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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agtcccacagctcaatataacatttcaattttgcttccctaatgactgataaattccttggtcatagaaaattcattactgagtccttttgatctttcagGTTATTGGAATTGATTTGCTGTCACAATCACTGTTACCGGCGATCGTAGAACTTGCAGAGGATAGGCACTGGAGGGTTCGGCTTGCAATAATTGAGTACA

Basic information

species Oryza sativa
transcript LOC_Os09g07510.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g07510.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G102858_T01 (Zea mays), 3'ss of exon 8
agtcccacagctcaatataacatttcaattttgcttccctaatgactgataaattccttgg--tcatagaa-aattcattactgagtccttttga-----tctttcagGTTATTGGAATTGATTTGCTGTCACAATCACTGTTACCGGCGATCGTAGAACTTGCAGAGGATAGGCACTGGAGGGTTCGGCTTGCAATAATTGAGTACA
        ||   |   |    ||| ||  |||  | |   |||  |  |    || ||    ||||  ||  ||  | |  | ||| || |        | |||||||||||||||||||| ||| |||| ||||||||  | || || || ||||| ||  | || |||||||||||||| ||||||||||| |||||||||||||
--------agaataggctttttttttaaacttgtgttcaagatgtttcctggcatcattcacttcattcaatgatgtacttgtaagttctctcctgtatttttttcagGTTATTGGAATTGACTTGTTGTCGCAATCACTTCTGCCAGCCATTGTAGAGCTCTCTGAAGATAGGCACTGGAGAGTTCGGCTTGCCATAATTGAGTACA

upper sequence: LOC_Os09g07510.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA09G31760.1 (Glycine max), 3'ss of exon 8
-----agtcccacagctcaatataacatttcaattttgcttccctaatgactgataaattccttggtcatagaaaattcattactgagtccttttgatc---------tttcagGTTATTGGAATTGATTTGCTGTCACAATCACTGTTACCGGCGATCGTAGAACTTGCAGAGGATAGGCACTGGAGGGTTCGGCTTGCAATAATTGAGTACA
      | |  | |  | |||||     ||||  ||  |       ||  |  | | | |  ||  |||||       |  || |||  | | |   |          || ||||||||||| ||||||||| | || || || ||||| || || || |||||||| || |||||| |||||||||| ||||| |||||||| || || || |
gtttgtggcttaaaattgaatat--tcattcaggttgaccgtgtacatttcaaacacaattatttttcatatgct-ccctctattgaagcttgtgatttacacatgaattgcagGTTATTGGTATTGATTTGTTATCTCAGTCTCTGTTGCCAGCCATAGTAGAACTAGCTGAGGATCGGCACTGGAGAGTTCGACTTGCAATCATAGAATATA

upper sequence: LOC_Os09g07510.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA10G42250.1 (Glycine max), 3'ss of exon 8
agtcccacagctca-atataacatttcaattttgcttccctaatga--ctgataaattccttggtcatagaaaattcatta-------ctgagtccttttgatctttcagGTTATTGGAATTGATTTGCTGTCACAATCACTGTTACCGGCGATCGTAGAACTTGCAGAGGATAGGCACTGGAGGGTTCGGCTTGCAATAATTGAGTACA
          || | || |||   || |  |  || | ||    ||  || | ||| | |   |  | |||||| |  |          | | ||  | |  | || |||||||| ||||||||| || | || || ||  ||||||| || || || || ||||| ||||||||||| |||||||| ||||||||||| || || || |
----------cttatatttaagcctttatgtccgcataccacccgatactcacaaaatacaaagcaaaagaaaacttttggaagacattttaatcaatatatttttgcagGTTATAGGAATTGATCTGTTATCTCAGTCTTTGTTACCAGCCATTGTTGAGCTTGCTGAGGATAGGCATTGGAGGGTCCGGCTTGCAATTATAGAATATA

upper sequence: LOC_Os09g07510.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA20G24790.1 (Glycine max), 3'ss of exon 8
agtcccacagctcaatata-acatttcaattttgcttccctaatgactgataaattccttggtcatagaaaattcattactgagtccttttgatctttcagGTTATTGGAATTGATTTGCTGTCACAATCACTGTTACCGGCGATCGTAGAACTTGCAGAGGATAGGCACTGGAGGGTTCGGCTTGCAATAATTGAGTACA
  |     |||   || |   |||  ||   |    || | ||  |   | |||      |   |      |   |    | | ||  | |  |||| |||||||| ||||| ||| || | || || ||  ||||||| || || || || ||||| ||||||||||| |||||||| ||||||||||| || || || |
-ttatttaagccttatgtctgcataccaccctatactcacaaaacatgtacaaagcaaaagaaaacctttgaaagacattttaatcaatgtattcttgcagGTTATAGGAATCGATCTGTTATCTCAGTCTTTGTTACCAGCCATTGTTGAGCTTGCTGAGGATAGGCATTGGAGGGTCCGGCTTGCAATTATAGAATATA

upper sequence: LOC_Os09g07510.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA07G10000.1 (Glycine max), 3'ss of exon 7
agtcccacagctcaatataacatttcaattttgcttcccta---atgactgataaattccttggtcatagaaaattcattactgagtccttttgatct----------ttcagGTTATTGGAATTGATTTGCTGTCACAATCACTGTTACCGGCGATCGTAGAACTTGCAGAGGATAGGCACTGGAGGGTTCGGCTTGCAATAATTGAGTACA
         ||| || ||   || |   ||  | ||  | |   |    | | | |||  |   |   | |   | | |   |     ||| |||| |          | ||||||||||| ||||||||| | || || || ||||| || || || |||||| | || |||||| |||||||||| ||||| |||||||| || || ||||
--gtttgtggcttaaaattgaatattccttcagattgaccatgtacatttcaaacattattatttttcatatgctccctctattgaagcttatgatttacacatggattgcagGTTATTGGTATTGATTTGTTATCTCAGTCTCTGTTGCCAGCCATAGTAGAATTAGCTGAGGATCGGCACTGGAGAGTTCGACTTGCAATCATAGAATACA

upper sequence: LOC_Os09g07510.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA02G10790.2 (Glycine max), 3'ss of exon 8
agtcccacagctcaatataacatttcaattttgcttccctaatgactgataaattccttggtcatagaaaattc------attactgagtccttttgatctttcagGTTATTGGAATTGATTTGCTGTCACAATCACTGTTACCGGCGATCGTAGAACTTGCAGAGGATAGGCACTGGAGGGTTCGGCTTGCAATAATTGAGTACA
      | |||| |  ||   ||  ||  ||   |             | ||||  | |    | | ||| ||       ||   |   ||   |   |||| ||||||||||||||  ||||| | || |||||  ||||||| || || || || ||||| ||||||||||| ||||||||||| ||||||||||| || || |
------agagcttatgatcttatgccaccttctatagagatgcagagtaaaaatcacataacgaaaaaaacttttcaaagatatgttgatcaagtcattcttgcagGTTATTGGAATCAATTTGTTATCTCAATCTTTGTTACCAGCCATTGTTGAGCTTGCTGAGGATAGGCATTGGAGGGTTCGACTTGCAATAATAGAATATA

upper sequence: LOC_Os09g07510.1 (Oryza sativa), 3'ss of exon 8
lower sequence: AT3G25800.2 (Arabidopsis thaliana), 3'ss of exon 7
--------------------------------agtcccacagctcaat-ataacatttcaattttg------cttccctaatgactgataaattccttggtcatagaaaattcattactgagtcct---tttgatcttt--cagGTTATTGGAATTGATTTGCTGTCACAATCACTGTTACCGGCGATCGTAGAACTTGCAGAGGATAGGCACTGGAGGGTTCGGCTTGCAATAATTGAGTACA
                                |  || |  |||  || ||||||| |    |||        ||| ||  |      |   || || |  |||  | | |   ||  ||| | ||   ||| || | |  ||||||||||| |||||| | || ||||||||  |||| || || || ||||||||||| || ||||| |||||||| ||  | ||||| ||||| ||||| |
gtttgttacaacagaaatacccaaaccagatcatgccaatggcttcatgataacatgttttgtttaaaagactttcactcttttaacttgcctttctcgcccatccatattcagttgatgacttctatattttatatgtggcagGTTATTGGGATTGATCTACTATCACAATCCTTGTTGCCAGCTATTGTAGAACTTGCTGAAGATAGACACTGGAGAGTAAGACTTGCTATAATCGAGTATA

upper sequence: LOC_Os09g07510.1 (Oryza sativa), 3'ss of exon 8
lower sequence: AT1G25490.1 (Arabidopsis thaliana), 3'ss of exon 8
agtcccacagctcaatataacatttcaattttgcttccctaatgactgataaattccttggtcatagaaaattcattactgagtccttttgatctttcagGTTATTGGAATTGATTTGCTGTCACAATCACTGTTACCGGCGATCGTAGAACTTGCAGAGGATAGGCACTGGAGGGTTCGGCTTGCAATAATTGAGTACA
               | |  ||| ||  || ||        ||      |  ||| |||   | ||   | ||  | ||||| |  | ||  |    |||||||||||||||||| | || || |||||  |||||||||| || ||||||||||| |||||| |||||||||| || || ||||||||||| |||||  
------------gtttgttgcatctctcttgtgtgctttagatactacttttattgctt--ccttatttagttggtgactgaattatcttt-tacggcagGTTATTGGAATTGATCTACTATCTCAATCCTTGTTACCGGCCATTGTAGAACTTGCTGAGGATCGGCACTGGAGAGTCCGACTTGCAATAATAGAGTATG

upper sequence: LOC_Os09g07510.1 (Oryza sativa), 3'ss of exon 8
lower sequence: Vv01s0011g03280.t01 (Vitis vinifera), 3'ss of exon 7
agtcccacagctcaatataacatttcaattttgcttccctaatgactgataaattccttggtcatagaaaattcattactgagtccttttga---------tctttcagGTTATTGGAATTGATTTGCTGTCACAATCACTGTTACCGGCGATCGTAGAACTTGCAGAGGATAGGCACTGGAGGGTTCGGCTTGCAATAATTGAGTACA
    |||   |    |  |    || ||   || | |    |||   ||  | |    ||  |||      |||     | || | |||| |         |||| ||||||||||||| |||| |  |||| ||||| || |||||||| || || || |||||||||||||| || ||||||||||| ||||||||||| ||||| |
---tccatgacaagcttcagggctttaaagatg-tccatgcatgtgagaggagtcttatgtgcatg-----ttcccctttcagacattttaaataagcgattcttgcagGTTATTGGAACTGATCTATTGTCCCAATCCCTATTACCGGCCATTGTTGAGCTTGCAGAGGATAGACATTGGAGGGTTCGACTTGCAATAATAGAGTATA

upper sequence: LOC_Os09g07510.1 (Oryza sativa), 3'ss of exon 8
lower sequence: Vv17s0000g03870.t01 (Vitis vinifera), 3'ss of exon 9
-----agtcccacagctcaatataacatttcaattttgcttccctaatgactgataaattccttggtcatagaaaattcattactgagtccttttgatctttcagGTTATTGGAATTGATTTGCTGTCACAATCACTGTTACCGGCGATCGTAGAACTTGCAGAGGATAGGCACTGGAGGGTTCGGCTTGCAATAATTGAGTACA
     | | | |||  | ||| |    || ||    ||  |||  ||  |   | || || | |     |  |  |||  ||     |    |||     ||||||| |||||||||||| ||||||| |||||  |  | ||||| || || || ||||| |||||||| |||||||||||||||||||||||||| || ||||
gcccaaattctacaaatgaatct---tttccatggctgaatcctgaaaaat--acaattttcattagtgttcagtatttcttttcatgcatatttttctgttcagGTGATTGGAATTGATCTGCTGTCTCAATCCTTACTGCCGGCCATTGTTGAGCTTGCTGAGGATAGACACTGGAGGGTTCGGCTTGCAATAATAGAATACA

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|58683974|gb|CK072661.1|CK072661
EST:     TTCCTGATGTTCGGCTCAATATAATCAGCAAGCTCGATCAAGTTAATCAG                         GTTATTGGAATTGATTTGCTGTCACAATCACTGTTACCGGCGATCGTAGAA
genomic: TTCCTGATGTTCGGCTCAATATAATCAGCAAGCTCGATCAAGTTAATCAGgtgatgttca ... gatctttcagGTTATTGGAATTGATTTGCTGTCACAATCACTGTTACCGGCGATCGTAGAA
EST: gi|30226842|gb|CB964734.1|CB964734
EST:     TTCCTGATGTTCGGCTCAATATAATCAGCAAGCTCGATCAAGTTAATCAG                         GTTATTGGAATTGATTTGCTGTCACAATCACTGTTACCGGCGATCGTAGAA
genomic: TTCCTGATGTTCGGCTCAATATAATCAGCAAGCTCGATCAAGTTAATCAGgtgatgttca ... gatctttcagGTTATTGGAATTGATTTGCTGTCACAATCACTGTTACCGGCGATCGTAGAA
EST: gi|38474762|gb|CF958895.1|CF958895
EST:     TTCCTGATGTTCGGCTCAATATAATCAGCAAGCTCGATCAAGTTAATCAG                         GTTATTGGAATTGATTTGCTGTCACAAATCACTGTTACCGGCGATCGTAGA
genomic: TTCCTGATGTTCGGCTCAATATAATCAGCAAGCTCGATCAAGTTAATCAGgtgatgttca ... gatctttcagGTTATTGGAATTGATTTGCTGTCACAA-TCACTGTTACCGGCGATCGTAGA
EST: gi|58593044|gb|CF991352.1|CF991352
EST:     TTCCTGATGTTCGGCTCAATATAATCAGCAAGCTCGATCAAGTTAATCAG                         GTTATTGGAATTGATTTGCTGTCACAATCACTGTTACCGGCGATCGTAGAA
genomic: TTCCTGATGTTCGGCTCAATATAATCAGCAAGCTCGATCAAGTTAATCAGgtgatgttca ... gatctttcagGTTATTGGAATTGATTTGCTGTCACAATCACTGTTACCGGCGATCGTAGAA
EST: gi|29635602|gb|CB640611.1|CB640611
EST:     TTCCTGATGTTCGGCTCAATATAATCAGCAAGCTCGATCAAGTTAATCAG                         GTTATTGGAATTGATTTGCTGTCACAATCACTGTTACCGGCGATCGTAGAA
genomic: TTCCTGATGTTCGGCTCAATATAATCAGCAAGCTCGATCAAGTTAATCAGgtgatgttca ... gatctttcagGTTATTGGAATTGATTTGCTGTCACAATCACTGTTACCGGCGATCGTAGAA
EST: gi|58598714|gb|CK009242.1|CK009242
EST:     TTCCTGATGTTCGGCTCAATATAATCAGCAAGCTCGATCAAGTTAATCAG                         GTTATTGGAATTGATTTGCTGTCACAATCACTGTTACCGGCGATCGTAGAA
genomic: TTCCTGATGTTCGGCTCAATATAATCAGCAAGCTCGATCAAGTTAATCAGgtgatgttca ... gatctttcagGTTATTGGAATTGATTTGCTGTCACAATCACTGTTACCGGCGATCGTAGAA
EST: gi|218487576|gb|FG960599.1|FG960599
EST:     TTCCTGATGTTCGGCTCAATATAATCAGCAAGCTCGATCAAGTTAGTCAG                         GTTATTGGAATTGATTTGCTGTCACAATCACTGTTACCGGCGATCGTAGAA
genomic: TTCCTGATGTTCGGCTCAATATAATCAGCAAGCTCGATCAAGTTAATCAGgtgatgttca ... gatctttcagGTTATTGGAATTGATTTGCTGTCACAATCACTGTTACCGGCGATCGTAGAA
EST: gi|3768380|gb|AU032407.1|AU032407
EST:     TCCTGATGTTCGGCTCAATATAATCAGCAAGCTCGATCAAAGTTAATCAG                         GTTATTGGAATTGANTTTGCTGTCACAATCACTGGTACCGGCGATCGTAGA
genomic: TCCTGATGTTCGGCTCAATATAATCAGCAAGCTCGATCAA-GTTAATCAGgtgatgttca ... gatctttcagGTTATTGGAATTGA-TTTGCTGTCACAATCACTGTTACCGGCGATCGTAGA
EST: gi|58655438|gb|CK044118.1|CK044118
EST:     TTCCTGATGTTCGGCTCAATATAATCAGCAAGCTCGATCAAGTTAATCAG                         GTTATTGGAATTGATTTGCTGTCACAATCACTGTTACCGGCGATCGTAGAA
genomic: TTCCTGATGTTCGGCTCAATATAATCAGCAAGCTCGATCAAGTTAATCAGgtgatgttca ... gatctttcagGTTATTGGAATTGATTTGCTGTCACAATCACTGTTACCGGCGATCGTAGAA
EST: gi|55409620|gb|CV721996.1|CV721996
EST:     TCCCTGATGTTCGGCTCAATATAATCAGCAAGCTCGATCAAGTTAATCAG                         GTTATTGGAATTGATTTGCTGTCACAATCACTGTTACCGGCGATCGTAGAA
genomic: TTCCTGATGTTCGGCTCAATATAATCAGCAAGCTCGATCAAGTTAATCAGgtgatgttca ... gatctttcagGTTATTGGAATTGATTTGCTGTCACAATCACTGTTACCGGCGATCGTAGAA
EST: gi|33676187|gb|CF304426.1|CF304426
EST:     TTCCTGATGTTCGGCTCAATATAATCAGCAAGCTCGATCAAGTTAATCAG                         GTTATTGGAATTGATTTGCTGTCACAATCACTGTTACCGGCGATCGTAGAA
genomic: TTCCTGATGTTCGGCTCAATATAATCAGCAAGCTCGATCAAGTTAATCAGgtgatgttca ... gatctttcagGTTATTGGAATTGATTTGCTGTCACAATCACTGTTACCGGCGATCGTAGAA
EST: gi|33656227|gb|CF278841.1|CF278841
EST:     TTCCTGATGTTCGGCTCAATATAATCAGCAAGCTCGATCAAGTTAATCAG                         GTTATTGGAATTGATTTGCTGTCACAATCACTGTTACCGGCGATCGTAGAA
genomic: TTCCTGATGTTCGGCTCAATATAATCAGCAAGCTCGATCAAGTTAATCAGgtgatgttca ... gatctttcagGTTATTGGAATTGATTTGCTGTCACAATCACTGTTACCGGCGATCGTAGAA
EST: gi|58678838|gb|CK067525.1|CK067525
EST:     TTCCTGATGTTCGGCTCAATATAATCAGCAAGCTCGATCAAGTTAATCAG                         GTTATTGGAATTGATTTGCTGTCACAATCACTGTTACCGGCGATCGTAGAA
genomic: TTCCTGATGTTCGGCTCAATATAATCAGCAAGCTCGATCAAGTTAATCAGgtgatgttca ... gatctttcagGTTATTGGAATTGATTTGCTGTCACAATCACTGTTACCGGCGATCGTAGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgataaattccttggtcatagaaaattcattactgagtccttttgatctttcagGTTATTGGAATTGATTTGCTGTCACAATCACTGTTACCGGCGATCGTAGAACTTGCAGAGGATAGGCACTGGAGGGTTCGGCTTGCAATAATTGAGTACA
                                      tccttttgatctttc  CT-rich tract
                  atagaaaattcatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agtcccacagctcaatataacatttcaattttgcttccctaatgactgataaattccttggtcatagaaaattcattactgagtccttttgatctttcagGTTATTGGAATTGATTTGCTGTCACAATCACTGTTACCGGCGATCGTAGAACTTGCAGAGGATAGGCACTGGAGGGTTCGGCTTGCAATAATTGAGTACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - -tgcttcc
- - - - - - - - - - - - - - - - - - - - -atgactg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -atagaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttactga