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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagtatcctacctattctttcatgaatctcttccaggatcgttggcatctgatggagctaaattgtcttcttttcagGTGAACTTGGTTGAATGGCTGAAGACCATGGTTGCTGAGAGGAAAGCAGAGGAGGTAGTAGACCCCAAGCTGCCCGAGAAGCCTTCTCCCAAAGCACTGA

Basic information

species Oryza sativa
transcript LOC_Os03g03410.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g03410.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G014366_T03 (Zea mays), 3'ss of exon 5
gtcagtatcctacctattctttcatgaatctcttccaggatcgttggcatctgatggagctaaattgtcttcttttc--------------agGTGAACTTGGTTGAATGGCTGAAGACCATGGTTGCTGAGAGGAAAGCAGAGGAGGTAGTAGACCCCAAGCTGCCCGAGAAGCCTTCTCCCAAAGCACTGA
||  | |   |  | ||  |   |    ||| |  || ||   | |    |      |||| |||| ||| | | ||              |||| ||||||||||| ||||| |||||||||||||| ||||||||||| ||||| ||  | ||||| ||| || | || ||||||||||||||| | ||||
gttggcacagtcgccatcttcataactttctttatcaagaatatggaggcccagcaaagctgaattctctacctgtctaccatgtgtgtgcagGTCAACTTGGTTGAGTGGCTCAAGACCATGGTTGCCGAGAGGAAAGCGGAGGAAGTTCTGGACCCAAAGATGGCTGAAAAGCCTTCTCCCAAAACGCTGA

upper sequence: LOC_Os03g03410.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G317938_T01 (Zea mays), 3'ss of exon 5
-----------------gtcagtatcctacctattctttcatgaatctcttccaggatcgttggca--tctgatggagctaaattgtct-tcttttcagGTGAACTTGGTTGAATGGCTGAAGACCATGGTTGCTGAGAGGAAAGCAGAGGAGGTAGTAGACCCCAAGCTGCCCGAGAAGCCTTCTCCCAAAGCACTGA
                  |   ||   || ||   || | ||   ||     |  |    |  | |  |||  |       |    | | | | | |||||| |  |||| || ||||| |||| |||||| || ||||||||||| ||||||||||| |||   ||| || |||||| |||| |||||||  | ||||
gtgccgtgccgtgttctatagataga-tagcttcactctgatctgtccgggtcgagtggctcagtaactctactaccatgcatgcatgtgtgtgtgcagGTGCAGCTGGTGGAGTGGCTCAAGAACATGGTGGCCGAGAGGAAAGCGGAGGAGGTAGTGGACAGTAAGATGGCCGAGAGGCCTCCTCCCAAGACGCTGA
















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|58586906|gb|CF985214.1|CF985214
EST:     AGATTATAACGGGTAGATCACCAGTAGATTACACCAGGGCACCTGGAGAG                         GTGAACTTGGTTGAATGGCTGAAGACCATGGTTGCTGAGAGGAAAGCAGAG
genomic: AGATTATAACGGGTAGATCACCAGTAGATTACACCAGGGCACCTGGAGAGgtcagtatcc ... ttcttttcagGTGAACTTGGTTGAATGGCTGAAGACCATGGTTGCTGAGAGGAAAGCAGAG
EST: gi|125863442|gb|EL586716.1|EL586716
EST:     AGATTATAACGGGTAGATCACCAGTAGATTACACCAGGGCACCTGGAGAG                         GTGAACTTGGTTGAATGGCTGAAGACCATGGTTGCTGAGAGGAAAGCAGAG
genomic: AGATTATAACGGGTAGATCACCAGTAGATTACACCAGGGCACCTGGAGAGgtcagtatcc ... ttcttttcagGTGAACTTGGTTGAATGGCTGAAGACCATGGTTGCTGAGAGGAAAGCAGAG
EST: gi|313080728|gb|HO213525.1|HO213525
EST:     AGATTATAACGGGTAGATCACCAGTAGATTACACCAGGGCACCTGGAGAG                         GTGAACTTGGTTGAATGGCTGAAGACCATGGTTGCTGAGAGGAAAGCAGAG
genomic: AGATTATAACGGGTAGATCACCAGTAGATTACACCAGGGCACCTGGAGAGgtcagtatcc ... ttcttttcagGTGAACTTGGTTGAATGGCTGAAGACCATGGTTGCTGAGAGGAAAGCAGAG
EST: gi|38480926|gb|CF965015.1|CF965015
EST:     AGATTATAACGGGTAGATCACCAGTAGATTACACCAGGGCACCTGGAGAG                         GTGAACTTGGTTGAATGGCTGAAGACCATGGTTGCTGAGAGGAAAGCAGAG
genomic: AGATTATAACGGGTAGATCACCAGTAGATTACACCAGGGCACCTGGAGAGgtcagtatcc ... ttcttttcagGTGAACTTGGTTGAATGGCTGAAGACCATGGTTGCTGAGAGGAAAGCAGAG
EST: gi|396941393|gb|HO188602.1|HO188602
EST:     GATTATAACGGGTAGATCACCAGTAGATTACACCAGGGCACCTGGGAGAG                         GTGAACTTGGTTGAATGGCTGAAGACCATGGTTGCTGAGAGGAAAGCAGA
genomic: GATTATAACGGGTAGATCACCAGTAGATTACACCAGGGCACCT-GGAGAGgtcagtatcc ... ttcttttcagGTGAACTTGGTTGAATGGCTGAAGACCATGGTTGCTGAGAGGAAAGCAGA
EST: gi|86496376|gb|CI139009.1|CI139009
EST:     GGCACCTGGAGAG                         GTGAACTTGGTTGAATGGCTGAAGACCATGGTTGCTGAGAGGAAAGCAGAG
genomic: GGCACCTGGAGAGgtcagtatcc ... ttcttttcagGTGAACTTGGTTGAATGGCTGAAGACCATGGTTGCTGAGAGGAAAGCAGAG
EST: gi|87040135|gb|CI193344.1|CI193344
EST:     AGATTATAACGGGTAGATCACCAGTAGATTACACCAGGGCACCTGGAGAG                         GTGAACTTGGTTGAATGGCTGAAGACCATGGTTGCTGAGAGGAAAGCAGAG
genomic: AGATTATAACGGGTAGATCACCAGTAGATTACACCAGGGCACCTGGAGAGgtcagtatcc ... ttcttttcagGTGAACTTGGTTGAATGGCTGAAGACCATGGTTGCTGAGAGGAAAGCAGAG
EST: gi|88366355|gb|CI553753.1|CI553753
EST:     TAGATTACACCAGGGCACCTGGAGAG                         GTGAACTTGGTTGAATGGCTGAAGACCATGGTTGCTGAGAGGAAAGCAGAG
genomic: TAGATTACACCAGGGCACCTGGAGAGgtcagtatcc ... ttcttttcagGTGAACTTGGTTGAATGGCTGAAGACCATGGTTGCTGAGAGGAAAGCAGAG
EST: gi|58588930|gb|CF987238.1|CF987238
EST:     AGATTATAACGGGTAGATCACCAGTAGATTACACCAGGGCACCTGGAGAG                         GTGAACTTGGTTGAATGGCTGAAGACCATGGTTGCTGAGAG
genomic: AGATTATAACGGGTAGATCACCAGTAGATTACACCAGGGCACCTGGAGAGgtcagtatcc ... ttcttttcagGTGAACTTGGTTGAATGGCTGAAGACCATGGTTGCTGAGAG
EST: gi|58694780|gb|CK083467.1|CK083467
EST:     AGATTATAACGGGTAGATCACCAGTAGATTACACCAGGGCACCTGGAGAG                         GTGAACTTGGTTGAATGGCTGAAGACCATGGTTGCTGAGAGGAAAGCAGAG
genomic: AGATTATAACGGGTAGATCACCAGTAGATTACACCAGGGCACCTGGAGAGgtcagtatcc ... ttcttttcagGTGAACTTGGTTGAATGGCTGAAGACCATGGTTGCTGAGAGGAAAGCAGAG
EST: gi|29677567|gb|CB673842.1|CB673842
EST:     AGATTATAACGGGTAGATCACCAGTAGATTACACCAGGGCACCTGGAGAG                         GTGAACTTGGTTGAATGGCTGAAGACCATGGTTGCTGAGAGGAAAGCAGAG
genomic: AGATTATAACGGGTAGATCACCAGTAGATTACACCAGGGCACCTGGAGAGgtcagtatcc ... ttcttttcagGTGAACTTGGTTGAATGGCTGAAGACCATGGTTGCTGAGAGGAAAGCAGAG
EST: gi|300215530|gb|HO088156.1|HO088156
EST:     AGATTATAACGGGTAGATCACCAGTAGATTACACCAGGGCACCTGGAGAG                         GTGAACTTGGTTGAATGGCTGAAGACCATGGTTGCTGAGAGGAAAGCAGAG
genomic: AGATTATAACGGGTAGATCACCAGTAGATTACACCAGGGCACCTGGAGAGgtcagtatcc ... ttcttttcagGTGAACTTGGTTGAATGGCTGAAGACCATGGTTGCTGAGAGGAAAGCAGAG
EST: gi|58693941|gb|CK082628.1|CK082628
EST:     AGATTATAACGGGTAGATCACCAGTAGATTACACCAGTGCACCTGGAGAG                         GTGAACTTGGTTGAATGGCTGAAGACCATGGTTGCTGAGAGGAAAGCAGAG
genomic: AGATTATAACGGGTAGATCACCAGTAGATTACACCAGGGCACCTGGAGAGgtcagtatcc ... ttcttttcagGTGAACTTGGTTGAATGGCTGAAGACCATGGTTGCTGAGAGGAAAGCAGAG
EST: gi|87017975|gb|CI275789.1|CI275789
EST:     AGATTATAACGGGTAGATCACCAGTAGATTACACCAGGGCACCTGGAGAG                         GTGAACTTGGTTGAATGGCTGAAGACCATGGTTGCTGAGAGGAAAGCAGAG
genomic: AGATTATAACGGGTAGATCACCAGTAGATTACACCAGGGCACCTGGAGAGgtcagtatcc ... ttcttttcagGTGAACTTGGTTGAATGGCTGAAGACCATGGTTGCTGAGAGGAAAGCAGAG
EST: gi|86828213|gb|CI276818.1|CI276818
EST:     AGATTATAACGGGTAGATCACCAGTAGATTACACCAGGGCACCTGGAGAG                         GTGAACTTGGTTGAATGGCTGAAGACCATGGTTGCTGAGAGGAAAGCAGAG
genomic: AGATTATAACGGGTAGATCACCAGTAGATTACACCAGGGCACCTGGAGAGgtcagtatcc ... ttcttttcagGTGAACTTGGTTGAATGGCTGAAGACCATGGTTGCTGAGAGGAAAGCAGAG
EST: gi|86435568|gb|CI106801.1|CI106801
EST:     AGATTATAACGGTTAGATCACCAGTAGATTACACCAGGGCACCTGGAGAG                         GTGAACTTGTTTGAATGGCTGAAGACCATGGTTGCTGAGAGGAAAGCAGAG
genomic: AGATTATAACGGGTAGATCACCAGTAGATTACACCAGGGCACCTGGAGAGgtcagtatcc ... ttcttttcagGTGAACTTGGTTGAATGGCTGAAGACCATGGTTGCTGAGAGGAAAGCAGAG

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: 73 (upstream exon), 61 (downstream exon)
Score: 32

GATGTTAAATGAGAGGAGCGATGTTTATAGCTTTGGAGTACTTATAATGGAGATTATAACGGGTAGATCACCAGTAGATTACACCAGGGCACCTGGAGAGgtcagtatcc ... ttcttttcagGTGAACTTGGTTGAATGGCTGAAGACCATGGTTGCTGAGAGGAAAGCAGAGGAGGTAGTAGACCCCAAGCTGCCCGAGAAGCCTTCTCCCAAAGCACTGA




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgaatctcttccaggatcgttggcatctgatggagctaaattgtcttcttttcagGTGAACTTGGTTGAATGGCTGAAGACCATGGTTGCTGAGAGGAAAGCAGAGGAGGTAGTAGACCCCAAGCTGCCCGAGAAGCCTTCTCCCAAAGCACTGA
                                 agctaaa  putative branch site (score: 32)
                                        ttgtcttcttttc  CT-rich tract
                                    taaattgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcagtatcctacctattctttcatgaatctcttccaggatcgttggcatctgatggagctaaattgtcttcttttcagGTGAACTTGGTTGAATGGCTGAAGACCATGGTTGCTGAGAGGAAAGCAGAGGAGGTAGTAGACCCCAAGCTGCCCGAGAAGCCTTCTCCCAAAGCACTGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC