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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGAAGCTGATTCTCGCCAAGGGCAACCCGCACTTCATCTGCGACGCCCGCGTGCTCGTCAAGCCATACAAGGAGAAGGGCAAGGTCCCCGACAAGTACAGgcaagccgagcttacttacagtccacattgcctctctaggttgatcccctataaccaatttgtaacttgctgttactttgcag

Basic information

species Oryza sativa
transcript LOC_Os07g48410.2
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g48410.2 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G311665_T01 (Zea mays), 5'ss of exon 3
TGAAGCTGATTCTCGCCAAGGGCAACCCGCACTTCATCTGCGACGCCCGCGTGCTCGTCAAGCCATACAAGGAGAAGGGCAAGGTCCCCGACAAGTACAGgcaagccgagcttacttacagtccacattgc-ctctcta-ggttgatcccct---ataaccaatttgtaacttgctgttactttgcag
|||||||||| || |||||||||||||||||||||||||||||||| ||||||||||| ||||| |||||||||||||||||||||||||||||||||||||| |||   |          | ||  | || ||  ||| | | ||   | |   || ||| ||   |    ||||| | || |||||
TGAAGCTGATCCTGGCCAAGGGCAACCCGCACTTCATCTGCGACGCGCGCGTGCTCGTGAAGCCCTACAAGGAGAAGGGCAAGGTCCCCGACAAGTACAGgcacgcctcccccttccttttttcaattcgctctacctacgatcgacatcatgtcatgaccgatcgctccgctgctgctgctctgcag

upper sequence: LOC_Os07g48410.2 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA12G01350.1 (Glycine max), 5'ss of exon 3
TGAAGCTGATTCTCGCCAAGGGCAACCCGCACTTCATCTGCGACGCCCGCGTGCTCGTCAAGCCATACAAGGAGAAGGGCAAGGTCCCCGACAAGTACAGgcaagccgagctt--acttacagtccacattgcctctctaggttgatcccctataaccaatttgta---acttgctgttactttgcag---------
||||||| |||||  | || || ||||| || ||  | || || || || ||||| || ||||| ||||||||||||||||| ||||| ||||||||||||||  ||    ||  |||   |    | | |   | | |  |||  |||| |        |||| |    ||  || ||  ||              
TGAAGCTTATTCTATCTAAAGGAAACCCTCATTTTGTGTGTGATGCACGAGTGCTTGTTAAGCCTTACAAGGAGAAGGGCAAAGTCCCAGACAAGTACAGgcaccccctctttctactcttatgtta-actttttgtttttgttattcccttgagtttgttttgaatgtgctcactattgtttcttgtgatttgcag

upper sequence: LOC_Os07g48410.2 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA11G01780.1 (Glycine max), 5'ss of exon 3
------TGAAGCTGATTCTCGCCAAGGGCAACCCGCACTTCATCTGCGACGCCCGCGTGCTCGTCAAGCCATACAAGGAGAAGGGCAAGGTCCCCGACAAGTACAGgcaagccgagcttacttacagtccacattgcctctctaggttgatcccctataaccaatttgtaacttgctgttactttgcag
      |||  || ||  |  |||| || || || || || ||||| ||  | || || || |||||||| |||||||||||||| || ||||| ||||||||         |  | ||       ||  | ||        |    | | |   | | || ||||| | |  ||| |           
AGACAGTGAGACTCATATTATCCAAAGGGAATCCTCATTTTATCTGTGATTCACGTGTACTTGTCAAGCCCTACAAGGAGAAGGGAAAAGTCCCTGACAAgtaagtatgcatcatgtttttaattggtttatatcttactatt--cctaaactaatgtgactaatttatta--tgcag-----------

upper sequence: LOC_Os07g48410.2 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA12G01350.2 (Glycine max), 5'ss of exon 3
------TGAAGCTGATTCTCGCCAAGGGCAACCCGCACTTCATCTGCGACGCCCGCGTGCTCGTCAAGCCATACAAGGAGAAGGGCAAGGTCCCCGACAAGTACAGgcaagccgagctt--acttacagtccacattgcctctctaggttgatcccctataaccaatttgta---acttgctgttactttgcag---------
      ||||||| |||||  | || || ||||| || ||  | || || || || ||||| || ||||| ||||||||||||||||| ||||| ||||||||||||||  ||    ||  |||   |    | | |   | | |  |||  |||| |        |||| |    ||  || ||  ||              
AGACCGTGAAGCTTATTCTATCTAAAGGAAACCCTCATTTTGTGTGTGATGCACGAGTGCTTGTTAAGCCTTACAAGGAGAAGGGCAAAGTCCCAGACAAgtacaggcaccccctctttctactcttatgtta-actttttgtttttgttattcccttgagtttgttttgaatgtgctcactattgtttcttgtgatttgcag

upper sequence: LOC_Os07g48410.2 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA01G43700.1 (Glycine max), 5'ss of exon 3
------TGAAGCTGATTCTCGCCAAGGGCAACCCGCACTTCATCTGCGACGCCCGCGTGCTCGTCAAGCCATACAAGGAGAAGGGCAAGGTCCCCGACAAGTACAGgcaagccgagcttacttacagtccacattgcctctctaggttgatcccctataaccaatttgtaacttgctgttactttgcag
      |||  || ||  |  |||| || || || || || ||||| ||  | || || || |||||||| |||||||||||||| || ||||| ||||||||         |  | ||  | |  |    |  |  ||  |||  ||  |   |||  || |  |||| |||   |  || | |||||
AGACAGTGAGACTCATATTATCCAAAGGGAATCCTCATTTTATCTGTGATTCACGTGTACTTGTCAAGCCCTACAAGGAGAAGGGAAAAGTCCCTGACAAgtaagtatgcatcatgttt--taattggtttctgtatcttacta--ttcctaaactaatacta--ttgtgactaatt--tattatgcag

upper sequence: LOC_Os07g48410.2 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA12G01340.1 (Glycine max), 5'ss of exon 4
------TGAAGCTGATTCTCGCCAAGGGCAACCCGCACTTCATCTGCGACGCCCGCGTGCTCGTCAAGCCATACAAGGAGAAGGGCAAGGTCCCCGACAAGTACAGgcaagccgagctta----cttacagtccacattgcctctctaggttgatcccctataaccaatttgta---acttgctgttactttgcag---------
      ||||||| |||||  | || || ||||| || ||  | || || || || ||||| || ||||| ||||||||||||||||| ||||| ||||||||||||||  ||    ||     ||||   |     ||   | | |  |||  |||| |        |||| |    ||  || ||  ||              
AGACCGTGAAGCTTATTCTATCTAAAGGAAACCCTCATTTTGTGTGTGATGCACGAGTGCTTGTTAAGCCTTACAAGGAGAAGGGCAAAGTCCCAGACAAgtacaggcaccccctctttctactcttatgttatcttttttttgtttttgttattcccttgagtttgttttgaatgtgctcactattgtttcttgtgatttgcag

upper sequence: LOC_Os07g48410.2 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA09G35990.1 (Glycine max), 5'ss of exon 7
TGAAGCTGATTCTCGCCAAGGGCAACCCGCACTTCATCTGCGACGCCCGCGTGCTCGTCAAGCCATACAAGGAGAAGGGCAAGGTCCCCGACAAGTACAGgcaagccgagcttacttacagtcc-acattgcctctctaggttgatcccctataaccaatttgtaa----cttgctgttactttgcag------------------------------
||||||| |||||  |||| || || || || ||  | || || || || ||||| || ||||| ||||||||||||||||| ||||| ||||||||||||||  |    | |  ||  | ||  |  ||  || | |   ||  |  | | |  |   || || |    ||||   ||| |||| |                               
TGAAGCTTATTCTATCCAAAGGAAATCCTCATTTTGTGTGTGATGCTCGAGTGCTTGTTAAGCCTTACAAGGAGAAGGGCAAAGTCCCAGACAAGTACAGgcacccaccccctctttctactcttatgttatcttttttttttcttttcttttttctttttggttattgtcttgagtttattttgaatgtcctcattgatgtttcttgtgatttgcag

upper sequence: LOC_Os07g48410.2 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA09G35980.1 (Glycine max), 5'ss of exon 4
------TGAAGCTGATTCTCGCCAAGGGCAACCCGCACTTCATCTGCGACGCCCGCGTGCTCGTCAAGCCATACAAGGAGAAGGGCAAGGTCCCCGACAAGTACAGgcaagccgagcttacttacagtcc-acattgcctctctaggttgatcccctataaccaatttgtaa----cttgctgttactttgcag------------------------------
      ||||||| |||||  |||| || || || || ||  | || || || || ||||| || ||||| ||||||||||||||||| ||||| ||||||||||||||  |    | |  ||  | ||  |  ||  || | |   ||  |  | | |  |   || || |    ||||   ||| |||| |                               
AGACTGTGAAGCTTATTCTATCCAAAGGAAATCCTCATTTTGTGTGTGATGCTCGAGTGCTTGTTAAGCCTTACAAGGAGAAGGGCAAAGTCCCAGACAAgtacaggcacccaccccctctttctactcttatgttatcttttttttttcttttcttttttctttttggttattgtcttgagtttattttgaatgtcctcattgatgtttcttgtgatttgcag

upper sequence: LOC_Os07g48410.2 (Oryza sativa), 5'ss of exon 3
lower sequence: AT3G63450.1 (Arabidopsis thaliana), 5'ss of exon 3
------TGAAGCTGATTCTCGCCAAGGGCAACCCGCACTTCATCTGCGACGCCCGCGTGCTCGTCAAGCCATACAAGGAGAAGGGCAAGGTCCCCGACAAGTACAGgcaagccgagcttacttacagtccacattgcctctctaggttgatcccctataaccaatttgtaacttgctgttactttgcag
      |||||   ||||| ||||| || ||||| |||||  | ||  |  || | || || || ||||| ||||||||||| ||||| ||||| |||||||||||| |    |   || | | |         |||  ||      | ||| | |     |  |||| |     ||| | |       
AGACTGTGAAGAGCATTCTGGCCAAAGGGAACCCTCACTTTGTGTGTCATTCCAGGGTTCTTGTTAAGCCTTACAAGGAGAAAGGCAAAGTCCCAGACAAgtacaggtactttggcttttcctcc---ttgagctgctcctgattcctcatctctttacgacgctttg-attcctctgctgcag-----

upper sequence: LOC_Os07g48410.2 (Oryza sativa), 5'ss of exon 3
lower sequence: AT3G51950.1 (Arabidopsis thaliana), 5'ss of exon 5
TGAAGCTGATTCTCGCCAAGGGCAACCCGCACTTCATCTGCGACGCCCGCGTGCTCGTCAAGCCATACAAGGAGAAGGGCAAGGTCCCCGACAAGTACAGgcaagccga--gct--tacttacagtccacattgcctctctaggttgatcccctataaccaatttgtaacttgctgttactt-tgcag
| |||   ||||||||||| || || || |||||  | || ||  || | || || |||||||| ||||||||||| ||||| ||||| ||||| |||||| |     |  |||  || |   |   |  ||    |  |  | ||| | || |  | ||  | |||    ||| |||  || |||||
TTAAGAGCATTCTCGCCAAAGGGAATCCTCACTTTGTGTGTGATTCCAGAGTTCTTGTCAAGCCTTACAAGGAGAAAGGCAAAGTCCCTGACAAATACAGgtacttatattgctagtattagtaactcttatactttggcctgattg-ttccttgaatcccttgtgtttactgcggtttgttgtgcag

upper sequence: LOC_Os07g48410.2 (Oryza sativa), 5'ss of exon 3
lower sequence: AT3G63450.3 (Arabidopsis thaliana), 5'ss of exon 3
TGAAGCTGATTCTCGCCAAGGGCAACCCGCACTTCATCTGCGACGCCCGCGTGCTCGTCAAGCCATACAAGGAGAAGGGCAAGGTCCCCGACAAGTACAGgcaagccgagcttacttacagtccacattgcctctctaggttgatcccctataaccaatttgtaacttgctgttactttgcag
|||||   ||||| ||||| || ||||| |||||  | ||  |  || | || || || ||||| ||||||||||| ||||| ||||| |||||||||||| |    |   || | | |         |||  ||      | ||| | |     |  |||| |     ||| | |       
TGAAGAGCATTCTGGCCAAAGGGAACCCTCACTTTGTGTGTCATTCCAGGGTTCTTGTTAAGCCTTACAAGGAGAAAGGCAAAGTCCCAGACAAGTACAGgtactttggcttttcctcc---ttgagctgctcctgattcctcatctctttacgacgctttg-attcctctgctgcag-----

upper sequence: LOC_Os07g48410.2 (Oryza sativa), 5'ss of exon 3
lower sequence: Vv13s0158g00370.t01 (Vitis vinifera), 5'ss of exon 4
------TGAAGCTGATTCTCGCCAAGGGCAACCCGCACTTCATCTGCGACGCCCGCGTGCTCGTCAAGCCATACAAGGAGAAGGGCAAGGTCCCCGACAAGTACAGgcaagccga---gcttacttacagtccacattgcctctctaggttgatcccctataaccaatttgtaacttgctgttactttgcag
      ||||||| ||| | || || || ||||| || ||  | || || || || || || || ||||| || |||||||||||||| ||||| ||||||||||||||  |      |||  |   |      | |||  | | | |||  |||    | |    |  ||    |   | ||  ||| |||
AGACAGTGAAGCTCATTTTGGCTAAAGGGAACCCTCATTTTGTTTGTGATGCTCGGGTTCTGGTTAAGCCCTATAAGGAGAAGGGCAAAGTCCCGGACAAgtacaggcactctcttctgctctccctctaaatgccttggtttttttggtgcatcttgcagagt--agctgatggtaatttttggttt-cag

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|58597206|gb|CK007734.1|CK007734
EST:     GTGCTCGTCAAGCCATACAAGGAGAAGGGCAAGGTCCCCGACAAGTACAG                         GAAGCAGCACCAGCCGGGCGAGAGGGTGGACTTCTCCAGCTGCACTACTCC
genomic: GTGCTCGTCAAGCCATACAAGGAGAAGGGCAAGGTCCCCGACAAGTACAGgcaagccgag ... tactttgcagGAAGCAGCACCAGCCGGGCGAGAGGGTGGACTTCTCCAGCTGCACTACTCC
EST: gi|58598485|gb|CK009013.1|CK009013
EST:     GTGCTCGTCAAGCCATACAAGGAGAAGGGCAAGGTCCCCGACAAGTACAG                         GAAGCAGCACCAGCCGGGCGAGAGGGTGGACTTCTCCAGCTGCACTACTCC
genomic: GTGCTCGTCAAGCCATACAAGGAGAAGGGCAAGGTCCCCGACAAGTACAGgcaagccgag ... tactttgcagGAAGCAGCACCAGCCGGGCGAGAGGGTGGACTTCTCCAGCTGCACTACTCC
EST: gi|86904436|gb|CI308646.1|CI308646
EST:     GTGCTCGTCAAGCCATACAAGGAGAAGGGCAAGGTCCCCGACAAGTACAG                         GAAGCAGCACCAGCCGGGCGAGAGGGTGGACTTCTCCAGCTGCACTACTCC
genomic: GTGCTCGTCAAGCCATACAAGGAGAAGGGCAAGGTCCCCGACAAGTACAGgcaagccgag ... tactttgcagGAAGCAGCACCAGCCGGGCGAGAGGGTGGACTTCTCCAGCTGCACTACTCC
EST: gi|58603862|gb|CK014390.1|CK014390
EST:     GGGCAAGGTCCCCGACAAGTACAG                         GAAGCAGCACCAGCCGGGCGAGAGGGTGGACTTCTCCAGCTGCACTACTCC
genomic: GGGCAAGGTCCCCGACAAGTACAGgcaagccgag ... tactttgcagGAAGCAGCACCAGCCGGGCGAGAGGGTGGACTTCTCCAGCTGCACTACTCC
EST: gi|58673551|gb|CK062237.1|CK062237
EST:     GTGCTCGTCAAGCCATACAAGGAGAAGGGCAAGGTCCCCGACAAGTACAG                         GAAGCAGCACCAGCCGGGCGAGAGGGTGGACTTCTCCAGCTGCACTACTCC
genomic: GTGCTCGTCAAGCCATACAAGGAGAAGGGCAAGGTCCCCGACAAGTACAGgcaagccgag ... tactttgcagGAAGCAGCACCAGCCGGGCGAGAGGGTGGACTTCTCCAGCTGCACTACTCC
EST: gi|58666711|gb|CK055397.1|CK055397
EST:     GTGCTCGTCAAGCCATACAAGGAGAAGGGCAAGGTCCCCGACAAGTACAG                         GAAGCAGCACCAGCCGGGCGAGAGGGTGGACTTCTCCAGCTGCACTACTCC
genomic: GTGCTCGTCAAGCCATACAAGGAGAAGGGCAAGGTCCCCGACAAGTACAGgcaagccgag ... tactttgcagGAAGCAGCACCAGCCGGGCGAGAGGGTGGACTTCTCCAGCTGCACTACTCC
EST: gi|58607189|gb|CK035222.1|CK035222
EST:     GTGCTCGTCAAGCCATACAAGGAGAAGGGCAAGGTCCCCGACAAGTACAG                         GAAGCGAGCACCAGCCGGGCGAGAGGGTGGACTTCTCCAGCTGCACTACTC
genomic: GTGCTCGTCAAGCCATACAAGGAGAAGGGCAAGGTCCCCGACAAGTACAGgcaagccgag ... tactttgcagGAAGC-AGCACCAGCCGGGCGAGAGGGTGGACTTCTCCAGCTGCACTACTC
EST: gi|58676590|gb|CK065277.1|CK065277
EST:     GTGCTCGTCAAGCCATACAAGGAGAAGGGCAAGGTCCCCGACAAGTACAG                         GAAGCAGCACCAGCCGGGCGAGAGGGTGGACTTCTCCAGCTGCACTACTCC
genomic: GTGCTCGTCAAGCCATACAAGGAGAAGGGCAAGGTCCCCGACAAGTACAGgcaagccgag ... tactttgcagGAAGCAGCACCAGCCGGGCGAGAGGGTGGACTTCTCCAGCTGCACTACTCC
EST: gi|7652196|gb|AU089733.1|AU089733
EST:     GTGCTCGTCAAGCCATACAAGGAGAAGGGCAAGGTCCCCGACAAGTACAG                         GAAGCAGCACCAGCCGGGCGAGAGGGTGGACTTCTCCAGCTGCACTACTCC
genomic: GTGCTCGTCAAGCCATACAAGGAGAAGGGCAAGGTCCCCGACAAGTACAGgcaagccgag ... tactttgcagGAAGCAGCACCAGCCGGGCGAGAGGGTGGACTTCTCCAGCTGCACTACTCC
EST: gi|58660017|gb|CK048697.1|CK048697
EST:     GTGCTCGTCAAGCCATACAAGGAGAAGGGCAAGGTCCCCGACAAGTACAG                         GAAGCAGCACCAGCCGGGCGAGAGGGTGGACTTCTCCAGCTGCACTACTCC
genomic: GTGCTCGTCAAGCCATACAAGGAGAAGGGCAAGGTCCCCGACAAGTACAGgcaagccgag ... tactttgcagGAAGCAGCACCAGCCGGGCGAGAGGGTGGACTTCTCCAGCTGCACTACTCC
EST: gi|29666734|gb|CB663009.1|CB663009
EST:     GTGCTCGTCAAGCCATACAAGGAGAAGGGCAAGGTCCCCGACAAGTACAG                         GAAGCAGCACCAGCCGGGCGAGAGGGTGGACTTCTCCAGCTGCACTACTCC
genomic: GTGCTCGTCAAGCCATACAAGGAGAAGGGCAAGGTCCCCGACAAGTACAGgcaagccgag ... tactttgcagGAAGCAGCACCAGCCGGGCGAGAGGGTGGACTTCTCCAGCTGCACTACTCC
EST: gi|58599584|gb|CK010112.1|CK010112
EST:     GTGCTCGTCAAGCCATACAAGGAGAAGGGCAAGGTCCCCGACAAGTACAG                         GAAGCAGCACCAGCCGGGCGAGAGGGTGGACTTCTCCAGCTGCACTACTCC
genomic: GTGCTCGTCAAGCCATACAAGGAGAAGGGCAAGGTCCCCGACAAGTACAGgcaagccgag ... tactttgcagGAAGCAGCACCAGCCGGGCGAGAGGGTGGACTTCTCCAGCTGCACTACTCC
EST: gi|58671842|gb|CK060528.1|CK060528
EST:     GTGCTCGTCAAGCCATACAAGGAGAAGGGCAAGGTCCCCGACAAGTACAG                         GAAGCAGCACCAGCCGGGCGAGAGGGTGGACTTCTCCAGCTGCACTACTCC
genomic: GTGCTCGTCAAGCCATACAAGGAGAAGGGCAAGGTCCCCGACAAGTACAGgcaagccgag ... tactttgcagGAAGCAGCACCAGCCGGGCGAGAGGGTGGACTTCTCCAGCTGCACTACTCC
EST: gi|58612737|gb|CK040449.1|CK040449
EST:     AGGGCAAGGTCCCCGACAAGTACAG                         GAAGCAGCACCAGCCGGGCGAGAGGGTGGACTTCTCCAGCTGCACTACTCC
genomic: AGGGCAAGGTCCCCGACAAGTACAGgcaagccgag ... tactttgcagGAAGCAGCACCAGCCGGGCGAGAGGGTGGACTTCTCCAGCTGCACTACTCC
EST: gi|29681057|gb|CB677332.1|CB677332
EST:     GTGCTCGTCAAGCCATACAAGGAGAAGGGCAAGGTCCCCGACAAGTACAG                         GAAGCAGCACCAGCCGGGCGAGAGGGTGGACTTCTCCAGCTGCACTACTCC
genomic: GTGCTCGTCAAGCCATACAAGGAGAAGGGCAAGGTCCCCGACAAGTACAGgcaagccgag ... tactttgcagGAAGCAGCACCAGCCGGGCGAGAGGGTGGACTTCTCCAGCTGCACTACTCC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGAAGCTGATTCTCGCCAAGGGCAACCCGCACTTCATCTGCGACGCCCGCGTGCTCGTCAAGCCATACAAGGAGAAGGGCAAGGTCCCCGACAAGTACAGgcaagccgagcttacttacagtccacattgcctctctaggttgatcccctataaccaatttgtaacttgctgttactttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA