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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tagcaattaaaacgttctcattccattataattcagttatgtcaggtaaaccatactgacttaatgtaccaatgcatgtattaatggatgctctctgaagACTAGTGAAAATTTCGAGGTTCTACAAGGTATTCCTGCAGAGAGAATGATGATAGAGACAGACTCTCCATACTGTGATATTAAAAATACTCATGCTGGAA

Basic information

species Oryza sativa
transcript LOC_Os07g06410.5
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g06410.5 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G095969_T01 (Zea mays), 3'ss of exon 8
------------------------tagcaattaaaacgttct-cattccattataattcagttatgtcaggtaaaccatactgacttaatgtaccaatgcatgtattaatggatgctctctgaagACTAGTGAAAATTTCGAGGTTCTACAAGGTATTCCTGCAGAGAGAATGATGATAGAGACAGACTCTCCATACTGTGATATTAAAAATACTCATGCTGGAA
                         | ||| |  |   ||    | ||  ||||  || |  | |  |||   |  || |      | |        |||| || ||||||| ||||||||||| ||||  |||||| | |||||||||| ||| |||||||  |||||  |||||||||| ||||| |||||||| |||||                       
tttccatttggatattgataactgaaacaactgtagaatttgatactctgttattcttta--tctcccagtcgagtcagatgattgtgaatcgtggttgcagGTGTTAATGGTTGCTCTCTGAAAACTAACGAAAATCTTGAGGTTCTACGAGGCATTCCTGTCGAGAGGTTGATGATAGAAACAGATTCTCCATATTGTGA-----------------------

upper sequence: LOC_Os07g06410.5 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G384762_T01 (Zea mays), 3'ss of exon 8
------------------------tagcaattaaaacgttct-cattccattataattcagttatgtcaggtaaaccatactgacttaatgtaccaatgcatgtattaatggatgctctctgaagACTAGTGAAAATTTCGAGGTTCTACAAGGTATTCCTGCAGAGAGAATGATGATAGAGACAGACTCTCCATACTGTGATATTAAAAATACTCATGCTGGAA
                         | ||| |  ||  ||    | ||  ||||  || |  | |  |||      || |      |          |||| || ||||||| ||||||||||| ||||  |||||| | |||||||||| ||| |||||||  |||||  |||||||||| ||| | |||||||| |||||                       
tttccatttggatattgataactgaaacaactgtaaaatttgatactctgttattcttta--tctcccagtcgggtcagatgattgtgcatcgtggttgcagGTGTTAATGGTTGCTCTCTGAAAACTAACGAAAATCTTGAGGTTCTACGAGGCATTCCTGTTGAGAGGTTGATGATAGAAACATATTCTCCATATTGTGA-----------------------

upper sequence: LOC_Os07g06410.5 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G058862_T01 (Zea mays), 3'ss of exon 1
------------------------tagcaattaaaacgttct-cattccattataattcagttatgtcaggtaaaccatactgacttaatgtaccaatgcatgtattaatggatgctctctgaagACTAGTGAAAATTTCGAGGTTCTACAAGGTATTCCTGCAGAGAGAATGATGATAGAGACAGACTCTCCATACTGTGATATTAAAAATACTCATGCTGGAA
                         | ||| |  ||  ||    | ||  ||||  || |  | |  |||      || |      |          |||| || | ||||| ||||||||||| ||||  |||||| | |||||||||| ||| |||||||  |||||  |||||||||| ||||| |||||||| |||||                       
tttccatttggatattgataactgaaacaactgtaaaatttgatactctgttattcttta--tctcccagtcgggtcagatgattgtgcatcgtggttgcagGTGT-AATGGTTGCTCTCTGAAAACTAACGAAAATCTTGAGGTTCTACGAGGCATTCCTGTCGAGAGGTTGATGATAGAAACAGATTCTCCATATTGTGAC----------------------

upper sequence: LOC_Os07g06410.5 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G051032_T01 (Zea mays), 3'ss of exon 10
------------------------tagcaattaaaacgttct-cattccattataattcagttatgtcaggtaaaccatactgacttaatgtaccaatgcatgtattaatggatgctctctgaagACTAGTGAAAATTTCGAGGTTCTACAAGGTATTCCTGCAGAGAGAATGATGATAGAGACAGACTCTCCATACTGTGATATTAAAAATACTCATGCTGGAA
                         | ||| || ||  ||    | ||  ||||  ||    | |   ||      || |      |          |||| || ||||||| ||||||||||| ||||  |||||| | |||||||||| ||| |||||||  |||||  |||||||||| ||||| |||||||| |||||                       
tttccatttggatattgataactgaaacaactataaaatttgatactctgttattctttg--tctcctagtggggtcagatgattatgcatcgtggttgcagGTGTTAATGGTTGCTCTCTGAAAACTAACGAAAATCTTGAGGTTCTACGAGGCATTCCTGTCGAGAGGTTGATGATAGAAACAGATTCTCCATATTGTGA-----------------------

upper sequence: LOC_Os07g06410.5 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G137367_T01 (Zea mays), 3'ss of exon 12
-----------------------tagcaattaaaacgttctcattccattataattcagttatgtcaggtaaaccatactgacttaatgtaccaatgcatgtattaatggatgctctctgaagACTAGTGAAAATTTCGAGGTTCTACAAGGTATTCCTGCAGAGAGAATGATGATAGAGACAGACTCTCCATACTGTGATATTAAAAATACTCATGCTGGAA
                        | ||| |  ||   | | || |  |  || |     | |  |||      || |      |          |||| || ||||||| ||||||||||| ||||  |||||| | |||||||||| ||| |||||||  |||||  |||||||||| ||||| |||||||| |||||                       
tccattttggatattgataactgaaacaactgtaaaaatttgatactctgttattctttatctcccagtcgggtcagatgattgtgcatcgtggttgcagGTGTTAATGGTTGCTCTCTGAAAACTAACGAAAATCTTGAGGTTCTACGAGGCATTCCTGTTGAGAGGTTGATGATAGAAACAGATTCTCCATATTGTGA-----------------------

upper sequence: LOC_Os07g06410.5 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA19G38780.1 (Glycine max), 3'ss of exon 9
-------------------tagcaattaaaacgttctcattccattataattcagttatgtcaggtaaaccatac---tgacttaatgtaccaatg-catgtattaatggatgctctctgaagACTAGTGAAAATTTCGAGGTTCTACAAGGTATTCCTGCAGAGAGAATGATGATAGAGACAGACTCTCCATACTGTGATATTAAAAATACTCATGCTGGAA
                    ||  |||  |  ||    |||  ||   | | |||| |  ||   | ||   |||   | | | | | |  |  || || | || ||||| |||||||||||||| | ||| ||  | || ||| |  | |||||||| |  |||||||||||||| ||||| ||||| |||||||||||                       
ttgcataaagtttcactttcagatattggattgtggggattaaatagcattccagtcaaatcccatgaatattacccatcattgattctgtctgtggcagGCATAAATGGGTGCTCTCTGAAGACGACTGAGAACCTTGATGTTGTTAAGGGTATTCCAGTTGAGAGAATGATGATTGAGACGGACTCACCATACTGTGA-----------------------

upper sequence: LOC_Os07g06410.5 (Oryza sativa), 3'ss of exon 7
lower sequence: Vv08s0032g01170.t01 (Vitis vinifera), 3'ss of exon 9
-----tagcaattaaaacgttctcattccat-tataa---ttcagtta--tgtcaggtaaaccatactgacttaa-------------tgtaccaatgcatgtattaatggatgctctctgaagACTAGTGAAAATTTCGAGGTTCTACAAGGTATTCCTGCAGAGAGAATGATGATAGAGACAGACTCTCCATACTGTGATATTAAAAATACTCATGCTGGAA
     |  |   |      || |  |    | ||| |   |||| |||  |||||| | || | || | |  |               |||||| |   | || | ||||| |||||||||||||||  ||||||| | || ||| ||   ||||||||||  |||||| ||||||| |||||||| |||||||| |||||                       
ataattttctgcttggtttttgttttcttgtatatgacttttcacttagatgtcagatgaatcttaataatctttgttcttttttctttgtaccca-atagGTGTAAATGGTTGCTCTCTGAAGACTGCTGAAAATCTTGAAGTTGTAAGGGGTATTCCTGTTGAGAGACTGATGATTGAGACAGATTCTCCATATTGTGA-----------------------

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|88970863|gb|CI385444.1|CI385444
EST:     AACTTCAGAGGACCGTGATAAGCTTCTTTCCTTTGAAAAGATGTTTATAG                         ACTAGTGAAAATTTCGAGGTTCTACAAGGTATTCCTGCAGAGAGAATGATG
genomic: AACTTCAGAGGACCGTGATAAGCTTCTTTCCTTTGAAAAGATGTTTATAGgtcatctccc ... ctctctgaagACTAGTGAAAATTTCGAGGTTCTACAAGGTATTCCTGCAGAGAGAATGATG
EST: gi|88303042|gb|CI505654.1|CI505654
EST:     GATGTTTATAG                         ACTAGTGAAAATTTCGAGGTTCTACAAGGTATTCCTGCAGAGAGAATGATG
genomic: GATGTTTATAGgtcatctccc ... ctctctgaagACTAGTGAAAATTTCGAGGTTCTACAAGGTATTCCTGCAGAGAGAATGATG
EST: gi|66923817|gb|CX110665.1|CX110665
EST:     AACTTCAGAGGACCGTGATAAGCTTCTTTCCTTTGAAAAGATGTTTATAG                         ACTAGTGAAAATCTCGAGGTTCTACAAGGTATTCCTGCAGAGAGAATGATG
genomic: AACTTCAGAGGACCGTGATAAGCTTCTTTCCTTTGAAAAGATGTTTATAGgtcatctccc ... ctctctgaagACTAGTGAAAATTTCGAGGTTCTACAAGGTATTCCTGCAGAGAGAATGATG
EST: gi|88318440|gb|CI505844.1|CI505844
EST:     CTTCTTTCCTTTGAAAAGATGTTTATAG                         ACTAGTGAAAATTTCGAGGTTCTACAAGGTATTCCTGCAGAGAGAATGATG
genomic: CTTCTTTCCTTTGAAAAGATGTTTATAGgtcatctccc ... ctctctgaagACTAGTGAAAATTTCGAGGTTCTACAAGGTATTCCTGCAGAGAGAATGATG
EST: gi|88566483|gb|CI497200.1|CI497200
EST:     AGCTTCTTTCCTTTGAAAAGATGTTTATAG                         ACTAGTGAAAATTTCGAGGTTCTACAAGGTATTCCTGCAGAGAGAATGATG
genomic: AGCTTCTTTCCTTTGAAAAGATGTTTATAGgtcatctccc ... ctctctgaagACTAGTGAAAATTTCGAGGTTCTACAAGGTATTCCTGCAGAGAGAATGATG
EST: gi|88562753|gb|CI493470.1|CI493470
EST:     GGACCGTGATAAGCTTCTTTCCTTTGAAAAGATGTTTATAG                         ACTAGTGAAAATTTCGAGGTTCTACAAGGTATTCCTGCAGAGAGAATGATG
genomic: GGACCGTGATAAGCTTCTTTCCTTTGAAAAGATGTTTATAGgtcatctccc ... ctctctgaagACTAGTGAAAATTTCGAGGTTCTACAAGGTATTCCTGCAGAGAGAATGATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtaaaccatactgacttaatgtaccaatgcatgtattaatggatgctctctgaagACTAGTGAAAATTTCGAGGTTCTACAAGGTATTCCTGCAGAGAGAATGATGATAGAGACAGACTCTCCATACTGTGATATTAAAAATACTCATGCTGGAA
                                           tgctctct  CT-rich tract
                              atgtattaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tagcaattaaaacgttctcattccattataattcagttatgtcaggtaaaccatactgacttaatgtaccaatgcatgtattaatggatgctctctgaagACTAGTGAAAATTTCGAGGTTCTACAAGGTATTCCTGCAGAGAGAATGATGATAGAGACAGACTCTCCATACTGTGATATTAAAAATACTCATGCTGGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA