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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCTTCCGCCGCGAGACACGAAGAGCAGCAGCTCACAGGTAGGCCTGCGCGTCGGCGGCCATGGGAGACAGCCAGTACTCCTTCTCCCTCACCACCTTCAGgtatgtgctgccttgcgcctccctcgcccggagatcgggcgtgatctggtgcggtttcggtttcgtcatctgtggtttttgtggcgatttcgtttgcag

Basic information

species Oryza sativa
transcript LOC_Os02g42320.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g42320.4 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM5G824831_T02 (Zea mays), 5'ss of exon 2
TCTTCCGCCGC-GAGACACGAAGA-GCAGCAGCTCACAGGTAGGCCTGCGCGTCGGCGGCCATGGGAGACAGCCAGTACTCCTTCTCCCTCACCACCTTCAGgtatgtgctgccttgc--gcctccctcgcccggagatcgggcgtgatctggt--gcggtttcggtttcgtcatctgtggttt--ttgtggcgatttcgtttgcag
 |    | ||| || || | |    | |  |||| ||  |  | |   | |  | ||| ||||||| |||||||||||||||||||||||||||||||||||||  ||||| |  | |  || || |||||  |     |      |    | |  | || ||  |  |||| | | |||||||  |   |    ||||| ||    
CCACGAGTCGCCGACACTCCATCCCGGAAGAGCTAACGAGGTGACT--CCCCACCGCGCCCATGGGTGACAGCCAGTACTCCTTCTCCCTCACCACCTTCAGgttcgtgctcctctccctgcatctctcgcttgctcgccttctccgtcgagatcgggggattttgcgtcgtta-cggtggtttgatccggattttttcggtt----

upper sequence: LOC_Os02g42320.4 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM5G824831_T08 (Zea mays), 5'ss of exon 2
TCTTCCGCCGC-GAGACACGAAGA-GCAGCAGCTCACAGGTAGGCCTGCGCGTCGGCGGCCATGGGAGACAGCCAGTACTCCTTCTCCCTCACCACCTTCAGgtatgtgctgccttgc--gcctccctcgcccg---------------gagatcgggcgtgatctggtgcggtttcggtttcgtcatctgtggtttttgtggcgatttcgtttgcag
 |    | ||| || || | |    | |  |||| ||  |  | |   | |  | ||| ||||||| |||||||||||||||||||||||||||||||||||||  ||||| |  | |  || || |||||  |               |||||||||   ||| | | |  ||| ||||    | ||| |   |||||  |  ||||| ||| ||||
CCACGAGTCGCCGACACTCCATCCCGGAAGAGCTAACGAGGTGACT--CCCCACCGCGCCCATGGGTGACAGCCAGTACTCCTTCTCCCTCACCACCTTCAGgttcgtgctcctctccctgcatctctcgcttgctcgccttctccgtcgagatcgggg--gattttgcgtcgttacggtggtttgatccggattttttcggttgattttgtt-gcag

upper sequence: LOC_Os02g42320.4 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM5G824831_T04 (Zea mays), 5'ss of exon 2
TCTTCCGCCGC-GAGACACGAAGA-GCAGCAGCTCACAGGTAGGCCTGCGCGTCGGCGGCCATGGGAGACAGCCAGTACTCCTTCTCCCTCACCACCTTCAGgtatgtgctgccttgc--gcctccctcgcccg---------------gagatcgggcgtgatctggtgcggtttcggtttcgtcatctgtggtttttgtggcgatttcgtttgcag
 |    | ||| || || | |    | |  |||| ||  |  | |   | |  | ||| ||||||| |||||||||||||||||||||||||||||||||||||  ||||| |  | |  || || |||||  |               |||||||||   ||| | | |  ||| ||||    | ||| |   |||||  |  ||||||||| ||||
CCACGAGTCGCCGACACTCCATCCCGGAAGAGCTAACGAGGTGACT--CCCCACCGCGCCCATGGGTGACAGCCAGTACTCCTTCTCCCTCACCACCTTCAGgttcgtgctcctctccctgcatctctcgcttgctcgccttctccgtcgagatcgggg--gattttgcgtcgttacggtggtttgatccggattttttcggttgatttcgtt-gcag

upper sequence: LOC_Os02g42320.4 (Oryza sativa), 5'ss of exon 1
lower sequence: AT1G79210.2 (Arabidopsis thaliana), 5'ss of exon 2
---TCTTCCGCCGCGAGACACGAAGAGCAGCAGCTCACAGGTAGGCCTGCGCGTCGGCGGCCA-TGGGAGACAGCCAGTACTCCTTCTCCCTCACCACCTTCAGgtatgtgctgccttgcgcctccctcgcccggagatcgggcgtgatctggtgcggtttcggtttcgtcatctgtggtttttgtggcgatttcgtttgcag
     ||||   |   ||||| |           |  ||| | |   |    || ||    || |||| ||||| |||||||| || || ||||||||||||||||||   ||   ||   | |  |           |        || |||  |||||||   ||||   | ||   ||  ||| | | |||      |||
TAAATTTCCAGAG-ATGACACTATTTCGCATTTTTTGCAGCTTGATTTA---GTTGGTTTTCAATGGGGGACAGTCAGTACTCGTTTTCTCTCACCACCTTCAGgtattaactttgtttatcatatcaatgttatctctttctgagcatttggaacggtttc---ttcggggtttg--attcatgttgtggtttatgaaacag

upper sequence: LOC_Os02g42320.4 (Oryza sativa), 5'ss of exon 1
lower sequence: AT1G79210.3 (Arabidopsis thaliana), 5'ss of exon 2
TCTTCCGCCGCGAGACACGAAGAGCAGCAGCTCACAGGTAGGCCTGCGCGTCGGCGGCCA-TGGGAGACAGCCAGTACTCCTTCTCCCTCACCACCTTCAGgtatgtgctgccttgcgcctccctcgcccggagatcgggcgtgatctggtgcggtttcggtttcgtcatctgtggtttttgtggcgatttcgtttgcag
             ||||| |           |  ||| | |   |    || ||    || |||| ||||| |||||||| || || ||||||||||||||||||   ||   ||   | |  |           |        || |||  |||||||   ||||   | ||   ||  ||| | | |||      |||
-----------ATGACACTATTTCGCATTTTTTGCAGCTTGATTTA---GTTGGTTTTCAATGGGGGACAGTCAGTACTCGTTTTCTCTCACCACCTTCAGgtattaactttgtttatcatatcaatgttatctctttctgagcatttggaacggtttc---ttcggggtttg--attcatgttgtggtttatgaaacag

upper sequence: LOC_Os02g42320.4 (Oryza sativa), 5'ss of exon 1
lower sequence: AT1G79210.1 (Arabidopsis thaliana), 5'ss of exon 2
TCTTCCGCCGCGAGACACGAAGAGCAGCAGCTCACAGGTAGGCCTGCGCGTCGGCGGCCA-TGGGAGACAGCCAGTACTCCTTCTCCCTCACCACCTTCAGgtatgtgctgccttgcgcctccctcgcccggagatcgggcgtgatctggtgcggtttcggtttcgtcatctgtggtttttgtggcgatttcgtttgcag
                                      | |   |    || ||    || |||| ||||| |||||||| || || ||||||||||||||||||   ||   ||   | |  |           |        || |||  |||||||   ||||   | ||   ||  ||| | | |||      |||
-------------------------------------CTTGATTTA---GTTGGTTTTCAATGGGGGACAGTCAGTACTCGTTTTCTCTCACCACCTTCAGgtattaactttgtttatcatatcaatgttatctctttctgagcatttggaacggtttc---ttcggggtttg--attcatgttgtggtttatgaaacag

upper sequence: LOC_Os02g42320.4 (Oryza sativa), 5'ss of exon 1
lower sequence: Vv01s0011g01960.t01 (Vitis vinifera), 5'ss of exon 1
----TCTTCCGCCGCGAGACACGAAGAGCAGCAGCTCACAGGTAGGCCTGCGCGTCGGCGGCCATGGGAGACAGCCAGTACTCCTTCTCCCTCACCACCTTCAGgtatgtgctgccttgcgcctccctcgcccggagatcgggcgtgatctggtgcggtttcggtttcgtcatctgtggtttttgtggcgatttcgtttgcag
      ||| | | |    | |         |  |||  || |     |    ||   |   |||||||||||| || ||||| |||||||||||||| |||||||| ||  |   || | |     || |  | |||   | |      |   |   ||      ||   || ||||  |   | | |              
CCAAGTTTCAGTCCCTTTTCTCTCTACTTTCCTTCTC-TAGAT---TTTCTCTGTAAACAAACATGGGAGACAGTCAATACTCATTCTCCCTCACCACTTTCAGgtaagtaatttatt-cactagattcacatgcaga---gactcatattttcgatcttctcacatctctatgtgtg--tcacgagacag------------

upper sequence: LOC_Os02g42320.4 (Oryza sativa), 5'ss of exon 1
lower sequence: PP1S2_595V6.1 (Physcomitrella patens), 5'ss of exon 1
---TCTTCCGCCGCGAGACACGAAGAGCAGCAGCTCACAGGTAGGCCTGCGCGTCGGCGGCCATGGGAGACAGCCAGTACTCCTTCTCCCTCACCACCTTCAGgtatgtgctgccttgcgcctccctcgcccggagatcgggcgtgatctggtgcggtttcggtttcgtcatctgtggtttttgtggcgatttcgtttgcag----
     | | ||  ||     | ||      |  |||    ||| |  |      | || |||||||| |||||||||||||| ||||| || |||||||||||||  ||||  | |    |  |  | |      | ||        ||| |       || |     ||    |    |  ||   ||||| ||   | ||    
ACCGGTGCAGCTTCGGTCTTCCAACTATTTCC-CTCGTGAGTAAGTTTTAAG--CTGCAGCCATGGGGGACAGCCAGTACTCGTTCTCGCTTACCACCTTCAGgttagtgc-acatcagtcggcttttgtgacacggtcccttaatttctcgacatcgatcagaggtatcgatagatagtcatgcaacgattgcgc--ggagttta

upper sequence: LOC_Os02g42320.4 (Oryza sativa), 5'ss of exon 1
lower sequence: PP1S61_202V6.1 (Physcomitrella patens), 5'ss of exon 1
TCTTCCGCCGCGAGACACGAAGAGCAGCAGCTCACAGGTAGGCCTGCGCGTCGGCGGCCATGGGAGACAGCCAGTACTCCTTCTCCCTCACCACCTTCAGgtatgtgctgccttgcgcctccctcgcccggagatcg-ggcgtgatctggtgcggtttcggtttcgtcatctgtggtttttgtggcgatttcgtttgcag-
   | |  |        | |       |   |  | |   ||      |     | || |||||||||||||||||||| || || |||||||| ||||||| |||||  |   |   | |   | |  |||  | | ||  ||  |   ||    |      | || ||   |      || |  |||| |   ||    
CAGTGCAGCATACCCACCTATACATCCCTTGTTGCTGTGGGGAACCTTCAATTTCAGCTATGGGAGACAGCCAGTACTCGTTTTCGCTCACCACTTTCAGgtttgtgcacctcggtcgcgcagcctcttggattttgtgggatgggcctctggcaatggtagatagtgattgatc-cgcatgcgaggattacccatgtctt

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|88590186|gb|CI709019.1|CI709019
EST:     TCGGCGGCCATGGGAGACAGCCAGTACTCCTTCTCCCTCACCACCTTCAG                         CCCGTCGGGGAAGCTGGTGCAGATCGAGCACGCGCTCACCGCGGTCGGATC
genomic: TCGGCGGCCATGGGAGACAGCCAGTACTCCTTCTCCCTCACCACCTTCAGgtatgtgctg ... tcgtttgcagCCCGTCGGGGAAGCTGGTGCAGATCGAGCACGCGCTCACCGCGGTCGGATC
EST: gi|88759914|gb|CI769470.1|CI769470
EST:     TCGGCGGCCATGGGAGACAGCCAGTACTCCTTCTCCCTCACCACCTTCAG                         CCCGTCGGGGAAGCTGGTGCAGATCGAGCACGCGCTCACCGCGGTCGGATC
genomic: TCGGCGGCCATGGGAGACAGCCAGTACTCCTTCTCCCTCACCACCTTCAGgtatgtgctg ... tcgtttgcagCCCGTCGGGGAAGCTGGTGCAGATCGAGCACGCGCTCACCGCGGTCGGATC
EST: gi|87011186|gb|CI287863.1|CI287863
EST:     TCGGCGGCCATGGGAGACAGCCAGTACTCCTTCTCCCTCACCACCTTCAG                         CCCGTCGGGGAAGCTGGTGCAGATCGAGCACGCGCTCACCGCGGTCGGATC
genomic: TCGGCGGCCATGGGAGACAGCCAGTACTCCTTCTCCCTCACCACCTTCAGgtatgtgctg ... tcgtttgcagCCCGTCGGGGAAGCTGGTGCAGATCGAGCACGCGCTCACCGCGGTCGGATC
EST: gi|86847609|gb|CI288727.1|CI288727
EST:     TCGGCGGCCATGGGAGACAGCCAGTACTCCTTCTCCCTCACCACCTTCAG                         CCCGTCGGGGAAGCTGGTGCAGATCGAGCACGCGCTCACCGCGGTCGGATC
genomic: TCGGCGGCCATGGGAGACAGCCAGTACTCCTTCTCCCTCACCACCTTCAGgtatgtgctg ... tcgtttgcagCCCGTCGGGGAAGCTGGTGCAGATCGAGCACGCGCTCACCGCGGTCGGATC
EST: gi|88391828|gb|CI603347.1|CI603347
EST:     TCGGCGGCCATGGGAGACAGCCAGTACTCCTTCTCCCTCACCACCTTCAG                         CCCGTCGGGGAAGCTGGTGCAGATCGAGCACGCGCTCACCGCCGGTCGGAT
genomic: TCGGCGGCCATGGGAGACAGCCAGTACTCCTTCTCCCTCACCACCTTCAGgtatgtgctg ... tcgtttgcagCCCGTCGGGGAAGCTGGTGCAGATCGAGCACGCGCTCACCGC-GGTCGGAT
EST: gi|88745867|gb|CI769227.1|CI769227
EST:     TCGGCGGCCATGGGAGACAGCCAGTACTCCTTCTCCCTCACCACCTTCAG                         CCCGTCGGGGAAGCTGGTGCAGATCGAGCACGCGCTCACCGNGGTCGGATT
genomic: TCGGCGGCCATGGGAGACAGCCAGTACTCCTTCTCCCTCACCACCTTCAGgtatgtgctg ... tcgtttgcagCCCGTCGGGGAAGCTGGTGCAGATCGAGCACGCGCTCACCGCGGTCGGATC
EST: gi|88294492|gb|CI667466.1|CI667466
EST:     TCGGCGGCCATGGGAGACAGCCAGTACTCCTTCTCCCTCACCACCTTCAG                         CCCGTCGGGGAAGCTGGTGCAGATCGAGCACGCGCTCACCGCGGTCGGATC
genomic: TCGGCGGCCATGGGAGACAGCCAGTACTCCTTCTCCCTCACCACCTTCAGgtatgtgctg ... tcgtttgcagCCCGTCGGGGAAGCTGGTGCAGATCGAGCACGCGCTCACCGCGGTCGGATC