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

...tttcaatgaagtgaaatattattttcattgatggaacttactgtcatttcttgctttttttcgttacttgatggaacttcaatcttcttttcttctgcagGATTAGTCTTTGTTCAGCTGATCTGCGCAATCCAATACCGAGTCGTGAAGGAACATGCTGATGATGCATTCTATGAATTGCAGAATCCCCAACAGCAAAT

Basic information

species Oryza sativa
transcript LOC_Os06g04399.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g04399.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G173858_T01 (Zea mays), 3'ss of exon 1
-------tttcaatga-agtgaaatattattttcattgatggaacttactgtcatttcttgctttttttcgttacttgatggaacttcaatcttcttttcttctgcagGATTA-GTCTTTGTTCAGCTGATCTGCGCAATCCAATACCGAGTCGTGAAGGAACATGCTGATGATGCATTCTATGAATTGCAGAATCCCCAACAGCAAAT
         ||  | | | |||| |   |    | |||      |  | ||  | |  |||||| ||||| ||  |  |        | || |  ||||  |||||||||| | ||||| || || ||||||||| ||||||| ||||| || || |||||| |||| |||||||| |||||||| |||||||||||||| ||||||| 
tctagttcctctgtaataatgaagtgaaacaccctttg------ccca-tgctactcattgcttgttttc-ttgttgaaacagttaacgatatcatttttctctgcagGATAATGTCTTCGTCCAACTGATCTGCACAATCCAGTACCGTGTTGTCAAGGAAAATGCAGATGATGCTTTCTATGAGTTGCAGAATCCCCAGCAGCAAA-
















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|88310755|gb|CI672624.1|CI672624
EST:     CTACGGTGCAGAAGCGAGCCTAAAGTGCCGCTCATTTTGGTTTATAATCG                         GATTAGTCTTTGTTCAGCTGATCTGCGCAATCCAATACCGAGTCGTGAAGG
genomic: CTACGGTGCAGAAGCGAGCCTAAAGTGCCGCTCATTTTGGTTTATAATCGgtgagatctt ... tcttctgcagGATTAGTCTTTGTTCAGCTGATCTGCGCAATCCAATACCGAGTCGTGAAGG
EST: gi|88325449|gb|CI675252.1|CI675252
EST:     CTACGGTGCAGAAGCGAGCCTAAAGTGCCGCTCATTTTGGTTTATAATCG                         GATTAGTCTTTGTTCAGCTGATCTGCGCAATCCAATACCGAGTCGTGAAGG
genomic: CTACGGTGCAGAAGCGAGCCTAAAGTGCCGCTCATTTTGGTTTATAATCGgtgagatctt ... tcttctgcagGATTAGTCTTTGTTCAGCTGATCTGCGCAATCCAATACCGAGTCGTGAAGG
EST: gi|88326645|gb|CI658366.1|CI658366
EST:     CTACGGTGCAGAAGCGAGCCTAAAGTGCCGCTCATTTTGGTTTATAATCG                         GATTAGTCTTTGTT
genomic: CTACGGTGCAGAAGCGAGCCTAAAGTGCCGCTCATTTTGGTTTATAATCGgtgagatctt ... tcttctgcagGATTAGTCTTTGTT
EST: gi|88357299|gb|CI622148.1|CI622148
EST:     CTACGGTGCACAAGCGAGCCTAAAGTGCCGCTCATTTTGGTTTATAATCG                         GATTAGTCTTTGTTCAGCTGATCTGCGCAATCCAATAC-GAGTCG
genomic: CTACGGTGCAGAAGCGAGCCTAAAGTGCCGCTCATTTTGGTTTATAATCGgtgagatctt ... tcttctgcagGATTAGTCTTTGTTCAGCTGATCTGCGCAATCCAATACCGAGTCG
EST: gi|88392034|gb|CI683860.1|CI683860
EST:     CTACGGTGCAGAAGCGAGCCTAAAGTGCCGCTCATTTTGGTTTATAATCG                         GATTAGTCTTTGTTCAGCTGATCTGCGCAATCCAATACCGAGTCGTGAAGG
genomic: CTACGGTGCAGAAGCGAGCCTAAAGTGCCGCTCATTTTGGTTTATAATCGgtgagatctt ... tcttctgcagGATTAGTCTTTGTTCAGCTGATCTGCGCAATCCAATACCGAGTCGTGAAGG
EST: gi|88355515|gb|CI679234.1|CI679234
EST:     CTACGGTGCAGAAGCGAGCCTAAAGTGCCGCTCATTTTGGTTTATAATCG                         GATTAGTCTTTGTTCAGCTGATCTGCGCAATCCAATACCGAGTCGTGAAGG
genomic: CTACGGTGCAGAAGCGAGCCTAAAGTGCCGCTCATTTTGGTTTATAATCGgtgagatctt ... tcttctgcagGATTAGTCTTTGTTCAGCTGATCTGCGCAATCCAATACCGAGTCGTGAAGG
EST: gi|88331173|gb|CI639584.1|CI639584
EST:     CTACGGTGCAGAAGCGAGCCTAAAGTGCCGCTCATTTTGGTTTATAATCG                         GATTAGTCTTTGTTCAGCTGATC
genomic: CTACGGTGCAGAAGCGAGCCTAAAGTGCCGCTCATTTTGGTTTATAATCGgtgagatctt ... tcttctgcagGATTAGTCTTTGTTCAGCTGATC
EST: gi|88579801|gb|CI691787.1|CI691787
EST:     CTACGGTGCAGAAGCGAGCCTAAAGTGCCGCTCATTTTGGTTTATAATCG                         GATTAGTCTTTGTTCAGCTGATCTGCGCAATCCAATACCGAGTCGTGAAGG
genomic: CTACGGTGCAGAAGCGAGCCTAAAGTGCCGCTCATTTTGGTTTATAATCGgtgagatctt ... tcttctgcagGATTAGTCTTTGTTCAGCTGATCTGCGCAATCCAATACCGAGTCGTGAAGG
EST: gi|88380705|gb|CI634730.1|CI634730
EST:     CTACGGTGCAGAAGCGAGCCTAAAGTGCCGCTCATTTTGGTTTATAATCG                         GATTAGTCTTTGTTCAGCTGATCTGCGCAATCC
genomic: CTACGGTGCAGAAGCGAGCCTAAAGTGCCGCTCATTTTGGTTTATAATCGgtgagatctt ... tcttctgcagGATTAGTCTTTGTTCAGCTGATCTGCGCAATCC
EST: gi|88349272|gb|CI678249.1|CI678249
EST:     CTACGGTGCAGAAGCGAGCCTAAAGTGCCGCTCATTTTGGTTTATAATCG                         GATTAGTCTTTGTTCAGCTGATCTGCGCAATCCAATACCGAGTCGTGAAGG
genomic: CTACGGTGCAGAAGCGAGCCTAAAGTGCCGCTCATTTTGGTTTATAATCGgtgagatctt ... tcttctgcagGATTAGTCTTTGTTCAGCTGATCTGCGCAATCCAATACCGAGTCGTGAAGG
EST: gi|88407046|gb|CI581133.1|CI581133
EST:     CTACGGTGCAGAAGCGAGCCTAAAGTGCCGCTCATTTTGGTTTATAATCG                         GATTAGTCTTTGTTCAGCTGATCTGCGCAATCCAATACCGAGTCGTGAAGG
genomic: CTACGGTGCAGAAGCGAGCCTAAAGTGCCGCTCATTTTGGTTTATAATCGgtgagatctt ... tcttctgcagGATTAGTCTTTGTTCAGCTGATCTGCGCAATCCAATACCGAGTCGTGAAGG
EST: gi|88444825|gb|CI696256.1|CI696256
EST:     CTACGGTGCAGAAGCGAGCCTAAAGTGCCGCTCATTTTGGTTTATAATCG                         GATTAGTCTTTGTTCAGCTGATCTGCGCAATCCAATACCGAGT
genomic: CTACGGTGCAGAAGCGAGCCTAAAGTGCCGCTCATTTTGGTTTATAATCGgtgagatctt ... tcttctgcagGATTAGTCTTTGTTCAGCTGATCTGCGCAATCCAATACCGAGT
EST: gi|88340766|gb|CI636926.1|CI636926
EST:     CTACGGTGCAGAAGCGAGCCTAAAGTGCCGCTCATTTTGGTTTATAATCG                         GATTAGTCTTTGTTCAGCTGATCTGCG
genomic: CTACGGTGCAGAAGCGAGCCTAAAGTGCCGCTCATTTTGGTTTATAATCGgtgagatctt ... tcttctgcagGATTAGTCTTTGTTCAGCTGATCTGCG
EST: gi|88575264|gb|CI669409.1|CI669409
EST:     CTACGGTGCAGAAGCGAGCCTAAAGTGCCGCTCATTTTGGTTTATAATCG                         GATTAGTCTTTGTTCAGCTGATCTGCGCAATCCAATACCGAGTCGTGAAGG
genomic: CTACGGTGCAGAAGCGAGCCTAAAGTGCCGCTCATTTTGGTTTATAATCGgtgagatctt ... tcttctgcagGATTAGTCTTTGTTCAGCTGATCTGCGCAATCCAATACCGAGTCGTGAAGG
EST: gi|88587481|gb|CI705231.1|CI705231
EST:     CTACGGTGCAGAAGCGAGCCTAAAGTGCCGCTCATTTTGGTTTATAATCG                         GATTAGTCTTTGTTCAGCTGATCTGCGCAAT
genomic: CTACGGTGCAGAAGCGAGCCTAAAGTGCCGCTCATTTTGGTTTATAATCGgtgagatctt ... tcttctgcagGATTAGTCTTTGTTCAGCTGATCTGCGCAAT
EST: gi|88589922|gb|CI708741.1|CI708741
EST:     CTACGGTGCAGAAGCGAGCCTAAAGTGCCGCTCATTTTGGTTTATAATCG                         GATTAGTCTTTGTTCAGCTGATCTGCGCAATCCAATACCGAGTCGTGAAGG
genomic: CTACGGTGCAGAAGCGAGCCTAAAGTGCCGCTCATTTTGGTTTATAATCGgtgagatctt ... tcttctgcagGATTAGTCTTTGTTCAGCTGATCTGCGCAATCCAATACCGAGTCGTGAAGG
EST: gi|88574376|gb|CI666145.1|CI666145
EST:     CTACGGTGCAGAAGCGAGCCTAAAGTGCCGCTCATTTTGGTTTATAATCG                         GATTAGTCTTTGTTCAGCTGATCTGCGCAATCCAATACCGAGTCGTGAAGG
genomic: CTACGGTGCAGAAGCGAGCCTAAAGTGCCGCTCATTTTGGTTTATAATCGgtgagatctt ... tcttctgcagGATTAGTCTTTGTTCAGCTGATCTGCGCAATCCAATACCGAGTCGTGAAGG
EST: gi|88340150|gb|CI650597.1|CI650597
EST:     CTACGGTGCAGAAGCGAGCCTAAAGTGCCGCTCATTTTGGTTTATAATCG                         GATTAGTCTTTGTTCAGCTGATCTGCGCAA
genomic: CTACGGTGCAGAAGCGAGCCTAAAGTGCCGCTCATTTTGGTTTATAATCGgtgagatctt ... tcttctgcagGATTAGTCTTTGTTCAGCTGATCTGCGCAA
EST: gi|88410563|gb|CI686897.1|CI686897
EST:     CTACGGTGCAGAAGCGAGCCTAAAGTGCCGCTCATTTTGGTTTATAATCG                         GATTAGTCTTTGTTCAGCTGATCTGCGCAATCCAATACCGAGTCGTGAAGG
genomic: CTACGGTGCAGAAGCGAGCCTAAAGTGCCGCTCATTTTGGTTTATAATCGgtgagatctt ... tcttctgcagGATTAGTCTTTGTTCAGCTGATCTGCGCAATCCAATACCGAGTCGTGAAGG
EST: gi|27546291|gb|CA764446.2|CA764446
EST:     CTACGGTGCAGAAGCGAGCCTAAAGTGCCGCTCATTTTGGTTTATAATCG                         GATTAGTCTTCGTTCAGCTGATCTGCGCAATCCAATACCGAGTCGTGAAGG
genomic: CTACGGTGCAGAAGCGAGCCTAAAGTGCCGCTCATTTTGGTTTATAATCGgtgagatctt ... tcttctgcagGATTAGTCTTTGTTCAGCTGATCTGCGCAATCCAATACCGAGTCGTGAAGG

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: 74 (upstream exon), 58 (downstream exon)
Score: 37

GGAATATGAAGGATTAAATACCTTAACAACTGCCAAGGCACCATTGTTCTCTACGGTGCAGAAGCGAGCCTAAAGTGCCGCTCATTTTGGTTTATAATCGgtgagatctt ... tcttctgcagGATTAGTCTTTGTTCAGCTGATCTGCGCAATCCAATACCGAGTCGTGAAGGAACATGCTGATGATGCATTCTATGAATTGCAGAATCCCCAACAGCAAAT




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttcttgctttttttcgttacttgatggaacttcaatcttcttttcttctgcagGATTAGTCTTTGTTCAGCTGATCTGCGCAATCCAATACCGAGTCGTGAAGGAACATGCTGATGATGCATTCTATGAATTGCAGAATCCCCAACAGCAAAT
                    acttgat  putative branch site (score: 37)
                               cttcaatcttcttttc  putative PPT
         ttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttcaatgaagtgaaatattattttcattgatggaacttactgtcatttcttgctttttttcgttacttgatggaacttcaatcttcttttcttctgcagGATTAGTCTTTGTTCAGCTGATCTGCGCAATCCAATACCGAGTCGTGAAGGAACATGCTGATGATGCATTCTATGAATTGCAGAATCCCCAACAGCAAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - aagtgaaa
- - - - - - - - - - - - - -ttgatgg
- - - - - - - - - - - - - - - - - - cttactg