Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGTACAGTACAAGAACGTGATGTTTACAGTATGGGATGTCGGTGGCCAAGAGAAGTTGAGGCCTCTGTGGAGGCATTACTTCAATAATACGGATGGTTTGgtatgttttgtttcctttgtggttatctttttgggaatacgtgaaagatttgtgcatcgttgcattaaagaaggaaagaagtggttatttgattttgaca...

Basic information

species Oryza sativa
transcript LOC_Os02g47110.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g47110.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G106795_T03 (Zea mays), 5'ss of exon 3
AGTACAGTACAAGAACGTGATGTTTACAGTATGGGATGTCGGTGGCCAAGAGAAGTTGAGGCCTCTGTGGAGGCATTACTTCAATAATACGGATGGTTTGgtatgttttgtttcctttgtggttatctttttgggaatacgtgaaagatttgtgcatcgttgcattaaagaaggaaaga-agtggttatttgattttgaca--
||| || |||||||| ||||||||||| || |||||||| ||||||||||| |||||||||||  |||||||||| |||||||| ||||| ||||| |||||||||||  | | ||||   |  | |||| ||  |  |  |  |   |||||  || |||    |  |   |    |  | |  || ||   || |      
AGTTCAATACAAGAATGTGATGTTTACTGTTTGGGATGTTGGTGGCCAAGAAAAGTTGAGGCCCTTGTGGAGGCACTACTTCAACAATACTGATGGCTTGgtatgtttattattcttttaag--acctttatgaaatgatatcgattgtttgta-attgttctgcttgacgggttgggttatttattcttcacttcttgagtt

upper sequence: LOC_Os02g47110.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G113995_T01 (Zea mays), 5'ss of exon 3
AGTACAGTACAAGAACGTGATGTTTACAGTATGGGATGTCGGTGGCCAAGAGAAGTTGAGGCCTCTGTGGAGGCATTACTTCAATAATACGGATGGTTTGgtatgttttgtttcctttgtggttatctttttgggaatacgtgaaagatttgtgcatcgttgcattaaagaaggaaagaagtggttatttgattttgaca-
||| || |||||||| ||||||||||| || |||||||| ||||||||||| |||||||||||  |||||||||| |||||||| ||||| ||||| |||||||||||| || |     || |  |  | |      ||| |   |  | |     | | ||  ||     |   | |   ||  |   ||| |||     
AGTTCAATACAAGAATGTGATGTTTACTGTGTGGGATGTTGGTGGCCAAGAAAAGTTGAGGCCCTTGTGGAGGCACTACTTCAACAATACTGATGGCTTGgtatgttttattgctaaaatgatattgatctgtactctactttgtaattgttctgcttgatgagttgggttacttatgtt-tgtcttggtgagtttatggg

upper sequence: LOC_Os02g47110.1 (Oryza sativa), 5'ss of exon 3
lower sequence: AT3G03120.1 (Arabidopsis thaliana), 5'ss of exon 3
AGTACAGTACAAGAACGTGATGTTTACAGTATGGGATGTCGGTGGCCAAGAGAAGTTGAGGCCTCTGTGGAGGCATTACTTCAATAATACGGATGGTTTGgtatgttttgtttcctttgtggttatctttttgggaatac-gtgaaagatttgtgcatcgttgcattaaagaaggaaagaagtggttatttg------attttgaca--------------------------
||| ||||||||||| || || || ||||| |||||||| ||||||||||||||| |||||||  ||||||||||||||||||||||||| |||||  | ||| || |    |  ||| |     |   | | |  | |  || ||    | | |  || |  | | |    ||   |    |  |  ||||      |||||                              
AGTTCAGTACAAGAATGTCATCTTCACAGTTTGGGATGTTGGTGGCCAAGAGAAGCTGAGGCCCTTGTGGAGGCATTACTTCAATAATACCGATGGACTTgtaagtctctacttatttttcacgctgcctctagttagatagttaactcatagagtctcttctcttcatgacagatgatttctcatgttttgtaaggaattttcctgattgatattggtcgatgcatttgcag

upper sequence: LOC_Os02g47110.1 (Oryza sativa), 5'ss of exon 3
lower sequence: AT5G17060.1 (Arabidopsis thaliana), 5'ss of exon 3
AGTACAGTACAAGAACGTGATGTTTACAGTATGGGATGTCGGTGGCCAAGAGAAGTTGAGGCCTCTGTGGAGGCATTACTTCAATAATACGGATGGTTTGgtatgtttt--gtttcctttgtggttatctttttggg---aatacgtga-----aagatttgtgcatcgttgcattaaagaaggaaagaagtggttatttgattttgaca------------------------------------------------------------------------------------------
||| ||||||||||| |||||||| ||||| |||||||| ||||||||||||||  |||| ||||| ||||||||||||||||||||||| |||||  | ||| || |   ||||  |||  | || |   |||  |    |||| | |     ||| ||| | ||||  |   ||     | |  |        |||||| || |||                                                                                            
AGTTCAGTACAAGAATGTGATGTTCACAGTTTGGGATGTTGGTGGCCAAGAGAAACTGAGACCTCTTTGGAGGCATTACTTCAATAATACTGATGGACTTgtacgtatatagtttttttttcgatttttgctttcagtcagatacttaactttcaaggtttttccatctctatgttggcatatgttat---cctatatttggttatgatgttgcagtatcatatgttgcttggccaatctttagatctttttccatctttatcgaccatggtataagactactctatgatgctcttgcag

upper sequence: LOC_Os02g47110.1 (Oryza sativa), 5'ss of exon 3
lower sequence: Vv16s0039g02240.t01 (Vitis vinifera), 5'ss of exon 3
AGTACAGTACAAGAACGTGATGTTTACAGTATGGGATGTCGGTGGCCAAGAGAAGTTGAGGCCTCTGTGGAGGCATTACTTCAATAATACGGATGGTTTGgtatgttttgtttcctttgtggttatctttttgggaatacgtgaaagatttgtgcatcgttgcattaaagaaggaaagaagtggttatttgattttgaca--
||| ||||| |||||||||||||| ||||| |||||||| ||||| ||||||||  | ||||| || |||||||||||||| |||||||| |||||  |||||    ||  ||  | |     ||| | || || |||   |   ||  |   |  || ||  |||  | |   |  |   |  || | | ||| | |    
AGTTCAGTATAAGAACGTGATGTTCACAGTGTGGGATGTAGGTGGACAAGAGAAACTCAGGCCACTCTGGAGGCATTACTTTAATAATACTGATGGACTGgtaatcattactttttatagccatatttgttcggtaattgttattagggtca-gtttcattttatttta-agttaccgttctctttgtataattctaaatgt

upper sequence: LOC_Os02g47110.1 (Oryza sativa), 5'ss of exon 3
lower sequence: PP1S91_59V6.1 (Physcomitrella patens), 5'ss of exon 3
AGTACAGTACAAGAACGTGATGTTTACAGTATGGGATGTCGGTGGCCAAGAGAAGTTGAGGCCTCTGTGGAGGCATTACTTCAATAATACGGATGGTTTGgtatgttttgtttcctttgtggttatctttttgggaatacgtgaaagattt--gtgcatcgttgcattaaagaaggaaagaagtggttatttgattttgaca
||| || |||||||| ||   ||| |||||||||||||| || || || ||||| ||| |||| || ||| ||||||||||||||||||| || ||||||||| || ||  ||  |  || | | | |   | |   |   |      |||   | || | ||  || | | |   | | |  |   ||| | || |  | |
AGTTCAATACAAGAATGTCGAGTTCACAGTATGGGATGTTGGAGGTCAGGAGAAATTGCGGCCCCTTTGGCGGCATTACTTCAATAATACTGACGGTTTGgtaagtatt-ctttataggttgctgtttcagtagacctttttttctttttttcatacaactttttatgatatatatatatatatatatatat-atatatata

upper sequence: LOC_Os02g47110.1 (Oryza sativa), 5'ss of exon 3
lower sequence: PP1S47_298V6.1 (Physcomitrella patens), 5'ss of exon 3
AGTACAGTACAAGAACGTGATGTTTACAGTATGGGATGTCGGTGGCCAAGAGAAGTTGAGGCCTCTGTGGAGGCATTACTTCAATAATACGGATGGTTTGgtatgttttgtttcctttgtggttatctttttgggaatacgtgaaagatttgtgcatcgttgcattaaagaaggaaagaagtggttatttgattttgaca--
||| ||||||||||||||   ||||||||| |||||||| || || |||||||| ||| ||||||||||| ||||||| ||||| || || ||||||||||||  || |  ||| || |   | |||| |   | ||| | | |  |  | |    |  ||  | || |||  |     ||      | | |   |      
AGTTCAGTACAAGAACGTCGAGTTTACAGTGTGGGATGTTGGAGGTCAAGAGAAATTGCGGCCTCTGTGGCGGCATTATTTCAACAACACTGATGGTTTGgtaaattat-cttcattggatatcatctctcaagtaat-catcattgtatggatattaattttactatagattgttgtgagcacaattctaacgctagatta

upper sequence: LOC_Os02g47110.1 (Oryza sativa), 5'ss of exon 3
lower sequence: PP1S37_304V6.1 (Physcomitrella patens), 5'ss of exon 3
AGTACAGTACAAGAACGTGATGTTTACAGTATGGGATGTCGGTGGCCAAGAGAAGTTGAGGCCTCTGTGGAGGCATTACTTCAATAATACGGATGGTTTGgtatgttttgtttcctttgtggttatctttttgggaatacgtgaaagatttgtgcatcgttgcattaaagaaggaaagaagtggttatttgattttgaca--
||| || |||||||| ||   ||||||||| ||||| || || ||||||||||| ||| | ||||||||| ||||||||||||| || || || |||||||||  || |  |||  |||   ||  |||    | | ||        |||  | |   |  | |  | | |  |  | |  |  ||||| |||   || |  
AGTTCAATACAAGAATGTTGAGTTTACAGTGTGGGACGTTGGAGGCCAAGAGAAATTGCGACCTCTGTGGCGGCATTACTTCAACAACACTGACGGTTTGgtaaattct-cttcacttgatattcccttacaagcagtatcatctttattgatactgagaaggagaatacatcgtgatacatttttatt-gatgccgatatt

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|66919065|gb|CX105913.1|CX105913
EST:     AGAAGTTGAGGCCTCTGTGGAGGCATTACTTCAATAATACGGATGGTTTG                         ATCTATGTAGTTGATTCATTGGATAGAGAGAGAATCGGAAAAGCGAAAGCG
genomic: AGAAGTTGAGGCCTCTGTGGAGGCATTACTTCAATAATACGGATGGTTTGgtatgttttg ... tgatttgcagATCTATGTAGTTGATTCATTGGATAGAGAGAGAATCGGAAAAGCGAAAGCG
EST: gi|2310427|gb|C26582.1|C26582
EST:     AGAAGTTGAGGCCTCTGTGGAGGCATTACTTCAATAATACGGATGGTTTG                         ATCTATGTAGTTGATTCATTGGNTAGAGGAGAGAATCGGAAAAGCGAAA-C
genomic: AGAAGTTGAGGCCTCTGTGGAGGCATTACTTCAATAATACGGATGGTTTGgtatgttttg ... tgatttgcagATCTATGTAGTTGATTCATTGGATAGAG-AGAGAATCGGAAAAGCGAAAGC
EST: gi|88311186|gb|CI570260.1|CI570260
EST:     AGAAGTTGACGCCTCTGTGGAGGCCTTACTTCACTAATACGGATGGTTTG                         ATCTATGTAGTTGATTCATTGGATACAGAGAGAAT-GGAAA-GCGAA
genomic: AGAAGTTGAGGCCTCTGTGGAGGCATTACTTCAATAATACGGATGGTTTGgtatgttttg ... tgatttgcagATCTATGTAGTTGATTCATTGGATAGAGAGAGAATCGGAAAAGCGAA
EST: gi|2310382|gb|C26537.1|C26537
EST:     AAGTTGAAGGCCTCTGTTGGAGGCATTACTTCAATAATACGGATGGTTTN                         ATCTATGTAGTTGATTCATT
genomic: AAGTTGA-GGCCTCTGT-GGAGGCATTACTTCAATAATACGGATGGTTTGgtatgttttg ... tgatttgcagATCTATGTAGTTGATTCATT
EST: gi|33692402|gb|CF320641.1|CF320641
EST:     AGAAGTTGAGGCCTCTGTGGAGGCATTACTTCAATAATACGGATGGTTTG                         ATCTATGTAGTTGATTCATTGGATAGAGAGAGAATCGGAAAAGCGAAAGCG
genomic: AGAAGTTGAGGCCTCTGTGGAGGCATTACTTCAATAATACGGATGGTTTGgtatgttttg ... tgatttgcagATCTATGTAGTTGATTCATTGGATAGAGAGAGAATCGGAAAAGCGAAAGCG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGTACAGTACAAGAACGTGATGTTTACAGTATGGGATGTCGGTGGCCAAGAGAAGTTGAGGCCTCTGTGGAGGCATTACTTCAATAATACGGATGGTTTGgtatgttttgtttcctttgtggttatctttttgggaatacgtgaaagatttgtgcatcgttgcattaaagaaggaaagaagtggttatttgattttgaca

- - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG