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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtgaatatctgtttactgatgcagatgcacttgaaacacttgcatatttctggtttctgacataaacatgtttctttttccagAAAATCAAGAACCCTAACTACCAAGGCAAATGGAAGGCACCGATGATCGACAACCCAG

Basic information

species Oryza sativa
transcript LOC_Os07g14270.3
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g14270.3 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G074687_T01 (Zea mays), 3'ss of exon 7
gtgtgaatatctgtttactga--tgcagatgcacttgaaacacttgcatatttctggtttctgacataaacatgtttctttttccagAAAATCAAGAACCCTAACTACCAAGGCAAATGGAAGGCACCGATGATCGACAACCCAG
    | ||  | |||   |||  || | |   |||   | || || |||||| ||| | ||||||   | ||||||||  || ||||||||||||||||||||||||||| || |||||||||||||| ||||| ||||||||||
----gtatggcagttccttgaactgtatacaaactgacatcaatt-catatt-ctgatatctgac---agcatgtttcacttgccagAAAATCAAGAACCCTAACTACCAGGGTAAATGGAAGGCACCTATGATTGACAACCCAG

upper sequence: LOC_Os07g14270.3 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G358059_T01 (Zea mays), 3'ss of exon 7
gtgtgaatatctgtttactgatgcagatgcacttgaaacacttgcatatttctggtttctgacataaacatgtttctttttccagAAAATCAAGAACCCTAACTACCAAGGCAAATGGAAGGCACCGATGATCGACAACCCAG
    | ||  | |||   |    |  ||  |||   | || || |||||| ||| | |||||||  |   ||||||  || |||||||||||||||||| |||||||| || |||||||||||||| ||||| ||||||||||
----gtatggcagttccttttaacctataaactgacagcaatt-catatt-ctgatatctgacagcatgttgtttcacttgccagAAAATCAAGAACCCGAACTACCAGGGTAAATGGAAGGCACCTATGATTGACAACCCAG

upper sequence: LOC_Os07g14270.3 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA20G23080.2 (Glycine max), 3'ss of exon 7
--gtgtgaatatctgtttactgatgcagatgcacttgaaacacttgcatatttc-tggtttctgacataaacatgtttctt------------------tttccagAAAATCAAGAACCCTAACTACCAAGGCAAATGGAAGGCACCGATGATCGACAACCCAG
   |||| | || |||||  | |    |    |  ||||| | |  |||||| | |  | | ||  || ||  || ||  |                  ||| ||||||||||||||||| |||||  |||| ||||||||||||||  |||| || |||||||
gtttgtggaaatttgttttgtaaatttgtaatatatgaaata-tgacatattccattatgtttggaatgaatttgctttataactttgcatgctacatatttgcagAAAATCAAGAACCCCAACTATAAAGGAAAATGGAAGGCACCATTGATTGATAACCCAG

upper sequence: LOC_Os07g14270.3 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA10G28890.1 (Glycine max), 3'ss of exon 7
-----------------gtgtgaatatctgtttactgatgca-gatgcacttgaa-acacttgc--atatttctggtttctgacataaacatgtttctt-tttccagAAAATCAAGAACCCTAACTACCAAGGCAAATGGAAGGCACCGATGATCGACAACCCAG
                  ||| ||| | |  |   |||   | ||   | |  |  |   |||   ||   | || ||||| || |   |||| | | | ||| ||||||||||||||||| |||||  |||| ||||||||||||||  |||| || |||||||
gtttgtggaaatttttattgtaaatttgtaatatttgaaatacgacatattccattatgtttggtaatgaatttgctttctaactttg-catgctacatatttgcagAAAATCAAGAACCCCAACTATAAAGGAAAATGGAAGGCACCATTGATTGATAACCCAG

upper sequence: LOC_Os07g14270.3 (Oryza sativa), 3'ss of exon 7
lower sequence: Vv07s0005g01390.t01 (Vitis vinifera), 3'ss of exon 7
gtgtgaatatctgtttactgatgcagatgcacttgaaacacttgcatatttctggtttctgacataaacatgttt---ctttttccagAAAATCAAGAACCCTAACTACCAAGGCAAATGGAAGGCACCGATGATCGACAACCCAG
||  |   |  |||||| |  |  |||||   ||     | ||    | ||   | |||  || |||   |  ||   |  ||  ||| |||| || ||||| |||||| | || |||||||||||||| ||||| ||||||||||
gttcgctgaaatgtttattagttaagatgatgttatggaattttggaagttgacggttc--acttaattgttcttgaaccattggcagCAAATAAAAAACCCCAACTACAAGGGAAAATGGAAGGCACCTATGATTGACAACCCAG

upper sequence: LOC_Os07g14270.3 (Oryza sativa), 3'ss of exon 7
lower sequence: Vv14s0060g01290.t01 (Vitis vinifera), 3'ss of exon 7
gtgtgaatatctgtt-tactgatgcagatgcacttgaaacacttgcatatttctggttt-----ctgacataaacatgtt---tctttttccagAAAATCAAGAACCCTAACTACCAAGGCAAATGGAAGGCACCGATGATCGACAACCCAG
         | |||   |  | |  || |  | |||||||| ||  || || |||||        || |||||      |   ||| ||  |||||||| ||||| || |||||| | || |||||||||||||| ||||| ||||||||||
--------gtttgtggcatggttttagtttaagttgaaacattta-attttgctggtaaaagagttgtcataattcctctctatctcttggcagAAAATTAAGAATCCCAACTACAAGGGAAAATGGAAGGCACCAATGATTGACAACCCAG

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|88729754|gb|CI753264.1|CI753264
EST:     CTGCACCAACCATTCCTAACCCTGAGTACAAGGGACCATGGAAGCAAAAG                         AAAATCAAGAACCCTAACTACCAAGGCAAATGGAAGGCACCGATGATCGAC
genomic: CTGCACCAACCATTCCTAACCCTGAGTACAAGGGACCATGGAAGCAAAAGgtgtgaatat ... ctttttccagAAAATCAAGAACCCTAACTACCAAGGCAAATGGAAGGCACCGATGATCGAC
EST: gi|29629339|gb|CB634350.1|CB634350
EST:     CTGCACCAACCATTCCTAACCCTGAGTACAAGGGACCATGGAAGCAAAAG                         AAAATCAAGAACCCTAACTACCAAGGCAAATGGAAGGCACCGATGATCGAC
genomic: CTGCACCAACCATTCCTAACCCTGAGTACAAGGGACCATGGAAGCAAAAGgtgtgaatat ... ctttttccagAAAATCAAGAACCCTAACTACCAAGGCAAATGGAAGGCACCGATGATCGAC
EST: gi|163920423|gb|EG710621.1|EG710621
EST:     CTGCACCAACCATTCCTAACCCTGAGTACAAGGGACCATGGAAGCAAAAG                         AAAATCAAGAACCCTAACTACCAAGGCAAATGGAAGGCACCGATGATCGAC
genomic: CTGCACCAACCATTCCTAACCCTGAGTACAAGGGACCATGGAAGCAAAAGgtgtgaatat ... ctttttccagAAAATCAAGAACCCTAACTACCAAGGCAAATGGAAGGCACCGATGATCGAC
EST: gi|33793505|gb|CF322636.1|CF322636
EST:     CTGCACCAACCATTCCTAACCCTGAGTACAAGGGACCATGGAAGCAAAAG                         AAAATCAAGAACCCTAACTACCAAGGCAAATGGAAGGCACCGATGATCGAC
genomic: CTGCACCAACCATTCCTAACCCTGAGTACAAGGGACCATGGAAGCAAAAGgtgtgaatat ... ctttttccagAAAATCAAGAACCCTAACTACCAAGGCAAATGGAAGGCACCGATGATCGAC
EST: gi|29658654|gb|CB654929.1|CB654929
EST:     CTGCACCAACCATTCCTAACCCTGAGTACAAGGGACCATGGAAGCAAAAG                         AAAATCAAGAACCCTAACTACCAAGGCAAATGGAAGGCACCGATGATCGAC
genomic: CTGCACCAACCATTCCTAACCCTGAGTACAAGGGACCATGGAAGCAAAAGgtgtgaatat ... ctttttccagAAAATCAAGAACCCTAACTACCAAGGCAAATGGAAGGCACCGATGATCGAC
EST: gi|88718533|gb|CI742043.1|CI742043
EST:     CTGCACCAACCATTCCTAACCCTGAGTACAAGGGACCATGGAAGCAAAAG                         AAAATCAAGAACCCTAACTACCAAGGCAAATGGAAGGCACCGATGATCGAC
genomic: CTGCACCAACCATTCCTAACCCTGAGTACAAGGGACCATGGAAGCAAAAGgtgtgaatat ... ctttttccagAAAATCAAGAACCCTAACTACCAAGGCAAATGGAAGGCACCGATGATCGAC
EST: gi|88722171|gb|CI745681.1|CI745681
EST:     CTGCACCAACCATTCCTAACCCTGAGTACAAGGGACCATGGAAGCAAAAG                         AAAATCAAGAACCCTAACTACCAAGGCAAATGGAAGGCACCGATGATCGAC
genomic: CTGCACCAACCATTCCTAACCCTGAGTACAAGGGACCATGGAAGCAAAAGgtgtgaatat ... ctttttccagAAAATCAAGAACCCTAACTACCAAGGCAAATGGAAGGCACCGATGATCGAC
EST: gi|88691187|gb|CI735266.1|CI735266
EST:     CTGCACCAACCATTCCTAACCCTGAGTACAAGGGACCATGGAAGCAAAAG                         AAAATCAAGAACCCTAACTACCAAGGCAAATGGAAGGCACCGATGATCGAC
genomic: CTGCACCAACCATTCCTAACCCTGAGTACAAGGGACCATGGAAGCAAAAGgtgtgaatat ... ctttttccagAAAATCAAGAACCCTAACTACCAAGGCAAATGGAAGGCACCGATGATCGAC
EST: gi|29675242|gb|CB671517.1|CB671517
EST:     CTGCACCAACCATTCCTAACCCTGAGTACAAGGGACCATGGAAGCAAAAG                         AAAATCAAGAACCCCTAACTACCAAGGCAAATGGAAGGCACCGATGATCGA
genomic: CTGCACCAACCATTCCTAACCCTGAGTACAAGGGACCATGGAAGCAAAAGgtgtgaatat ... ctttttccagAAAATCAAGAACCC-TAACTACCAAGGCAAATGGAAGGCACCGATGATCGA
EST: gi|396941542|gb|HO188751.1|HO188751
EST:     CTGCACCAACCATTCCTAACCCTGAGTACAAGGGACCATGGAAGCAAAAG                         AAAATCAAGAACCCTAACTACCAAGGCAAATGGAAGGCACCGATGATCGAC
genomic: CTGCACCAACCATTCCTAACCCTGAGTACAAGGGACCATGGAAGCAAAAGgtgtgaatat ... ctttttccagAAAATCAAGAACCCTAACTACCAAGGCAAATGGAAGGCACCGATGATCGAC
EST: gi|14192066|gb|AU184277.1|AU184277
EST:     CTGCACCAACCATTCCTAACCCTGAGTACAAGGGACCATGGAAGCAAAAG                         AAAATCAAGAACCCTAACTACCAAGGCAAATGGAAGGCACCGATGATCGAC
genomic: CTGCACCAACCATTCCTAACCCTGAGTACAAGGGACCATGGAAGCAAAAGgtgtgaatat ... ctttttccagAAAATCAAGAACCCTAACTACCAAGGCAAATGGAAGGCACCGATGATCGAC
EST: gi|29662654|gb|CB658929.1|CB658929
EST:     CTGCACCAACCATTCCTAACCCTGAGTACAAGGGACCATGGAAGCAAAAG                         AAAATCAAGAACCCTAACTACCAAGGCAAATGGAAGGCACCGATGATCGAC
genomic: CTGCACCAACCATTCCTAACCCTGAGTACAAGGGACCATGGAAGCAAAAGgtgtgaatat ... ctttttccagAAAATCAAGAACCCTAACTACCAAGGCAAATGGAAGGCACCGATGATCGAC
EST: gi|86497286|gb|CI139919.1|CI139919
EST:     TCCTAACCCTGAGTACAAGGGACCATGGAAGCAAAAG                         AAAATCAAGAACCCTAACTACCAAGGCAAATGGAAGGCACCGATGATCGAC
genomic: TCCTAACCCTGAGTACAAGGGACCATGGAAGCAAAAGgtgtgaatat ... ctttttccagAAAATCAAGAACCCTAACTACCAAGGCAAATGGAAGGCACCGATGATCGAC
EST: gi|29644253|gb|CB649260.1|CB649260
EST:     CTGCACCAACCATTCCTAACCCTGAGTACAAGGGACCATGGAAGCAAAAG                         AAAATCAAGAACCCTAACTACCAAGGCAAATGGAAGGCACCGATGATCGAC
genomic: CTGCACCAACCATTCCTAACCCTGAGTACAAGGGACCATGGAAGCAAAAGgtgtgaatat ... ctttttccagAAAATCAAGAACCCTAACTACCAAGGCAAATGGAAGGCACCGATGATCGAC
EST: gi|33793940|gb|CF322858.1|CF322858
EST:     CTGCACCAACCATTCCTAACCCTGAGTACAAGGGACCATGGAAGCAAAAG                         AAAATCAAGAACCCTAACTACCAAGGCAAATGGAAGGCACCGATGATCGAC
genomic: CTGCACCAACCATTCCTAACCCTGAGTACAAGGGACCATGGAAGCAAAAGgtgtgaatat ... ctttttccagAAAATCAAGAACCCTAACTACCAAGGCAAATGGAAGGCACCGATGATCGAC
EST: gi|58596614|gb|CK007142.1|CK007142
EST:     CTGGACCAACCATTCCTAACCCTGAGTACAAGGGACCATGGAAGCCAAAG                         AAAATCAAGAACCCTAACTA
genomic: CTGCACCAACCATTCCTAACCCTGAGTACAAGGGACCATGGAAGCAAAAGgtgtgaatat ... ctttttccagAAAATCAAGAACCCTAACTA
EST: gi|88690114|gb|CI734193.1|CI734193
EST:     CTGCACCAACCATTCCTAACCCTGAGTACAAGGGACCATGGAAGCAAAAG                         AAAATCAAGAACCCTAACTACCAAGGCAAATGGAAGGCACCGATGATCGAC
genomic: CTGCACCAACCATTCCTAACCCTGAGTACAAGGGACCATGGAAGCAAAAGgtgtgaatat ... ctttttccagAAAATCAAGAACCCTAACTACCAAGGCAAATGGAAGGCACCGATGATCGAC
EST: gi|88730078|gb|CI753693.1|CI753693
EST:     CTGCACCAACCATTCCTAACCCTGAGTACAAGGGACCATGGAAGCAAAAG                         AAAATCAAGAACCCTAACTACCAAGGCAAATGGAAGGCACCGATGATCGAC
genomic: CTGCACCAACCATTCCTAACCCTGAGTACAAGGGACCATGGAAGCAAAAGgtgtgaatat ... ctttttccagAAAATCAAGAACCCTAACTACCAAGGCAAATGGAAGGCACCGATGATCGAC
EST: gi|29673077|gb|CB669352.1|CB669352
EST:     CTGCACCAACCATTCCTAACCGTGAGTACAAGGGACCATGGAAGCAAAAG                         AAAATCAAGAACCTTATCTACCAAGGCAAATGGAAGGCACCGATGATCGAC
genomic: CTGCACCAACCATTCCTAACCCTGAGTACAAGGGACCATGGAAGCAAAAGgtgtgaatat ... ctttttccagAAAATCAAGAACCCTAACTACCAAGGCAAATGGAAGGCACCGATGATCGAC
EST: gi|66915891|gb|CX102739.1|CX102739
EST:     CTGCACCAACCATTCCTAACCCTGAGTACAAGGGACCATGGAAGCAAAAG                         AAAATCAAGAACCCTAACTACCAAGGCAAATGGAAGGCACCGATGATCGAC
genomic: CTGCACCAACCATTCCTAACCCTGAGTACAAGGGACCATGGAAGCAAAAGgtgtgaatat ... ctttttccagAAAATCAAGAACCCTAACTACCAAGGCAAATGGAAGGCACCGATGATCGAC
EST: gi|8856749|gb|AU094067.1|AU094067
EST:     CTGCACCAACCATTCCTAACCCTGAGTACAAGGGACCATGGAAGCAAAAG                         AAAATCAAGAACCCTAACTACCAAGGCAAATGGAAGGCACCGATGATCGAC
genomic: CTGCACCAACCATTCCTAACCCTGAGTACAAGGGACCATGGAAGCAAAAGgtgtgaatat ... ctttttccagAAAATCAAGAACCCTAACTACCAAGGCAAATGGAAGGCACCGATGATCGAC
EST: gi|58592538|gb|CF990846.1|CF990846
EST:     GGGACCATGGAAGCAAAAG                         AAAATCAAGAACCCTAAGTAGCAAGGCAAATGGAAGGCACCGATGATCGAC
genomic: GGGACCATGGAAGCAAAAGgtgtgaatat ... ctttttccagAAAATCAAGAACCCTAACTACCAAGGCAAATGGAAGGCACCGATGATCGAC
EST: gi|29662655|gb|CB658930.1|CB658930
EST:     CTGCACCAACCATTCCTAACCCTGAGTACAAGGGACCATGGAAGCAAAAG                         AAAATCAAGAACCCTAACTACCAAGGCAAATGGAAGGCACCGATGATCGAC
genomic: CTGCACCAACCATTCCTAACCCTGAGTACAAGGGACCATGGAAGCAAAAGgtgtgaatat ... ctttttccagAAAATCAAGAACCCTAACTACCAAGGCAAATGGAAGGCACCGATGATCGAC
EST: gi|88996495|gb|CI259999.1|CI259999
EST:     CTGCACCAACCATTCCTAAGCCTGAGTACAAGGGACCATGGAAGCAAAAG                         AAAATCAAGAACCCTAACTACCAAGGCAAATGGAAGGCACCGATGATCGAC
genomic: CTGCACCAACCATTCCTAACCCTGAGTACAAGGGACCATGGAAGCAAAAGgtgtgaatat ... ctttttccagAAAATCAAGAACCCTAACTACCAAGGCAAATGGAAGGCACCGATGATCGAC
EST: gi|86600080|gb|CI258420.1|CI258420
EST:     CTGCACCAACCATTCCTAACCCTGAGTACAAGGGACCATGGAAGCAAAAG                         AAAATCAAGAACCCTAACTACCAAGGCAAATGGAAGGCACCGATGATCGAC
genomic: CTGCACCAACCATTCCTAACCCTGAGTACAAGGGACCATGGAAGCAAAAGgtgtgaatat ... ctttttccagAAAATCAAGAACCCTAACTACCAAGGCAAATGGAAGGCACCGATGATCGAC
EST: gi|3760360|gb|C97614.1|C97614
EST:     TGGAAGCAAAAG                         AAAATCAAG-ACCCTAACTACCAAGGCAAATGGAAGGCACCGATGATCGAC
genomic: TGGAAGCAAAAGgtgtgaatat ... ctttttccagAAAATCAAGAACCCTAACTACCAAGGCAAATGGAAGGCACCGATGATCGAC
EST: gi|29663170|gb|CB659445.1|CB659445
EST:     CTGCACCAACCATTCCTAACCCTGAGTACAAGGGACCATGGAAGCAAAAG                         AAAATCAAGAACCCTAACTACCAAGGCAAATGGAAGGCACCGATGATCGAC
genomic: CTGCACCAACCATTCCTAACCCTGAGTACAAGGGACCATGGAAGCAAAAGgtgtgaatat ... ctttttccagAAAATCAAGAACCCTAACTACCAAGGCAAATGGAAGGCACCGATGATCGAC
EST: gi|8528286|gb|AU093101.1|AU093101
EST:     CCAACCATTCCCTAACCNTGAGT-CCAGGG-CCATGGAAGCAAAAG                         AAAATCAAG-ACCCTAACTACCAAGGCAAATGGAAGGCACCGATGATCGAC
genomic: CCAACCATT-CCTAACCCTGAGTACAAGGGACCATGGAAGCAAAAGgtgtgaatat ... ctttttccagAAAATCAAGAACCCTAACTACCAAGGCAAATGGAAGGCACCGATGATCGAC
EST: gi|29660493|gb|CB656768.1|CB656768
EST:     CTGCACCAACCATTCCTAACCCTGAGTACAAGGGACCATGGAAGCAAAAG                         AAAATCAAGAACCCTAACTACCAAGGCAAATGGAAGGCACCGATGATCGAC
genomic: CTGCACCAACCATTCCTAACCCTGAGTACAAGGGACCATGGAAGCAAAAGgtgtgaatat ... ctttttccagAAAATCAAGAACCCTAACTACCAAGGCAAATGGAAGGCACCGATGATCGAC
EST: gi|29660220|gb|CB656495.1|CB656495
EST:     CTGCACCAACCATTCCTAACCCTGAGTACAAGGGACCATGGAAGCAAAAG                         AAAATCAAGAACCCTAACTACCAAGGCAAATGGAAGGCACCGATGATCGAC
genomic: CTGCACCAACCATTCCTAACCCTGAGTACAAGGGACCATGGAAGCAAAAGgtgtgaatat ... ctttttccagAAAATCAAGAACCCTAACTACCAAGGCAAATGGAAGGCACCGATGATCGAC
EST: gi|29629338|gb|CB634349.1|CB634349
EST:     CTGCACCAACCATTCCTAACCCTGAGTACAAGGGACCATGGAAGCAAAAG                         AAAATCAAGAACCCTAACTACCAAGGCAAATGGAAGGCACCGATGATCGAC
genomic: CTGCACCAACCATTCCTAACCCTGAGTACAAGGGACCATGGAAGCAAAAGgtgtgaatat ... ctttttccagAAAATCAAGAACCCTAACTACCAAGGCAAATGGAAGGCACCGATGATCGAC
EST: gi|58679227|gb|CK067914.1|CK067914
EST:     CTGCACCAACCATTCCTAACCCTGAGTACAAGGGACCATGGAAGCAAAAG                         AAAATCAAGAACCCTAACTACCAAGGCAAATGGAAGGCACCGATGATCGAC
genomic: CTGCACCAACCATTCCTAACCCTGAGTACAAGGGACCATGGAAGCAAAAGgtgtgaatat ... ctttttccagAAAATCAAGAACCCTAACTACCAAGGCAAATGGAAGGCACCGATGATCGAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acttgaaacacttgcatatttctggtttctgacataaacatgtttctttttccagAAAATCAAGAACCCTAACTACCAAGGCAAATGGAAGGCACCGATGATCGACAACCCAG
                          ttctgac  putative branch site (score: 2)
                                      catgtttctttttcc  putative PPT
                                          tttcttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgtgaatatctgtttactgatgcagatgcacttgaaacacttgcatatttctggtttctgacataaacatgtttctttttccagAAAATCAAGAACCCTAACTACCAAGGCAAATGGAAGGCACCGATGATCGACAACCCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG