Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGCCCTGAGGAGGTCAGTGCTATGATCCTTGGAAAGATGAAGGAGACTGCTGAGGCATACCTTGGCAAGAAGATCAACGATGCTGTCGTGACTGTTCCTGgttagtaatgacaagacattcatgtgcttagttaactcaagcggtgattctgtggaagccattgctcacttctgctctttcatgttttcag

Basic information

species Oryza sativa
transcript LOC_Os02g02410.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g02410.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G415007_T01 (Zea mays), 5'ss of exon 3
AGCCCTGAGGAGGTCAGTGCTATGATCCTTGGAAAGATGAAGGAGACTGCTGAGGCATACCTTGGCAAGAAGATCAACGATGCTGTCGTGACTGTTCCTGgttagtaatgacaagacattcatgtgcttagttaactcaagcggtgattctgtggaa--gccattgctcacttc--tgctctttcatgttttcag
|||||||||||| ||||||| ||||| ||||| ||||||||||| ||||||||||| |||||||||||||||||||||||||||||||| ||||| ||||||||||||     |  |||||   ||||  |||| ||| ||  ||  || |||  ||  |   | ||| |||||  |    |||  | ||| |||
AGCCCTGAGGAGATCAGTGCCATGATTCTTGGCAAGATGAAGGATACTGCTGAGGCGTACCTTGGCAAGAAGATCAACGATGCTGTCGTCACTGTCCCTGgttagtaac--tgaaccattc---tgct-ggttacctctagtagttgttatgtaaaaatgtggtggcttacttccttatgttttgttttttgcag

upper sequence: LOC_Os02g02410.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G114793_T01 (Zea mays), 5'ss of exon 3
AGCCCTGAGGAGGTCAGTGCTATGATCCTTGGAAAGATGAAGGAGACTGCTGAGGCATACCTTGGCAAGAAGATCAACGATGCTGTCGTGACTGTTCCTGgttagtaatgacaagacattcatgtgcttagttaactcaagcggtgattctgtggaagcc--attgctcacttctgctctttcatgttttcag----
|||||||||||| ||||||| ||||| ||||| ||||||||||| |||||||||||||||||||||||||||||||| ||||||||||| |||||||||||||||||   ||   ||| |  ||    | |||| ||| ||  ||  || |||  || |      |||||||||   | | |  ||||||       
AGCCCTGAGGAGATCAGTGCCATGATTCTTGGCAAGATGAAGGATACTGCTGAGGCATACCTTGGCAAGAAGATCAATGATGCTGTCGTCACTGTTCCTGgttagta---actgaacaattctgc---tggttacctctagtagttgttatgtaaaaacgtggcggctcacttcc-ttgtgttgtgtttttttgcag

upper sequence: LOC_Os02g02410.1 (Oryza sativa), 5'ss of exon 3
lower sequence: AT5G28540.1 (Arabidopsis thaliana), 5'ss of exon 3
AGCCCTGAGGAGGTCAGTGCTATGATCCTTGGAAAGATGAAGGAGACTGCTGAGGCATACCTTGGCAAGAAGATCAACGATGCTGTCGTGACTGTTCCTGgttagtaatgacaagacattcatg-tgcttagttaactcaagcggtgattctgtggaagccattgctcacttctgctctttcatgtttt-cag
|| ||||||||| | ||||||||||| ||    |||||||||||||| ||||| || |||||||| ||||| ||||| || ||||| || |||||||| |||||||  ||     | ||   || ||   || || ||  |       |  |  |  |   |||| | | ||    | ||| |  ||    ||
AGTCCTGAGGAGATTAGTGCTATGATTCTGACTAAGATGAAGGAGACAGCTGAAGCCTACCTTGGAAAGAAAATCAAGGACGCTGTTGTCACTGTTCCAGgttagtt-tgttgttatatatgtggtggagaggtatctttattatctgtatttggtgattgattgtttatttggtgtttttgactttgcgtag

upper sequence: LOC_Os02g02410.1 (Oryza sativa), 5'ss of exon 3
lower sequence: AT5G42020.1 (Arabidopsis thaliana), 5'ss of exon 3
AGCCCTGAGGAGGTCAGTGCTATGATCCTTGGAAAGATGAAGGAGACTGCTGAGGCATACCTTGGCAAGAAGATCAACGATGCTGTCGTGACTGTTCCTGgttagt-----aatgacaagacattcatgtgcttagttaactcaagcggtgattctgtggaagccattgctcacttctgctctttcatgttttcag----------
|| ||||||||| ||||||| ||||| ||    |||||||||||||| || || || |||||||| ||||| ||||| || ||||| || |||||||| |||||||       | |   |   ||  |||  |   |  | |  || | | | | | |       |||| | | |  |  | | |   || ||             
AGTCCTGAGGAGATCAGTGCCATGATTCTGACTAAGATGAAGGAGACAGCCGAAGCCTACCTTGGAAAGAAAATCAAGGACGCTGTTGTCACTGTTCCAGgttagtttgttgttaattcgggttttctgttatatatgtagtggagagataaatttcttatctgtattggtgattgattgtttatttggtgtttgactatgcgcag

upper sequence: LOC_Os02g02410.1 (Oryza sativa), 5'ss of exon 3
lower sequence: Vv02s0025g02140.t01 (Vitis vinifera), 5'ss of exon 3
AGCCCTGAGGAGGTCAGTGCTATGATCCTTGGAAAGATGAAGGAGACTGCTGAGGCATACCTTGGCAAGAAGATCAACGATGCTGTCGTGACTGTTCCTGgttagtaatga----caagacatt-catgtgcttagttaactcaagcggtga---ttctgtggaagccattgctcac-ttctgctctttcatgttttcag-----------------------------
|||||||||||| ||||||| |||||  |    |||||||||||||| ||||| |||| |||||| ||||||||||| ||||||||||| ||||| || ||| ||||        | ||| ||  | ||||     || |      || | |   |  | | |||        |  | || || || ||    | ||                                
AGCCCTGAGGAGATCAGTGCAATGATTTTGACTAAGATGAAGGAGACAGCTGAAGCATTCCTTGGGAAGAAGATCAAGGATGCTGTCGTTACTGTGCCCGgtgagtatcactcttctagatataacgtgtgaggttttgaactgcccgcttacactcttcttgaaatgtgaattagcattttgttcattaggatgttttactcatattagctttccatgcaacccgcag

upper sequence: LOC_Os02g02410.1 (Oryza sativa), 5'ss of exon 3
lower sequence: EDP06859 (Chlamydomonas reinhardtii), 5'ss of exon 2
AGCCCTGAGGAGGTCAGTGCTATGATCCTTGGAAAGATGAAGGAGACTGCTGAGGCATACCTTGGCAAGAAGATCAACGATGCTGTCGTGACTGTTCCTGgttagtaatgacaagacattcatgtgcttagttaactcaagcggtgattctgtggaagccattgctcacttctgctctttcatgttttcag----------------------------------------
                           |||   ||||||||||| ||||||||||| ||||| |||||||   ||||  | ||||| || || || || |    ||| |   | ||    || | ||   ||        |  ||     |||| | |     || |      | | |   ||| |   ||                                        
--------------------------TCTTCAGAAGATGAAGGACACTGCTGAGGCCTACCTGGGCAAGACTGTCAAGCACGCTGTGGTCACCGTGCCCGC---GTACTTTAACGATGCCCA-GCGCCAGgtgcgtatgtggcgttgggatgtgtaggagggggcacggcggggttgtgg-atggtgggagggggtggaggggggccagctggcgttggcacggtactcca

upper sequence: LOC_Os02g02410.1 (Oryza sativa), 5'ss of exon 3
lower sequence: EDP06660 (Chlamydomonas reinhardtii), 5'ss of exon 3
AGCCCTGAGGAGGTCAGTGCTATGATCCTTGGAAAGATGAAGGAGACTGCTGAGGCATACCTTGGCAAGAAGATCAACGATGCTGTCGTGACTGTTCCTGgttagt--aatgacaagacat-tcatgtgcttagttaactcaagcggtgattctgtggaagc-cattgctcacttctgctctttcatgttttcag--------------------------------
                           |||   ||||||||||| ||||||||||| ||||| |||||||   ||||  | ||||| || || || || |  || |  || ||          || |||| |   |  |    | | ||  | || ||  || |   |   ||  | |   | |  |||  |                                   
--------------------------TCTTCAGAAGATGAAGGACACTGCTGAGGCCTACCTGGGCAAGACTGTCAAGCACGCTGTGGTCACCGTGCCCGCGTACTTCAACGATGCCCAGCGCCAGgtgcgtgcgtggcgttgg-gatgtgtatgagggggcacggcgggtacggcggggttgtggtgtgctggaggggggccggctggcgttggcacggtactacg

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|29624638|gb|CB629649.1|CB629649
EST:     TGAGGCATACCTTGGCAAGAAGATCAACGATGCTGTCGTGACTGTTCCTG                         CGTACTTCAATGACGCGCAGAGGCAGGCAACCAAGGATGCCGGTGTCATTG
genomic: TGAGGCATACCTTGGCAAGAAGATCAACGATGCTGTCGTGACTGTTCCTGgttagtaatg ... atgttttcagCGTACTTCAATGACGCGCAGAGGCAGGCAACCAAGGATGCCGGTGTCATTG
EST: gi|29630263|gb|CB635272.1|CB635272
EST:     TGAGGCATACCTTGGCAAGAAGATCAACGATGCTGTCGTGACTGTTCCTG                         CGTACTTCAATGACGCGCAGAGGCAGGCAACCAAGGATGCCGGTGTCATTG
genomic: TGAGGCATACCTTGGCAAGAAGATCAACGATGCTGTCGTGACTGTTCCTGgttagtaatg ... atgttttcagCGTACTTCAATGACGCGCAGAGGCAGGCAACCAAGGATGCCGGTGTCATTG
EST: gi|86884177|gb|CI311639.1|CI311639
EST:     TGAGGCATACCTTGGCAAGAAGATCAACGATGCTGTCGTGACTGTTCCTG                         CGTACTTCAATGACGCGCAGAGGCAGGCAACCAAGGATGCCGGTGTCATTG
genomic: TGAGGCATACCTTGGCAAGAAGATCAACGATGCTGTCGTGACTGTTCCTGgttagtaatg ... atgttttcagCGTACTTCAATGACGCGCAGAGGCAGGCAACCAAGGATGCCGGTGTCATTG
EST: gi|86826293|gb|CI311115.1|CI311115
EST:     TGAGGCATACCTTGGCAAGAAGATCAACGATGCTGTCGTGACTGTTCCTG                         CGTACTTCAATGACGCGCAGAGGCAGGCAACCAAGGATGCCGGTGTCATTG
genomic: TGAGGCATACCTTGGCAAGAAGATCAACGATGCTGTCGTGACTGTTCCTGgttagtaatg ... atgttttcagCGTACTTCAATGACGCGCAGAGGCAGGCAACCAAGGATGCCGGTGTCATTG
EST: gi|58672968|gb|CK061654.1|CK061654
EST:     TGAGGCATACCTTGGCAAGAAGATCAACGATGCTGTCGTGACTGTTCCTG                         CGTACTTCAATGACGCGCAGAGGCAGGCAACCAAGGATGCCGGTGTCATTG
genomic: TGAGGCATACCTTGGCAAGAAGATCAACGATGCTGTCGTGACTGTTCCTGgttagtaatg ... atgttttcagCGTACTTCAATGACGCGCAGAGGCAGGCAACCAAGGATGCCGGTGTCATTG
EST: gi|29628132|gb|CB633143.1|CB633143
EST:     TGAGGCATACCTTGGCAAGAAGATCAACGATGCTGTCGTGACTGTTCCTG                         CGTACTTCAATGACGCGCAGAGGCAGGCAACCAAGGATGCCGGTGTCATTG
genomic: TGAGGCATACCTTGGCAAGAAGATCAACGATGCTGTCGTGACTGTTCCTGgttagtaatg ... atgttttcagCGTACTTCAATGACGCGCAGAGGCAGGCAACCAAGGATGCCGGTGTCATTG
EST: gi|396941184|gb|HO188393.1|HO188393
EST:     TGAGGCATACCTTGGCAAGAAGATCAACGATGCTGTCGTGACTGTTCCTG                         CGTACTTCAATGACGCGCAGAGGCAGGCAACCAAGGATGCCGGTGTCATTG
genomic: TGAGGCATACCTTGGCAAGAAGATCAACGATGCTGTCGTGACTGTTCCTGgttagtaatg ... atgttttcagCGTACTTCAATGACGCGCAGAGGCAGGCAACCAAGGATGCCGGTGTCATTG
EST: gi|29628408|gb|CB633419.1|CB633419
EST:     TGAGGCATACCTTGGCAAGAAGATCAACGATGCTGTCGTGACTGTTCCTG                         CGTACTTCAATGACGCGCAGAGGCAGGCAACCAAGGATGCCGGTGTCATTG
genomic: TGAGGCATACCTTGGCAAGAAGATCAACGATGCTGTCGTGACTGTTCCTGgttagtaatg ... atgttttcagCGTACTTCAATGACGCGCAGAGGCAGGCAACCAAGGATGCCGGTGTCATTG
EST: gi|86904389|gb|CI308599.1|CI308599
EST:     TGAGGCATACCTTGGCAAGAAGATCAACGATCCTGTCGTGACTGTTCCTG                         CGTACTTCAATGACGCGCAGAGGCAGGCAACCAAGGATGCCGGTGTCATTG
genomic: TGAGGCATACCTTGGCAAGAAGATCAACGATGCTGTCGTGACTGTTCCTGgttagtaatg ... atgttttcagCGTACTTCAATGACGCGCAGAGGCAGGCAACCAAGGATGCCGGTGTCATTG
EST: gi|29628702|gb|CB633713.1|CB633713
EST:     TGAGGCATACCTTGGCAAGAAGATCAACGATGCTGTCGTGACTGTTCCTG                         CGTACTTCAATGACGCGCAGAGGCAGGCAACCAAGGATGCCGGTGTCATTG
genomic: TGAGGCATACCTTGGCAAGAAGATCAACGATGCTGTCGTGACTGTTCCTGgttagtaatg ... atgttttcagCGTACTTCAATGACGCGCAGAGGCAGGCAACCAAGGATGCCGGTGTCATTG
EST: gi|29631218|gb|CB636227.1|CB636227
EST:     TGAGGCATACCTTGGCAAGAAGATCAACGATGCTGTCGTGACTGTTCCTG                         CGTACTTCAATGACGCGCAGAGGCAGGCAACCAAGGATGCCGGTGTCATTG
genomic: TGAGGCATACCTTGGCAAGAAGATCAACGATGCTGTCGTGACTGTTCCTGgttagtaatg ... atgttttcagCGTACTTCAATGACGCGCAGAGGCAGGCAACCAAGGATGCCGGTGTCATTG
EST: gi|29630767|gb|CB635776.1|CB635776
EST:     TGAGGCATACCTTGGCAAGAAGATCAACGATGCTGTCGTGACTGTTCCTG                         CGTACTTCAATGACGCGCAGAGGCAGGCAACCAAGGATGCCGGTGTCATTG
genomic: TGAGGCATACCTTGGCAAGAAGATCAACGATGCTGTCGTGACTGTTCCTGgttagtaatg ... atgttttcagCGTACTTCAATGACGCGCAGAGGCAGGCAACCAAGGATGCCGGTGTCATTG
EST: gi|86902315|gb|CI302346.1|CI302346
EST:     TGAGGCATACCTTGGCAAGAAGATCAACGATGCTGTCGTGACTGTTCCTG                         CGTACTTCAATGACGCGC
genomic: TGAGGCATACCTTGGCAAGAAGATCAACGATGCTGTCGTGACTGTTCCTGgttagtaatg ... atgttttcagCGTACTTCAATGACGCGC

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 75 (upstream exon), 71 (downstream exon)
Score: 303

AGCCCTGAGGAGGTCAGTGCTATGATCCTTGGAAAGATGAAGGAGACTGCTGAGGCATACCTTGGCAAGAAGATCAACGATGCTGTCGTGACTGTTCCTGgttagtaatg ... atgttttcagCGTACTTCAATGACGCGCAGAGGCAGGCAACCAAGGATGCCGGTGTCATTGCTGGCCTGAATGTTGCTAGGATCATCAATGAGCCAACTGCTGCTGCTAT




<











<


<









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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGCCCTGAGGAGGTCAGTGCTATGATCCTTGGAAAGATGAAGGAGACTGCTGAGGCATACCTTGGCAAGAAGATCAACGATGCTGTCGTGACTGTTCCTGgttagtaatgacaagacattcatgtgcttagttaactcaagcggtgattctgtggaagccattgctcacttctgctctttcatgttttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG