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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgttgttgggtgcaatatttggtttgtattctatcacaacaacagcaggatttttgagttacgaaagctaccgcagGGAGAAGCATTGTTTCAGACCCATGAAAACTTGGAGCATCTTGCTATGATGGAGAGGGTATTTGGTCCTTTGCCATGTCACATGCTCAAAAGGGCAGA

Basic information

species Oryza sativa
transcript LOC_Os12g27520.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g27520.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G179308_T03 (Zea mays), 3'ss of exon 8
gtatgttgttgggtgcaatatttggtttgtattctatcacaacaacagcaggatttttgagttacgaaagctaccgcagGGAGAAGCATTGTTTCAGACCCATGAAAACTTGGAGCATCTTGCTATGATGGAGAGGGTATTTGGTCCTTTGCCATGTCACATGCTCAAAAGGGCAGA
||||||| ||| |        |||||||| ||| |      ||||   |||    | |||||||| || | | | |||||| || ||  | || ||||| || ||||||||||| ||||| |||||||||||||||||  |||| ||||||||||  || ||| |||| ||||||||
gtatgttattgtgc------cttggtttg-attttgcatgtacaagtacagaggatctgagttaccaaggtt-ctgcagGGTGAGGCGATATTCCAGACTCACGAAAACTTGGAACATCTGGCTATGATGGAGAGGGTTCTTGGACCTTTGCCATACCATATGTTCAAGAGGGCAGA

upper sequence: LOC_Os12g27520.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G063792_T04 (Zea mays), 3'ss of exon 9
gtatgttgttgggtgcaatatttggtttgtattctatcacaacaacagcaggatttttgagttacgaaagctaccgcagGGAGAAGCATTGTTTCAGACCCATGAAAACTTGGAGCATCTTGCTATGATGGAGAGGGTATTTGGTCCTTTGCCATGTCACATGCTCAAAAGGGCAGA--
|||||||  ||||    |  || | ||  | |   ||   |  |  | ||||   | |||||||| || | |   |||||| || || || || ||||| || ||||||||||| ||||| |||||||||||||| ||  |||| |||||||| |  || ||||| || ||||||||  
gtatgttaatggg----accttggcttcatttggcat-gtacaagtaccaggggatctgagttaccaaggttgt-gcagGGTGAGGCGTTATTCCAGACTCACGAAAACTTGGAACATCTGGCTATGATGGAGAGAGTTCTTGGACCTTTGCCGTACCATATGCTTAAGAGGGCAGAGT

upper sequence: LOC_Os12g27520.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G063792_T06 (Zea mays), 3'ss of exon 7
gtatgttgttgggtgcaatatttggtttgtattctatcacaacaacagcaggatttttgagttacgaaagctaccgcagGGAGAAGCATTGTTTCAGACCCATGAAAACTTGGAGCATCTTGCTATGATGGAGAGGGTATTTGGTCCTTTGCCATGTCACATGCTCAAAAGGGCAGA
|||||||  ||||    |  || | ||  | |   ||   |  |  | ||||   | |||||||| || | |   |||||| || || || || ||||| || ||||||||||| ||||| |||||||||||||| ||  |||| |||||||| |  || ||||| || ||||||||
gtatgttaatggg----accttggcttcatttggcat-gtacaagtaccaggggatctgagttaccaaggttgt-gcagGGTGAGGCGTTATTCCAGACTCACGAAAACTTGGAACATCTGGCTATGATGGAGAGAGTTCTTGGACCTTTGCCGTACCATATGCTTAAGAGGGCAGA

upper sequence: LOC_Os12g27520.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GLYMA05G02740.1 (Glycine max), 3'ss of exon 8
gtatgttg-------ttgggtgcaatatttggtttgtattc-----tatcacaacaacagcaggatttt-tgagttacgaaagc-taccgcagGGAGAAGCATTGTTTCAGACCCATGAAAACTTGGAGCATCTTGCTATGATGGAGAGGGTATTTGGTCCTTTGCCATGTCACATGCTCAAAAGGGCAGA
|||||||        |      |  |||         |||      | ||| | ||      | ||| | | | | | |||    ||   ||||| ||||| ||||||||||| |||||||| || ||||||||||| |||||||| |||||| ||||| | || |||     |||| | || || |  ||
gtatgtttggctctttcaaaacctttatacaaagcacatttatccatctcatatcatagattgtattctataattcatgaatttgtattacagGGTGAAGCTTTGTTTCAGACTCATGAAAATTTAGAGCATCTTGCAATGATGGAAAGGGTACTTGGTTCATTACCACAGACCATGATGAAGAGAGTCGA

upper sequence: LOC_Os12g27520.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GLYMA04G36360.1 (Glycine max), 3'ss of exon 8
gtatgtt--gttgggtgcaatatttggtttgtattctatcacaacaacagcaggatttttgag-ttacgaaag-ctaccgcagGGAGAAGCATTGTTTCAGACCCATGAAAACTTGGAGCATCTTGCTATGATGGAGAGGGTATTTGGTCCTTTGCCATGTCACATGCTCAAAAGGGCAGA
||| |||  | |   ||  ||| ||  |  | | | |    ||         |  |   | || ||| |     |||  |||||| ||||| ||||||||||| |||||||| || |||||||| |||||||||||||||||  |||||||| | |||   || ||| | || || |  ||
gtaagtttggctctctg-gatactttttaggcaattttatccagttttgtttgtttaaatcagcttatgggcttctattgcagGGTGAAGCTTTGTTTCAGACTCATGAAAATTTAGAGCATCTGGCTATGATGGAGAGGGTGCTTGGTCCTATACCACAGCAGATGTTAAAGAGAGTTGA

upper sequence: LOC_Os12g27520.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GLYMA17G13440.1 (Glycine max), 3'ss of exon 7
gtatgtt--gttgggtgcaatatttggtttgtattctatcacaacaacagcaggatttt------tgagttacgaaagc-taccgcagGGAGAAGCATTGTTTCAGACCCATGAAAACTTGGAGCATCTTGCTATGATGGAGAGGGTATTTGGTCCTTTGCCATGTCACATGCTCAAAAGGGCAGA
|||||||  | |   |  |||  |   |    |   |||     || |     |||| |      | | ||  |||    ||   ||||| | ||| ||||||||||| || ||||| |||||||||||||| |||||||| |||||| ||||||| || |||   | |||| | || || |  ||
gtatgtttggctctctcaaatcctgtataaaaaacatatttatccatctcttagattctattccataatttgtgaatttatattacagGGCGGAGCTTTGTTTCAGACTCACGAAAATTTGGAGCATCTTGCCATGATGGAAAGGGTACTTGGTCCATTACCACAGCCCATGTTGAAGAGAGTCGA

upper sequence: LOC_Os12g27520.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GLYMA06G18530.1 (Glycine max), 3'ss of exon 8
gtatgtt--gttgggtgca-atatttggtttgtattctatcacaacaacagcaggatttttgag-ttacgaaag-ctaccgcagGGAGAAGCATTGTTTCAGACCCATGAAAACTTGGAGCATCTTGCTATGATGGAGAGGGTATTTGGTCCTTTGCCATGTCACATGCTCAAAAGGGCAGA
||| |||  | |   || | |  ||||   |  ||  |||| ||      |  |  |   | || ||| ||    |||  |||||| ||||| ||||||||||| |||||||| || |||||||| || ||||||||||||||  |||||||| | |||   || ||| | || || |  ||
gtaagtttggctctctggatacttttgaggttaatattatc-cagtttttgttgtttaaatcagcttatgagtttctattgcagGGTGAAGCTTTGTTTCAGACTCATGAAAATTTAGAGCATCTGGCCATGATGGAGAGGGTGCTTGGTCCTATACCACAGCAGATGTTAAAGAGAGTTGA

upper sequence: LOC_Os12g27520.1 (Oryza sativa), 3'ss of exon 9
lower sequence: AT4G24740.2 (Arabidopsis thaliana), 3'ss of exon 8
gtatgttgttgggtgcaatatttggtttgtattctatcacaacaacagcaggatttttgagttacgaaagctaccgcagGGAGAAGCATTGTTTCAGACCCATGAAAACTTGGAGCATCTTGCTATGATGGAGAGGGTATTTGGTCCTTTGCCATGTCACATGCTCAAAAGGGCAGA
    ||   ||  || | || ||| ||  || |  ||       |        || ||||   |    || |   | |||| ||||||||||| || || ||||||||| |||||||||| || ||||||||| | ||  |||| || || ||    || ||||| || |  |  ||
----gtgtgtgtctgaagtagttgattgttaatgaatgtttgggagtct---tttattgaaagatttgagat-ttgtagGGTGAAGCATTGTTCCAAACACATGAAAACCTGGAGCATCTAGCGATGATGGAGCGTGTTCTTGGGCCGTTTCCTCAACAAATGCTGAAGAAAGTGGA

upper sequence: LOC_Os12g27520.1 (Oryza sativa), 3'ss of exon 9
lower sequence: Vv01s0137g00580.t01 (Vitis vinifera), 3'ss of exon 9
--------------------gtat-----gttgttgggtgcaatatttggtttgtattctatcacaacaacagcaggatttttgagttacgaaagctacc----gcagGGAGAAGCATTGTTTCAGACCCATGAAAACTTGGAGCATCTTGCTATGATGGAGAGGGTATTTGGTCCTTTGCCATGTCACATGCTCAAAAGGGCAGA
                    ||||      |  |||  |  |||   ||| | ||| |  ||    |  |   |   ||     |  |  |   ||| ||    |||||||||||| ||||||||||| ||||| ||||||||||| || || |||||||| ||||| || || ||  | ||   ||| ||| | ||||| |  ||
gtatgcttaatctctctgtagtattaatgatctttgcatcaaatggctggatggtaatacat-gtcatgaagtcctaatgcaaaacatgtggctgcttcctgttgcagGGAGAAGCTTTGTTTCAGACACATGAGAACTTGGAGCACCTGGCCATGATGGAAAGGGTTTTAGGCCCCATACCTCCTCATATGTTGAAAAGAGTGGA

upper sequence: LOC_Os12g27520.1 (Oryza sativa), 3'ss of exon 9
lower sequence: Vv17s0000g09500.t01 (Vitis vinifera), 3'ss of exon 9
----gtatgttgttggg--tgcaatatttggtttgtattctatcacaacaacagcaggattt--ttgagttacgaaagctac------cgcagGGAGAAGCATTGTTTCAGACCCATGAAAACTTGGAGCATCTTGCTATGATGGAGAGGGTATTTGGTCCTTTGCCATGTCACATGCTCAAAAGGGCAGA
    || | ||  |     ||||||   || | | | || | |  |  ||   | | |||    ||  | | | | |  ||       | ||||||||||||||||||||||| ||||| ||  ||||||| ||||| |||||||| ||||| || |||||  ||||    |||||||| || || | |||
gtacgtttattaattaaattgcaatgcatgttgtctctttt-tgtcggcattggaatgatgaggttatgatgcaacatttattcattacacagGGAGAAGCATTGTTTCAGACTCATGAGAATCTGGAGCACCTTGCCATGATGGAAAGGGTGTTGGGTCCACTGCCGCAGCACATGCTGAAGAGAGTAGA

upper sequence: LOC_Os12g27520.1 (Oryza sativa), 3'ss of exon 9
lower sequence: PP1S100_121V6.1 (Physcomitrella patens), 3'ss of exon 11
--------------gta-tgttgttgggtgcaatatttg-gtttgtattctatcacaacaacagcaggatttttgag----ttacgaa--agctaccgcagGGAGAAGCATTGTTTCAGACCCATGAAAACTTGGAGCATCTTGCTATGATGGAGAGGGTATTTGGTCCTTTGCCATGTCACATGCTCAAAAGGGCAGA
               || ||| | ||  |  | ||     |   |||  |   ||    | ||  | |  |||| |     |||   |     |     |||| || ||  |||||||||| ||||| |||||||||||| | |||||||||||| |||| || |||||  | ||   ||||||| | |  ||||||||
tccctcgaagaaggctactgtagctgtatctactacacatgacggtagccgtacatgg-atcaatatgtcttttaataactttattcattgtttgttttagGGTGATGCGCTGTTTCAGACTCATGAGAACTTGGAGCATTTGGCTATGATGGAGCGGGTTTTAGGTCCCATTCCCGTTCACATGATAAGGAGGGCAGA

upper sequence: LOC_Os12g27520.1 (Oryza sativa), 3'ss of exon 9
lower sequence: PP1S132_58V6.1 (Physcomitrella patens), 3'ss of exon 9
------------------------------------------------------------------------------------------gtatgttgttg--ggtgcaatatttggtttgtattctatcacaacaacagcaggatttttgagt---tacgaaa---gctaccgcagGGAGAAGCATTGTTTCAGACCCATGAAAACTTGGAGCATCTTGCTATGATGGAGAGGGTATTTGGTCCTTTGCCATGTCACATGCTCAAAAGGGCAGA
                                                                                          | |  |  |||  |    | | |||  |  | |     | | | |||    |   ||||| |||   |||   |   ||||  |||||| || |||||||||||||| || || || ||||||||| | |||||||||||  | || || |||||| | ||    |||||| |||| ||||||||
gtatgggattcctatcgccttcctttctcttttatattcctctattatccagtaattccctatactttctcttcaaacttgtaaatttgagaaaatctttgatgtcatagtttttcatgcgaagatgttgaaaccaatgtaaatgtttttcagtggttacagtatttgctatggcagGGTGATGCATTGTTTCAGACTCACGAGAATTTGGAGCATTTGGCTATGATGGAACGAGTCTTAGGTCCTATTCCTGTACACATGATCAAGAGGGCAGA

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|58030560|gb|CX728103.1|CX728103
EST:     GTTGAGCTATGCACG                         GGAGAAGCATTGTTTCAGACCCATGAAAACTTGGAGCATCTTGCTATGATG
genomic: GTTGAGCTATGCACGgtatgttgtt ... gctaccgcagGGAGAAGCATTGTTTCAGACCCATGAAAACTTGGAGCATCTTGCTATGATG
EST: gi|86250790|gb|CI007653.1|CI007653
EST:     GTGATATATGGAGTGTTGGTTGTATACTGGTTGAGCTATGCACG                         GGAGAAGCATTTTTTCAGACCCATGAAAACTTGGAGCATCTTGCTATGATG
genomic: GTGATATATGGAGTGTTGGTTGTATACTGGTTGAGCTATGCACGgtatgttgtt ... gctaccgcagGGAGAAGCATTGTTTCAGACCCATGAAAACTTGGAGCATCTTGCTATGATG
EST: gi|29632958|gb|CB637967.1|CB637967
EST:     ACCCCTGTGATATATGGAGTGTTGGTTGTATACTGGTTGAGCTATGCACG                         GGAGAAGCATTGTTTCAGACCCATGAAAACTTGGAGCATCTTGCTATGATG
genomic: ACCCCTGTGATATATGGAGTGTTGGTTGTATACTGGTTGAGCTATGCACGgtatgttgtt ... gctaccgcagGGAGAAGCATTGTTTCAGACCCATGAAAACTTGGAGCATCTTGCTATGATG
EST: gi|86421246|gb|CI057235.1|CI057235
EST:     AGCTATGCACG                         GGAGAAGCATTGTTTCAGACCCATGAAAACTTGGAGCATCTTGCTATGATG
genomic: AGCTATGCACGgtatgttgtt ... gctaccgcagGGAGAAGCATTGTTTCAGACCCATGAAAACTTGGAGCATCTTGCTATGATG
EST: gi|29670716|gb|CB666991.1|CB666991
EST:     GGTTGAGCTATGCACG                         GGAGAAGCATTGTTTCAGACCCATGAAAACTTGGAGCATCTTGCTATGATG
genomic: GGTTGAGCTATGCACGgtatgttgtt ... gctaccgcagGGAGAAGCATTGTTTCAGACCCATGAAAACTTGGAGCATCTTGCTATGATG
EST: gi|88841022|gb|CI000984.1|CI000984
EST:     ACTGGTTGAGCTATGCACG                         GGAGAAGCATTGTTTCAGACCCATGAAAACTTGGAGCATCTTGCTATGATG
genomic: ACTGGTTGAGCTATGCACGgtatgttgtt ... gctaccgcagGGAGAAGCATTGTTTCAGACCCATGAAAACTTGGAGCATCTTGCTATGATG
EST: gi|86416061|gb|CI030072.1|CI030072
EST:     TATGGAGTGTTGGTTGTATACTGNTTGAGCTATGCACG                         GGAGAAGCATTGTTTCAGACCCATGAAAACTTGGAGCATCTTGCTATGATG
genomic: TATGGAGTGTTGGTTGTATACTGGTTGAGCTATGCACGgtatgttgtt ... gctaccgcagGGAGAAGCATTGTTTCAGACCCATGAAAACTTGGAGCATCTTGCTATGATG
EST: gi|88958327|gb|CI095846.1|CI095846
EST:     GAGCTATGCACG                         GGAGAAGCATTGTTTCAGACCCATGAAAACTTGGAGCATCTTGCTATGATG
genomic: GAGCTATGCACGgtatgttgtt ... gctaccgcagGGAGAAGCATTGTTTCAGACCCATGAAAACTTGGAGCATCTTGCTATGATG
EST: gi|88845676|gb|CI008673.1|CI008673
EST:     ACCCCTGTGATATATGGAGTGTTGGTTGTATACTGGTTGAGCTATGCACG                         GGAGAAGCATTGTTTCAGACCCATGAAAACTTTGAGCATCTTGCTATGATG
genomic: ACCCCTGTGATATATGGAGTGTTGGTTGTATACTGGTTGAGCTATGCACGgtatgttgtt ... gctaccgcagGGAGAAGCATTGTTTCAGACCCATGAAAACTTGGAGCATCTTGCTATGATG
EST: gi|29675908|gb|CB672183.1|CB672183
EST:     ACCCCTGTGATATATGGAGTGTTGGTTGTATACTGGTTGAGCTATGCACG                         GGAGAAGCATTGTTTCAGACCCATGAAAACTTGGAGCATCTTGCTATGATG
genomic: ACCCCTGTGATATATGGAGTGTTGGTTGTATACTGGTTGAGCTATGCACGgtatgttgtt ... gctaccgcagGGAGAAGCATTGTTTCAGACCCATGAAAACTTGGAGCATCTTGCTATGATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttgtattctatcacaacaacagcaggatttttgagttacgaaagctaccgcagGGAGAAGCATTGTTTCAGACCCATGAAAACTTGGAGCATCTTGCTATGATGGAGAGGGTATTTGGTCCTTTGCCATGTCACATGCTCAAAAGGGCAGA
     tattctat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgttgttgggtgcaatatttggtttgtattctatcacaacaacagcaggatttttgagttacgaaagctaccgcagGGAGAAGCATTGTTTCAGACCCATGAAAACTTGGAGCATCTTGCTATGATGGAGAGGGTATTTGGTCCTTTGCCATGTCACATGCTCAAAAGGGCAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG