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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cgtggtggtgtttaattatttttttgcgggattttggttgattttgggatgtattatgttctgacgaaatcgtttacttcgttgtttgtttgcgcagcagCTTGCCCTGTAGCCGCGTGCTCCGGCCATGGCGTTCTTCAGGGGCCTGACCGCGGTGTCGAGGCTTCGATCCCGCGTG

Basic information

species Oryza sativa
transcript LOC_Os02g10070.2
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g10070.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G064023_T02 (Zea mays), 3'ss of exon 1
cgtggtggtgtttaattatttttttgcgggattttggttgattttgggatgtattatgttctgacgaaatcgtttacttcgttgttt-----gtttgcgcagcagCT----TGCCCTG-TAGCCGCGTGCTCCGGCCATGGCGTTCTTCAGGGGCCTGACCGCGGTGTCGAGGCTTCGATCCCGCGTG
     | |  |    |  |||  |   ||  ||| |||| | || ||      | | |   ||| |  ||||| |  ||  ||| ||     || || |||||||      |||  || |||||| | ||||||||||||||||||||| ||||||| |||||||| |||||||| ||||||||| ||
--catttgcttcccgtagtttcctctgggagtttcggttaaattcggttgtggtgaggacatgatgggatcgtctgtttgtttggttcctgtgtctgtgcagCAGTGCAGGTGCGGTGGTAGCCGAGCGCTCCGGCCATGGCGTTCTTCCGGGGCCTCACCGCGGTCTCGAGGCTGCGATCCCGCATG

upper sequence: LOC_Os02g10070.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G064023_T04 (Zea mays), 3'ss of exon 1
cgtggtggtgtttaattatttttttgcgggattttggttgattttgggatgtattatgttctgacgaaatcgtttacttcgttgttt-----gtttgcgcagcagCT----TGCCCTG-TAGCCGCGTGCTCCGGCCATGGCGTTCTTCAGGGGCCTGACCGCGGTGTCGAGGCTTCGATCCCGCGTG
               |  |||  |   ||  ||| |||| | || ||      | | |   ||| |  ||||| |  ||  ||| ||     || || |||||||      |||  || |||||| | ||||||||||||||||||||| ||||||| |||||||| |||||||| ||||||||| ||
--------------gtagtttcctctgggagtttcggttaaattcggttgtggtgaggacatgatgggatcgtctgtttgtttggttcctgtgtctgtgcagcagTGCAGGTGCGGTGGTAGCCGAGCGCTCCGGCCATGGCGTTCTTCCGGGGCCTCACCGCGGTCTCGAGGCTGCGATCCCGCATG

upper sequence: LOC_Os02g10070.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G064023_T01 (Zea mays), 3'ss of exon 2
-------cgtggtggtgtttaattatttttttgcgggattttggttgattttgggatgtattatgttctgacgaaatcgtttacttcgttgttt-----gtttgcgcagcagCT----TGCCCTG-TAGCCGCGTGCTCCGGCCATGGCGTTCTTCAGGGGCCTGACCGCGGTGTCGAGGCTTCGATCCCGCGTG
            | |  |    |  |||  |   ||  ||| |||| | || ||      | | |   ||| |  ||||| |  ||  ||| ||     || || |||||||      |||  || |||||| | ||||||||||||||||||||| ||||||| |||||||| |||||||| ||||||||| ||
gtaactatccatttgcttcccgtagtttcctctgggagtttcggttaaattcggttgtggtgaggacatgatgggatcgtctgtttgtttggttcctgtgtctgtgcagCAGTGCAGGTGCGGTGGTAGCCGAGCGCTCCGGCCATGGCGTTCTTCCGGGGCCTCACCGCGGTCTCGAGGCTGCGATCCCGCATG

upper sequence: LOC_Os02g10070.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G064023_T03 (Zea mays), 3'ss of exon 1
cgtggtggtgtttaattatttttttgcgggattttggttgattttgggatgtattatgttctgacgaaatcgtttacttcgttgttt-----gtttgcgcagcagCT----TGCCCTG-TAGCCGCGTGCTCCGGCCATGGCGTTCTTCAGGGGCCTGACCGCGGTGTCGAGGCTTCGATCCCGCGTG
     | |  |    |  |||  |   ||  ||| |||| | || ||      | | |   ||| |  ||||| |  ||  ||| ||     || || |||||||      |||  || |||||| | ||||||||||||||||||||| ||||||| |||||||| |||||||| ||||||||| ||
-----ttgcttcccgtagtttcctctgggagtttcggttaaattcggttgtggtgaggacatgatgggatcgtctgtttgtttggttcctgtgtctgtgcagcagTGCAGGTGCGGTGGTAGCCGAGCGCTCCGGCCATGGCGTTCTTCCGGGGCCTCACCGCGGTCTCGAGGCTGCGATCCCGCATG

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|29614058|gb|CB619071.1|CB619071
EST:     CCTCCCCGATTCGATTCAATTCGCGACGCCTCCGTGAAATTCTCCAAAGCC                         A
genomic: CCTCCCCGATTCGATTCAATTCGCGACGCCTCCGTGAAATTCTCCAAAG-Cgtaagtgcat ... tgcgcagcag-
EST: gi|29614058|gb|CB619071.1|CB619071
EST:     CCTCCCCGATTCGATTCAATTCGCGACGCCTCCGTGAAATTCTCCAAAGCC                         A
genomic: CCTCCCCGATTCGATTCAATTCGCGACGCCTCCGTGAAATTCTCCAAAG-Cgtaagtgcat ... tgcgcagcag-
EST: gi|29614058|gb|CB619071.1|CB619071
EST:     CCTCCCCGATTCGATTCAATTCGCGACGCCTCCGTGAAATTCTCCAAAGCC                         A
genomic: CCTCCCCGATTCGATTCAATTCGCGACGCCTCCGTGAAATTCTCCAAAG-Cgtaagtgcat ... tgcgcagcag-
EST: gi|58693317|gb|CK082004.1|CK082004
EST:     CCTCCCCGATTCGATTCAATTCGCGACGCCTCCGTGAAATTCTCCAAAGC                         CTTGCCCTGTAGCCGCGTGCTCCGGCCATGGCGTTCTTCAGGGGCCTGACC
genomic: CCTCCCCGATTCGATTCAATTCGCGACGCCTCCGTGAAATTCTCCAAAGCgtaagtgcat ... tgcgcagcagCTTGCCCTGTAGCCGCGTGCTCCGGCCATGGCGTTCTTCAGGGGCCTGACC
EST: gi|58658570|gb|CK047250.1|CK047250
EST:     CCTCCCCGATTCGATTCAATTCGCGACGCCTCCGGGAAATTCTCCAAAGCC                         A
genomic: CCTCCCCGATTCGATTCAATTCGCGACGCCTCCGTGAAATTCTCCAAAG-Cgtaagtgcat ... tgcgcagcag-
EST: gi|58658570|gb|CK047250.1|CK047250
EST:     CCTCCCCGATTCGATTCAATTCGCGACGCCTCCGGGAAATTCTCCAAAGCC                         A
genomic: CCTCCCCGATTCGATTCAATTCGCGACGCCTCCGTGAAATTCTCCAAAG-Cgtaagtgcat ... tgcgcagcag-
EST: gi|58658570|gb|CK047250.1|CK047250
EST:     CCTCCCCGATTCGATTCAATTCGCGACGCCTCCGGGAAATTCTCCAAAGCC                         A
genomic: CCTCCCCGATTCGATTCAATTCGCGACGCCTCCGTGAAATTCTCCAAAG-Cgtaagtgcat ... tgcgcagcag-
EST: gi|29667252|gb|CB663527.1|CB663527
EST:     CCTCCCCGATTCGATTCAATTCGCGACGCCTCCGTGAAATTCTCCAAAGCC                         A
genomic: CCTCCCCGATTCGATTCAATTCGCGACGCCTCCGTGAAATTCTCCAAAG-Cgtaagtgcat ... tgcgcagcag-
EST: gi|29667252|gb|CB663527.1|CB663527
EST:     CCTCCCCGATTCGATTCAATTCGCGACGCCTCCGTGAAATTCTCCAAAGCC                         A
genomic: CCTCCCCGATTCGATTCAATTCGCGACGCCTCCGTGAAATTCTCCAAAG-Cgtaagtgcat ... tgcgcagcag-
EST: gi|29667252|gb|CB663527.1|CB663527
EST:     CCTCCCCGATTCGATTCAATTCGCGACGCCTCCGTGAAATTCTCCAAAGCC                         A
genomic: CCTCCCCGATTCGATTCAATTCGCGACGCCTCCGTGAAATTCTCCAAAG-Cgtaagtgcat ... tgcgcagcag-
EST: gi|88400849|gb|CI616854.1|CI616854
EST:     CCTCCCCGATTCGATTCAATTCGCGACGCCTCCGTGAAATTCTCCAAAGCC                         A
genomic: CCTCCCCGATTCGATTCAATTCGCGACGCCTCCGTGAAATTCTCCAAAG-Cgtaagtgcat ... tgcgcagcag-
EST: gi|88400849|gb|CI616854.1|CI616854
EST:     CCTCCCCGATTCGATTCAATTCGCGACGCCTCCGTGAAATTCTCCAAAGCC                         A
genomic: CCTCCCCGATTCGATTCAATTCGCGACGCCTCCGTGAAATTCTCCAAAG-Cgtaagtgcat ... tgcgcagcag-
EST: gi|88400849|gb|CI616854.1|CI616854
EST:     CCTCCCCGATTCGATTCAATTCGCGACGCCTCCGTGAAATTCTCCAAAGCC                         A
genomic: CCTCCCCGATTCGATTCAATTCGCGACGCCTCCGTGAAATTCTCCAAAG-Cgtaagtgcat ... tgcgcagcag-
EST: gi|58611144|gb|CK038856.1|CK038856
EST:     CCTCCCCGATTCGATTCAATTCGCGACGCCTCCGTGAAATTCTCCAAAGCC                         A
genomic: CCTCCCCGATTCGATTCAATTCGCGACGCCTCCGTGAAATTCTCCAAAG-Cgtaagtgcat ... tgcgcagcag-
EST: gi|58611144|gb|CK038856.1|CK038856
EST:     CCTCCCCGATTCGATTCAATTCGCGACGCCTCCGTGAAATTCTCCAAAGCC                         A
genomic: CCTCCCCGATTCGATTCAATTCGCGACGCCTCCGTGAAATTCTCCAAAG-Cgtaagtgcat ... tgcgcagcag-
EST: gi|58611144|gb|CK038856.1|CK038856
EST:     CCTCCCCGATTCGATTCAATTCGCGACGCCTCCGTGAAATTCTCCAAAGCC                         A
genomic: CCTCCCCGATTCGATTCAATTCGCGACGCCTCCGTGAAATTCTCCAAAG-Cgtaagtgcat ... tgcgcagcag-
EST: gi|29614020|gb|CB619033.1|CB619033
EST:     CCTCCCCGATTCGATTCAATTCGCGACGCCTCCGTGAAATTCTCCAAAGCC                         A
genomic: CCTCCCCGATTCGATTCAATTCGCGACGCCTCCGTGAAATTCTCCAAAG-Cgtaagtgcat ... tgcgcagcag-
EST: gi|29614020|gb|CB619033.1|CB619033
EST:     CCTCCCCGATTCGATTCAATTCGCGACGCCTCCGTGAAATTCTCCAAAGCC                         A
genomic: CCTCCCCGATTCGATTCAATTCGCGACGCCTCCGTGAAATTCTCCAAAG-Cgtaagtgcat ... tgcgcagcag-
EST: gi|29614020|gb|CB619033.1|CB619033
EST:     CCTCCCCGATTCGATTCAATTCGCGACGCCTCCGTGAAATTCTCCAAAGCC                         A
genomic: CCTCCCCGATTCGATTCAATTCGCGACGCCTCCGTGAAATTCTCCAAAG-Cgtaagtgcat ... tgcgcagcag-
EST: gi|58695278|gb|CK083965.1|CK083965
EST:     CCTCCCCGATTCGATTCAATTCGCGACGCCTCCGTGAAATTCTCCAAAGCC                         A
genomic: CCTCCCCGATTCGATTCAATTCGCGACGCCTCCGTGAAATTCTCCAAAG-Cgtaagtgcat ... tgcgcagcag-
EST: gi|58695278|gb|CK083965.1|CK083965
EST:     CCTCCCCGATTCGATTCAATTCGCGACGCCTCCGTGAAATTCTCCAAAGCC                         A
genomic: CCTCCCCGATTCGATTCAATTCGCGACGCCTCCGTGAAATTCTCCAAAG-Cgtaagtgcat ... tgcgcagcag-
EST: gi|58695278|gb|CK083965.1|CK083965
EST:     CCTCCCCGATTCGATTCAATTCGCGACGCCTCCGTGAAATTCTCCAAAGCC                         A
genomic: CCTCCCCGATTCGATTCAATTCGCGACGCCTCCGTGAAATTCTCCAAAG-Cgtaagtgcat ... tgcgcagcag-
EST: gi|58690828|gb|CK079515.1|CK079515
EST:     CCTCCCCGATTCGATTCAATTCGCGACGCCTCCGTGAAATTCTCCAAAGCC                         A
genomic: CCTCCCCGATTCGATTCAATTCGCGACGCCTCCGTGAAATTCTCCAAAG-Cgtaagtgcat ... tgcgcagcag-
EST: gi|58690828|gb|CK079515.1|CK079515
EST:     CCTCCCCGATTCGATTCAATTCGCGACGCCTCCGTGAAATTCTCCAAAGCC                         A
genomic: CCTCCCCGATTCGATTCAATTCGCGACGCCTCCGTGAAATTCTCCAAAG-Cgtaagtgcat ... tgcgcagcag-
EST: gi|58690828|gb|CK079515.1|CK079515
EST:     CCTCCCCGATTCGATTCAATTCGCGACGCCTCCGTGAAATTCTCCAAAGCC                         A
genomic: CCTCCCCGATTCGATTCAATTCGCGACGCCTCCGTGAAATTCTCCAAAG-Cgtaagtgcat ... tgcgcagcag-


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gggatgtattatgttctgacgaaatcgtttacttcgttgtttgtttgcgcagcagCTTGCCCTGTAGCCGCGTGCTCCGGCCATGGCGTTCTTCAGGGGCCTGACCGCGGTGTCGAGGCTTCGATCCCGCGTG
             ttctgac  putative branch site (score: 2)
                                       tttgttt  putative PPT
      tattatgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cgtggtggtgtttaattatttttttgcgggattttggttgattttgggatgtattatgttctgacgaaatcgtttacttcgttgtttgtttgcgcagcagCTTGCCCTGTAGCCGCGTGCTCCGGCCATGGCGTTCTTCAGGGGCCTGACCGCGGTGTCGAGGCTTCGATCCCGCGTG

- -ggtggtg
- - - - - - - - - - tttttgc
- - - - - - - - - - - - - - - - - - gttgatt
- - - - - - - - - - - - - - - - - - - - - - tgggatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - tgttctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgtttgt