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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACCTCTTCCATGgtgagattctccccctttcttctcctctatacgccgactctgtacattgtgtatgtgctgatcgtgattgcaagcttcgacttgatgtggtgttgcagta...

Basic information

species Oryza sativa
transcript LOC_Os01g73160.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g73160.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G446960_T01 (Zea mays), 5'ss of exon 2
ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACCTCTTCCATGgtgagatt----ctccccctttcttctc--ctctatacgccgactctgtacattgtgtatgtgctgatcgtgattgcaagcttcgacttgatgtggtgttgcagta
||||||||||||||||||||||||||||||||||| |||||||||||||||||| |     ||||  ||  ||| ||   ||  || ||   | |  ||| || || |  |  | ||    || ||  || |    |   |       ||     
ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAATACCTCTTCCATGgtgagctctgagctccttctcccttttcgtttccctaggcgcgcccaatacgttatgcagattgtcattcccat-gcgtgcgttagttcattagatgcctg-----

upper sequence: LOC_Os01g73160.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G171484_T01 (Zea mays), 5'ss of exon 2
ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACCTCTTCCATGgtgagattctccccctttcttctcctctatacgccga------ctctgtacattgtgtatgtgctgatcgtgattgcaagcttcgacttgatgtggtgttgcagta-------------------------------------------------------------------
||||||||||||||||||||||||||||||||||||||| |||||||||||||| | || | |||  ||  ||  |  | | || |      | |  || |   |   |    |     |   | | |  |  ||| | |   |   | ||| ||                                                                   
ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACATCTTCCATGgtgagctccttctcctccctcttcgcccgtccccctaggcgcgcccaatataagattatttcattagatttagataccaattcagacattacaagcattagcaatattcggatcgtgtacgacccaagcccgtccttgtcttagattgagaaccgttcaactttatgttgcag
















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|88388732|gb|CI683519.1|CI683519
EST:     ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACCTCTTCCATG                         AGGGAGTCTTGTATGCCAAGAAGGACTACAACCTGGCCAAGCACCCAAAGG
genomic: ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACCTCTTCCATGgtgagattct ... ctatatgcagAGGGAGTCTTGTATGCCAAGAAGGACTACAACCTGGCCAAGCACCCAAAGG
EST: gi|88392465|gb|CI612939.1|CI612939
EST:     ATCATCTGCAAGAAGAACCGCCGCGAGATCTGCAAGTACCTCTTCCATG                         AGGGAGTCTTGTATGCCAAGAAGGACTACAACCTGGCCAAGCACCCAAAGG
genomic: ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACCTCTTCCATGgtgagattct ... ctatatgcagAGGGAGTCTTGTATGCCAAGAAGGACTACAACCTGGCCAAGCACCCAAAGG
EST: gi|58611267|gb|CK038979.1|CK038979
EST:     GATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACCTCTTCCATG                         AGGGAGTC-TGTATGCCAAGAAGGACTACAACCTGGCCAAGCACCCAAAGG
genomic: GATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACCTCTTCCATGgtgagattct ... ctatatgcagAGGGAGTCTTGTATGCCAAGAAGGACTACAACCTGGCCAAGCACCCAAAGG
EST: gi|88311142|gb|CI658055.1|CI658055
EST:     ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACCTCTTCCATG                         AGGGAGTCTTGTATGCCAAGAAGGACTACAACCTGGCCAAGCACCCAAAGG
genomic: ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACCTCTTCCATGgtgagattct ... ctatatgcagAGGGAGTCTTGTATGCCAAGAAGGACTACAACCTGGCCAAGCACCCAAAGG
EST: gi|25800605|gb|CA756566.1|CA756566
EST:     ATCATCTCCNAGAAGAACCGCCGCGAGATCTGCAAGTACCTCTTCCATG                         AGGGAGTCTTGTATGCCAAGAAGGACTACAACCTGGCCAAGCACCCAAAGG
genomic: ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACCTCTTCCATGgtgagattct ... ctatatgcagAGGGAGTCTTGTATGCCAAGAAGGACTACAACCTGGCCAAGCACCCAAAGG
EST: gi|33673989|gb|CF302228.1|CF302228
EST:     ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACCTCTTCCATG                         AGGGAGTCTTGTATGCCAAGAAGGACTACAACCTGGCCAAGCACCCAAAGG
genomic: ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACCTCTTCCATGgtgagattct ... ctatatgcagAGGGAGTCTTGTATGCCAAGAAGGACTACAACCTGGCCAAGCACCCAAAGG
EST: gi|88724659|gb|CI747918.1|CI747918
EST:     ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACCTCTTCCATG                         AGGGAGTCTTGTATGCCAAGAAGGACTACAACCTGGCCAAGCACCCAAAGG
genomic: ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACCTCTTCCATGgtgagattct ... ctatatgcagAGGGAGTCTTGTATGCCAAGAAGGACTACAACCTGGCCAAGCACCCAAAGG
EST: gi|33660783|gb|CF291750.1|CF291750
EST:     ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACCTCTTCCATG                         AGGGAGTCTTGTATGCCAAGAAGGACTACAACCTGGCCAAGCACCCAAAGG
genomic: ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACCTCTTCCATGgtgagattct ... ctatatgcagAGGGAGTCTTGTATGCCAAGAAGGACTACAACCTGGCCAAGCACCCAAAGG
EST: gi|88301884|gb|CI667730.1|CI667730
EST:     ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACCTCTTCCATG                         AGGGAGTCTTGTATGCCAAGAAGGACTACAACCTGGCCAAGCACCCAAAGG
genomic: ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACCTCTTCCATGgtgagattct ... ctatatgcagAGGGAGTCTTGTATGCCAAGAAGGACTACAACCTGGCCAAGCACCCAAAGG
EST: gi|88739378|gb|CI762886.1|CI762886
EST:     ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACCTCTTCCATG                         AGGGAGTCTTGTATGCCAAGAAGGACTACAACCTGGCCAAGCACCCAAAGG
genomic: ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACCTCTTCCATGgtgagattct ... ctatatgcagAGGGAGTCTTGTATGCCAAGAAGGACTACAACCTGGCCAAGCACCCAAAGG
EST: gi|55435427|gb|CV730845.1|CV730845
EST:     ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACCTCTTCCATG                         AGGGAGTCTTGTATGCCAAGAAGGACTACAACCTGGCCAAGCACCCAAAGG
genomic: ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACCTCTTCCATGgtgagattct ... ctatatgcagAGGGAGTCTTGTATGCCAAGAAGGACTACAACCTGGCCAAGCACCCAAAGG
EST: gi|88378851|gb|CI681669.1|CI681669
EST:     ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACCTCTTCCATG                         AGGGAGTCTTGTATGCCAAGAAGGACTACAACCTGGCCAAGCACCCAAAGG
genomic: ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACCTCTTCCATGgtgagattct ... ctatatgcagAGGGAGTCTTGTATGCCAAGAAGGACTACAACCTGGCCAAGCACCCAAAGG
EST: gi|88353557|gb|CI632948.1|CI632948
EST:     ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACCTCTTCCATG                         AGGGAGTCTTGTATGCCAAGAAGGACTACAACCTGGCCAAGCACCCAAAGG
genomic: ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACCTCTTCCATGgtgagattct ... ctatatgcagAGGGAGTCTTGTATGCCAAGAAGGACTACAACCTGGCCAAGCACCCAAAGG
EST: gi|2428870|gb|C73333.1|C73333
EST:     ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACCTCTTCCATG                         AGGGAGTCTTGTATGCCAAGAAGGACTACAACCTGGCCAAGCACCCAAAGG
genomic: ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACCTCTTCCATGgtgagattct ... ctatatgcagAGGGAGTCTTGTATGCCAAGAAGGACTACAACCTGGCCAAGCACCCAAAGG
EST: gi|33670983|gb|CF299222.1|CF299222
EST:     ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACCTCTTCCATG                         AGGGAGTCTTGTATGCCAAGAAGGACTACAACCTGGCCAAGCACCCAAAGG
genomic: ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACCTCTTCCATGgtgagattct ... ctatatgcagAGGGAGTCTTGTATGCCAAGAAGGACTACAACCTGGCCAAGCACCCAAAGG
EST: gi|66918131|gb|CX104979.1|CX104979
EST:     ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACCTCTTCCATG                         AGGGAGTCTTGTATGCCAAGAAGGACTACAACCTGGCCAAGCACCCAAAGG
genomic: ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACCTCTTCCATGgtgagattct ... ctatatgcagAGGGAGTCTTGTATGCCAAGAAGGACTACAACCTGGCCAAGCACCCAAAGG
EST: gi|88364474|gb|CI644552.1|CI644552
EST:     ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACCTCTTCCATG                         AGGGAGTCTTGTATGCCAAGAAGGACTACAACCTGGCCAAGCACCCAAAGG
genomic: ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACCTCTTCCATGgtgagattct ... ctatatgcagAGGGAGTCTTGTATGCCAAGAAGGACTACAACCTGGCCAAGCACCCAAAGG
EST: gi|88360769|gb|CI647779.1|CI647779
EST:     ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACCTCTTCCATG                         AGGGAGTCTTGTATGCCAAGAAGGACTACAACCTGGCCAAGCACCCAAAGG
genomic: ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACCTCTTCCATGgtgagattct ... ctatatgcagAGGGAGTCTTGTATGCCAAGAAGGACTACAACCTGGCCAAGCACCCAAAGG
EST: gi|88325019|gb|CI645035.1|CI645035
EST:     ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACCTCTTCCATG                         AGGGAGTCTTGTATGCCAAGAAGGACTACAACCTGGCCAAGCACCCAAAGG
genomic: ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACCTCTTCCATGgtgagattct ... ctatatgcagAGGGAGTCTTGTATGCCAAGAAGGACTACAACCTGGCCAAGCACCCAAAGG
EST: gi|88334750|gb|CI676543.1|CI676543
EST:     ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACCTCTTCCATG                         AGGGAGTCTTGTATGCCAAGAAGGACTACAACCTGGCCAAGCACCCAAAGG
genomic: ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACCTCTTCCATGgtgagattct ... ctatatgcagAGGGAGTCTTGTATGCCAAGAAGGACTACAACCTGGCCAAGCACCCAAAGG
EST: gi|88341101|gb|CI638657.1|CI638657
EST:     ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACCTCTTCCATG                         AGGGAGTCTTGTATGCCAAGAAGGACTACAACCTGGCCAAGCACCCAAAGG
genomic: ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACCTCTTCCATGgtgagattct ... ctatatgcagAGGGAGTCTTGTATGCCAAGAAGGACTACAACCTGGCCAAGCACCCAAAGG
EST: gi|88290586|gb|CI666959.1|CI666959
EST:     ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACCTCTTCCATG                         AGGGAGTCTTGTATGCCAAGAAGGACTACAACCTGGCCAAGCACCCAAAGG
genomic: ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACCTCTTCCATGgtgagattct ... ctatatgcagAGGGAGTCTTGTATGCCAAGAAGGACTACAACCTGGCCAAGCACCCAAAGG
EST: gi|86831237|gb|CI297506.1|CI297506
EST:     ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACCTCTTCCATG                         AGGGAGTCTTGTATGCCAAGAAGGACTACAACCTGGCCAAGCACCCAAAGG
genomic: ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACCTCTTCCATGgtgagattct ... ctatatgcagAGGGAGTCTTGTATGCCAAGAAGGACTACAACCTGGCCAAGCACCCAAAGG
EST: gi|88343622|gb|CI677601.1|CI677601
EST:     ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACCTCTTCCATG                         AGGGAGTCTTGTATGCCAAGAAGGACTACAACCTGGCCAAGCACCCAAAGG
genomic: ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACCTCTTCCATGgtgagattct ... ctatatgcagAGGGAGTCTTGTATGCCAAGAAGGACTACAACCTGGCCAAGCACCCAAAGG
EST: gi|33659995|gb|CF290962.1|CF290962
EST:     ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACCTCTTCCATG                         AGGGAGTCTTGTATGCCAAGAAGGACTACAACCTGGCCAAGCACCCAAAGG
genomic: ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACCTCTTCCATGgtgagattct ... ctatatgcagAGGGAGTCTTGTATGCCAAGAAGGACTACAACCTGGCCAAGCACCCAAAGG
EST: gi|88313669|gb|CI671802.1|CI671802
EST:     ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACCTCTTCCATG                         AGGGAGTCTTGTATGCCAAGAAGGACTACAACCTGGCCAAGCACCCAAAGG
genomic: ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACCTCTTCCATGgtgagattct ... ctatatgcagAGGGAGTCTTGTATGCCAAGAAGGACTACAACCTGGCCAAGCACCCAAAGG
EST: gi|88727672|gb|CI749474.1|CI749474
EST:     ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACCTCTTCCATG                         AGGGAGTCTTGTATGCCAAGAAGGACTACAACCTGGCCAAGCACCCAAAGG
genomic: ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACCTCTTCCATGgtgagattct ... ctatatgcagAGGGAGTCTTGTATGCCAAGAAGGACTACAACCTGGCCAAGCACCCAAAGG
EST: gi|88338425|gb|CI645679.1|CI645679
EST:     ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACCTCTTCCATG                         AGGGAGTCTTGTATGCCAAGAAGGACTACAACCTGGCCAAGCACCCAAAGG
genomic: ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACCTCTTCCATGgtgagattct ... ctatatgcagAGGGAGTCTTGTATGCCAAGAAGGACTACAACCTGGCCAAGCACCCAAAGG
EST: gi|33815878|gb|CF333786.1|CF333786
EST:     ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACCTCTTCCATG                         AGGGAGTCTTGTATGCCAAGAAGGACTACAACCTGGCCAAGCACCCAAAGG
genomic: ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACCTCTTCCATGgtgagattct ... ctatatgcagAGGGAGTCTTGTATGCCAAGAAGGACTACAACCTGGCCAAGCACCCAAAGG
EST: gi|88329374|gb|CI653291.1|CI653291
EST:     ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACCTCTTCCATG                         AGGGAGTCTTGTATGCCAAGAAGGACTACAACCTGGCCAAGCACCCAAAGG
genomic: ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACCTCTTCCATGgtgagattct ... ctatatgcagAGGGAGTCTTGTATGCCAAGAAGGACTACAACCTGGCCAAGCACCCAAAGG
EST: gi|88734384|gb|CI757892.1|CI757892
EST:     ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACCTCTTCCATG                         AGGGAGTCTTGTATGCCAAGAAGGACTACAACCTGGCCAAGCACCCAAAGG
genomic: ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACCTCTTCCATGgtgagattct ... ctatatgcagAGGGAGTCTTGTATGCCAAGAAGGACTACAACCTGGCCAAGCACCCAAAGG
EST: gi|88342338|gb|CI645860.1|CI645860
EST:     ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACCTCTTCCATG                         AGGGAGTCTTGTATGCCAAGAAGGACTACAACCTGGCCAAGCACCCAAAGG
genomic: ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACCTCTTCCATGgtgagattct ... ctatatgcagAGGGAGTCTTGTATGCCAAGAAGGACTACAACCTGGCCAAGCACCCAAAGG
EST: gi|55435537|gb|CV730899.1|CV730899
EST:     ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACCTCTTCCATG                         T
genomic: ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACCTCTTCCATGgtgagattct ... ctatatgcag-
EST: gi|55435537|gb|CV730899.1|CV730899
EST:     ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACCTCTTCCATG                         T
genomic: ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACCTCTTCCATGgtgagattct ... ctatatgcag-

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: 38 (upstream exon), 69 (downstream exon)
Score: 7

ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACCTCTTCCATGgtgagattct ... ctatatgcagAGGGAGTCTTGTATGCCAAGAAGGACTACAACCTGGCCAAGCACCCAAAGGTTGATGTGCCCAACTTGGAGGTGATTAAGCTCATGCAGAGCTTCAAGTC




<











<


<









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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACCTCTTCCATGgtgagattctccccctttcttctcctctatacgccgactctgtacattgtgtatgtgctgatcgtgattgcaagcttcgacttgatgtggtgttgcagta

- - - -  AAGAAG
- - - - - - AAGAAC
- - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctccccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cttctcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cgccgac