAGAGACGGCTTGCTATATCAACGATCACCTATTCCACCATCTGAAAA                         GGTTTGCATCTGAACAGAATTCGATGTCTGCTGATGTGCTGAAGAAAGCAT
genomic: CCCAGAGACGGCTTGCTATATCAACGATCACCTATTCCACCATCTGAAAAgtaattgata ... tatattgcagGGTTTGCATCTGAACAGAATTCGATATCTGCTGATGTGCTGAAGAAAGCAT
EST: gi|117240320|gb|CT842746.1|CT842746
EST:     CCCAGAGACGGCTTGCTATATCAACGATCACCTATTCCACCATCTGAAAA                         GGTTTGCATCTGAACAGAATTCGATGTCTGCTGATGTGCTGAAGAAAGCAT
genomic: CCCAGAGACGGCTTGCTATATCAACGATCACCTATTCCACCATCTGAAAAgtaattgata ... tatattgcagGGTTTGCATCTGAACAGAATTCGATATCTGCTGATGTGCTGAAGAAAGCAT
EST: gi|33793893|gb|CF322835.1|CF322835
EST:     CGGCTTGCTATATCAACGATCACCTATTCCACCATCTGAAAA                         GGTTTGCATCTGAACAGAATTCGATATCTGCTGATGTGCTGAAGAAAGCAT
genomic: CGGCTTGCTATATCAACGATCACCTATTCCACCATCTGAAAAgtaattgata ... tatattgcagGGTTTGCATCTGAACAGAATTCGATATCTGCTGATGTGCTGAAGAAAGCAT
EST: gi|33653808|gb|CF276422.1|CF276422
EST:     CCCAGAGACGGCTTACTATATCAACGATCACCTATTCCACCATCTGAAAA                         GGTTTGCATCTGAACAGAATTCGATATCTGGCTGATGGTGCTGAAGAAAGC
genomic: CCCAGAGACGGCTTGCTATATCAACGATCACCTATTCCACCATCTGAAAAgtaattgata ... tatattgcagGGTTTGCATCTGAACAGAATTCGATATCTG-CTGATG-TGCTGAAGAAAGC
EST: gi|29679794|gb|CB676069.1|CB676069
EST:     CCCAGAGACGGCTTGCTATATCAACGATCACCTATTCCACCATCTGAAAA                         GGTTTGCATCTGAACAGAATTCGATATCTGCTGATGTGCTGAAGAAAGCAT
genomic: CCCAGAGACGGCTTGCTATATCAACGATCACCTATTCCACCATCTGAAAAgtaattgata ... tatattgcagGGTTTGCATCTGAACAGAATTCGATATCTGCTGATGTGCTGAAGAAAGCAT
EST: gi|58612365|gb|CK040077.1|CK040077
EST:     CCCAGAGACGGCTTGCTATATCAACGATCACCTATTCCACCATCTGAAAA                         GGTTTGCATCTGAACAGAATTCGATGTCTGCTGATGTGCTGAAGAAAGCAT
genomic: CCCAGAGACGGCTTGCTATATCAACGATCACCTATTCCACCATCTGAAAAgtaattgata ... tatattgcagGGTTTGCATCTGAACAGAATTCGATATCTGCTGATGTGCTGAAGAAAGCAT
EST: gi|29664135|gb|CB660410.1|CB660410
EST:     CCCAGAGACGGCTTGCTATATCAACGATCACCTATTCCACCATCTGAAAA                         GGTTTGCATCTGAACAGAATTCGATATCTGCTGATGTGCTGAAGAAAGCAT
genomic: CCCAGAGACGGCTTGCTATATCAACGATCACCTATTCCACCATCTGAAAAgtaattgata ... tatattgcagGGTTTGCATCTGAACAGAATTCGATATCTGCTGATGTGCTGAAGAAAGCAT
EST: gi|29677202|gb|CB673477.1|CB673477
EST:     CCCAGAGACGGCTTGCTATATCAACGATCACCTATTCCACCATCTGAAAA                         GGTTTGCATCTGAACAGAATTCGATATCTGCTGATGTGCTGAAGAAAGCAT
genomic: CCCAGAGACGGCTTGCTATATCAACGATCACCTATTCCACCATCTGAAAAgtaattgata ... tatattgcagGGTTTGCATCTGAACAGAATTCGATATCTGCTGATGTGCTGAAGAAAGCAT
EST: gi|33653665|gb|CF276279.1|CF276279
EST:     CCCAGAGACGGCTTGCTATATCAACGATCACCTATTCCACCATCTGAAAA                         GGTTTGCATCTGAACAGAATTCGATAT
genomic: CCCAGAGACGGCTTGCTATATCAACGATCACCTATTCCACCATCTGAAAAgtaattgata ... tatattgcagGGTTTGCATCTGAACAGAATTCGATAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgtgttttagagcaattccatgaccatttcattcttccatggcttatattgcagGGTTTGCATCTGAACAGAATTCGATATCTGCTGATGTGCTGAAGAAAGCATATGAAGCTACAGAAGATGGGTTCTTCTCTGTTGTCACCAAGCAATGGCC
                                            ttatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaattgatactgacagtatgcactagtgttgttttgcactacttccatactgtgttttagagcaattccatgaccatttcattcttccatggcttatattgcagGGTTTGCATCTGAACAGAATTCGATATCTGCTGATGTGCTGAAGAAAGCATATGAAGCTACAGAAGATGGGTTCTTCTCTGTTGTCACCAAGCAATGGCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA