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'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCCTCGCAAAGGAGTTCCTTGGTGCTGCCAATGACAAGCGGAAGGAAATCCTCTCCAATATGGAAGAGGAGGTTGTGAAGCTCAGTGGTTCTGCTGCAAAgtaaactctagtctaagttgcatttattatttttgcaatgacgttatctgtacatgcaagttgaaccttggcatttacatatttaaatcag

Basic information

species Oryza sativa
transcript LOC_Os01g23740.1
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g23740.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM2G128171_T04 (Zea mays), 5'ss of exon 8
CCCTCGCAAAGGAGTTCCTTGGTGCTGCCAATGACAAGCGGAAGGAAATCCTCTCCAATATGGAAGAGGAGGTTGTGAAGCTCAGTGGTTCTGCTGCAAAgtaaactctagtctaagttgcatttattatttttgcaatgacgttatctgtacatgcaagttgaacctt--ggcatttacatatttaaatcag------------------------------
 ||| || |||||||||||||||||| ||  ||||||||| |||||| ||||||||| |||||| |||||||  |  |||||||||||||||||||||| |||||||||   || ||||    ||    | | |||  ||| | |||   |  ||   | || |   |    | || |   || |||| | ||                              
TCCTGGCTAAGGAGTTCCTTGGTGCTTCCGGTGACAAGCGAAAGGAAGTCCTCTCCAGTATGGAGGAGGAGGCAGATAAGCTCAGTGGTTCTGCTGCAAGgtaaactcttcccttagtta---ttggcctatctgccttga-gctattcattgatctcaattaacgttataagaatgttattagttaagtgagttgaattttccttattgcgtaataaatcag
















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|29613480|gb|CB618493.1|CB618493
EST:     CTCTCCAATATGGAAGAGGAGGTTGTGAAGCTCAGTGGTTCTGCTGCAAA                         GCATGGAAAGGTCTACATTGCCATTGCAAAGAAAATCCTGGACAAAGGTCA
genomic: CTCTCCAATATGGAAGAGGAGGTTGTGAAGCTCAGTGGTTCTGCTGCAAAgtaaactcta ... tttaaatcagGCATGGAAAGGTCTACATTGCCATTGCAAAGAAAATCCTGGACAAAGGTCA
EST: gi|86601985|gb|CI258661.1|CI258661
EST:     CTCTCCAATATGGAAGAGGAGGTTGTGAAGCTCAGTGGTTCTGCTGCAAA                         GCATGGAAAGGTCTACATTGCCATTGCAAAGAAAATCCTGGACAAAGGTCA
genomic: CTCTCCAATATGGAAGAGGAGGTTGTGAAGCTCAGTGGTTCTGCTGCAAAgtaaactcta ... tttaaatcagGCATGGAAAGGTCTACATTGCCATTGCAAAGAAAATCCTGGACAAAGGTCA
EST: gi|88965062|gb|CI097930.1|CI097930
EST:     CTCTCCAATATGGAAGAGGAGGTTGTGAAGCTCAGTGGTTCTGCTGCAAA                         GCATGGAAAGGTCTACATTGCCATTGCAAAGAAAATCCTGGACAAAGGTCA
genomic: CTCTCCAATATGGAAGAGGAGGTTGTGAAGCTCAGTGGTTCTGCTGCAAAgtaaactcta ... tttaaatcagGCATGGAAAGGTCTACATTGCCATTGCAAAGAAAATCCTGGACAAAGGTCA
EST: gi|88836436|gb|CI078333.1|CI078333
EST:     CTCCAATATGGAAGAGGAGGTTGTGAAGCTCAGTGGTTCTGCTGCAAA                         GCATGGAAAGGTCTACATTGCCATTGCAAAGAAAATCCTGGACAAAGGTCA
genomic: CTCCAATATGGAAGAGGAGGTTGTGAAGCTCAGTGGTTCTGCTGCAAAgtaaactcta ... tttaaatcagGCATGGAAAGGTCTACATTGCCATTGCAAAGAAAATCCTGGACAAAGGTCA
EST: gi|86413125|gb|CI067530.1|CI067530
EST:     CTCTCCAATATGGAAGAGGAGGTTGTGAAGCTCAGTGGTTCTGCTGCAAA                         GCATGGAAAGGTCTACATTGCCATTGCAAAGAAAATCCTGGACAAAGGTCA
genomic: CTCTCCAATATGGAAGAGGAGGTTGTGAAGCTCAGTGGTTCTGCTGCAAAgtaaactcta ... tttaaatcagGCATGGAAAGGTCTACATTGCCATTGCAAAGAAAATCCTGGACAAAGGTCA
EST: gi|88247610|gb|CI247459.1|CI247459
EST:     CTCTCCAATATGGAAGAGGAGGTTGTGAAGCTCAGTGGTTCTGCTGCAAA                         GCATGGAAAGGTTTACATTGCCATTGCAAAGAAAATCCTGGACAAAGGTCA
genomic: CTCTCCAATATGGAAGAGGAGGTTGTGAAGCTCAGTGGTTCTGCTGCAAAgtaaactcta ... tttaaatcagGCATGGAAAGGTCTACATTGCCATTGCAAAGAAAATCCTGGACAAAGGTCA
EST: gi|89183635|gb|CI046200.1|CI046200
EST:     CTCTCCAATATGGAAGAGGAGGTTGTGAAGCTCAGTGGTTCTGCTGCAAA                         GCATGGAAAGGTCTACATTGCCATTGCAAAGAAAATCCTGGACAAAGGTCA
genomic: CTCTCCAATATGGAAGAGGAGGTTGTGAAGCTCAGTGGTTCTGCTGCAAAgtaaactcta ... tttaaatcagGCATGGAAAGGTCTACATTGCCATTGCAAAGAAAATCCTGGACAAAGGTCA
EST: gi|88266700|gb|CI377602.1|CI377602
EST:     CTCTCCAATATGGAAGAGGAGGTTGTGAAGCTCAGTGGTTCTGCTGCAAA                         GCATGGAAAGGTCTACATTGCCATTGCAAAGAAAATCCTGGACAAAGGTCA
genomic: CTCTCCAATATGGAAGAGGAGGTTGTGAAGCTCAGTGGTTCTGCTGCAAAgtaaactcta ... tttaaatcagGCATGGAAAGGTCTACATTGCCATTGCAAAGAAAATCCTGGACAAAGGTCA
EST: gi|87029638|gb|CI257433.1|CI257433
EST:     CTCTCCAATATGGAAGAGGAGGTTGTGAAGCTCAGTGGTTCTGCTGCAAA                         GCATGGAAAGGTCTACATTGCCATTGCAAAGAAAATCCTGGACAAAGGTCA
genomic: CTCTCCAATATGGAAGAGGAGGTTGTGAAGCTCAGTGGTTCTGCTGCAAAgtaaactcta ... tttaaatcagGCATGGAAAGGTCTACATTGCCATTGCAAAGAAAATCCTGGACAAAGGTCA
EST: gi|87034904|gb|CI188707.1|CI188707
EST:     CTCTCCAATATGGAAGAGGAGGTTGTGAAGCTCAGTGGTTCTGCTGCAAA                         GCATGGAAAGGTCTACATTGCCATTGCAAAGAAAATCCTGGACAAAGGTCA
genomic: CTCTCCAATATGGAAGAGGAGGTTGTGAAGCTCAGTGGTTCTGCTGCAAAgtaaactcta ... tttaaatcagGCATGGAAAGGTCTACATTGCCATTGCAAAGAAAATCCTGGACAAAGGTCA
EST: gi|87031239|gb|CI259819.1|CI259819
EST:     CTCTCCAATATGGAAGAGGAGGTTGTGAAGCTCAGTGGTTCTGCTGCAAA                         GCATGGAAAGGTCTACATTGCCATTGCAAAGAAAATCCTGGACAAAGGTCA
genomic: CTCTCCAATATGGAAGAGGAGGTTGTGAAGCTCAGTGGTTCTGCTGCAAAgtaaactcta ... tttaaatcagGCATGGAAAGGTCTACATTGCCATTGCAAAGAAAATCCTGGACAAAGGTCA
EST: gi|88959312|gb|CI093007.1|CI093007
EST:     CTCCAATATGGAAGAGGAGGTTGTGAAGCTCAGTGGTTCTGCTGCAAA                         GCATGGAAAGGTCTACATTGCCATTGCAAAGAAAATCCTGGACAAAGGTCA
genomic: CTCCAATATGGAAGAGGAGGTTGTGAAGCTCAGTGGTTCTGCTGCAAAgtaaactcta ... tttaaatcagGCATGGAAAGGTCTACATTGCCATTGCAAAGAAAATCCTGGACAAAGGTCA
EST: gi|27548511|gb|CA766443.2|CA766443
EST:     CTCTCCAATATGGAAGAGGAGGTTGTGAAGCTCAGTGGTTCTGCTGCAAA                         GCATGGAAAGGTCTACATTGCCATTGCAAAGAAAATCCTGGACAAAGGTCA
genomic: CTCTCCAATATGGAAGAGGAGGTTGTGAAGCTCAGTGGTTCTGCTGCAAAgtaaactcta ... tttaaatcagGCATGGAAAGGTCTACATTGCCATTGCAAAGAAAATCCTGGACAAAGGTCA
EST: gi|88250135|gb|CI249984.1|CI249984
EST:     CTCTCCAATATGGAAGAGGAGGTTGTGAAGCTCAGTGGTTCTGCTGCAAA                         GCATGGAAAGGTCTACATTGCCATTGCAAAGAAAATCCTGGACAAAGGTCA
genomic: CTCTCCAATATGGAAGAGGAGGTTGTGAAGCTCAGTGGTTCTGCTGCAAAgtaaactcta ... tttaaatcagGCATGGAAAGGTCTACATTGCCATTGCAAAGAAAATCCTGGACAAAGGTCA
EST: gi|86603606|gb|CI112366.1|CI112366
EST:     CTCTCCAATATGGAAGAGGAGGTTGTGAAGCTCAGTGGTTCTGCTGCAAA                         GCATGGAAAGGTCTACATTGCCATTGCAAAGAAAATCCTGGACAAAGGTCA
genomic: CTCTCCAATATGGAAGAGGAGGTTGTGAAGCTCAGTGGTTCTGCTGCAAAgtaaactcta ... tttaaatcagGCATGGAAAGGTCTACATTGCCATTGCAAAGAAAATCCTGGACAAAGGTCA
EST: gi|86538109|gb|CI178315.1|CI178315
EST:     TGGTTCTGCTGCAAA                         GCATGGAAAGGTCTACATTGCCATTGCAAAGAAAATCCTGGACAAAGGTCA
genomic: TGGTTCTGCTGCAAAgtaaactcta ... tttaaatcagGCATGGAAAGGTCTACATTGCCATTGCAAAGAAAATCCTGGACAAAGGTCA
EST: gi|89197971|gb|CI117449.1|CI117449
EST:     CTCTCCAATATGGAAGAGGAGGTTGTGAAGCTCAGTGGTTCTGCTGCAAA                         GCATGGAAAGGTCTACATTGCCATTGCAAAGAAAATCCTGGACAAAGGTCA
genomic: CTCTCCAATATGGAAGAGGAGGTTGTGAAGCTCAGTGGTTCTGCTGCAAAgtaaactcta ... tttaaatcagGCATGGAAAGGTCTACATTGCCATTGCAAAGAAAATCCTGGACAAAGGTCA
EST: gi|86503530|gb|CI146163.1|CI146163
EST:     CTCTCCAATATGGAAGAGGAGGTTGTGAAGCTCAGTGGTTCTGCTGCAAA                         GCATGGAAAGGTCTACATTGCCATTGCAAAGAAAATCCTGGACAAAGGTCA
genomic: CTCTCCAATATGGAAGAGGAGGTTGTGAAGCTCAGTGGTTCTGCTGCAAAgtaaactcta ... tttaaatcagGCATGGAAAGGTCTACATTGCCATTGCAAAGAAAATCCTGGACAAAGGTCA
EST: gi|88828953|gb|CI073823.1|CI073823
EST:     CTCTCCAATATGGAAGAGGAGGTTGTGAAGCTCAGTGGTTCTGCTGCAAA                         GCATGGAAAGGTCTACATTGCCATTGCAAAGAAAATCCTGGACAAAGGTCA
genomic: CTCTCCAATATGGAAGAGGAGGTTGTGAAGCTCAGTGGTTCTGCTGCAAAgtaaactcta ... tttaaatcagGCATGGAAAGGTCTACATTGCCATTGCAAAGAAAATCCTGGACAAAGGTCA
EST: gi|88976785|gb|CI257527.1|CI257527
EST:     CTCTCCAATATGGAAGAGGAGGTTGTGAAGCTCAGTGGTTCTGCTGCAAA                         GCATGGAAAGGTCTACATTGCCATTGCAAAGAAAATCCTGGACAAAGGTCA
genomic: CTCTCCAATATGGAAGAGGAGGTTGTGAAGCTCAGTGGTTCTGCTGCAAAgtaaactcta ... tttaaatcagGCATGGAAAGGTCTACATTGCCATTGCAAAGAAAATCCTGGACAAAGGTCA
EST: gi|87016611|gb|CI275613.1|CI275613
EST:     CTCTCCAATATGGAAGAGGAGGTTGTGAAGCTCAGTGGTTCTGCTGCAAA                         GCATGGAAAGGTCTACATTGCCATTGCAAAGAAAATCCTGGACAAAGGTCA
genomic: CTCTCCAATATGGAAGAGGAGGTTGTGAAGCTCAGTGGTTCTGCTGCAAAgtaaactcta ... tttaaatcagGCATGGAAAGGTCTACATTGCCATTGCAAAGAAAATCCTGGACAAAGGTCA
EST: gi|86601984|gb|CI258660.1|CI258660
EST:     CTCTCCAATATGGAAGAGGAGGTTGTGAAGCTCAGTGGTTCTGCTGCAAA                         GCATGGAAAGGTCTACATTGCCATTGCAAAGAAAATCCTGGACAAAGGTCA
genomic: CTCTCCAATATGGAAGAGGAGGTTGTGAAGCTCAGTGGTTCTGCTGCAAAgtaaactcta ... tttaaatcagGCATGGAAAGGTCTACATTGCCATTGCAAAGAAAATCCTGGACAAAGGTCA

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), 75 (downstream exon)
Score: 46

CCCTCGCAAAGGAGTTCCTTGGTGCTGCCAATGACAAGCGGAAGGAAATCCTCTCCAATATGGAAGAGGAGGTTGTGAAGCTCAGTGGTTCTGCTGCAAAgtaaactcta ... tttaaatcagGCATGGAAAGGTCTACATTGCCATTGCAAAGAAAATCCTGGACAAAGGTCACGACTATACCAAGAAGGAAACAGAGAGGCTTGAACGCATGTTGGAGAAG




<











<


<









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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCCTCGCAAAGGAGTTCCTTGGTGCTGCCAATGACAAGCGGAAGGAAATCCTCTCCAATATGGAAGAGGAGGTTGTGAAGCTCAGTGGTTCTGCTGCAAAgtaaactctagtctaagttgcatttattatttttgcaatgacgttatctgtacatgcaagttgaaccttggcatttacatatttaaatcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC