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

GCATGGAAAGGTCTACATTGCCATTGCAAAGAAAATCCTGGACAAAGGTCACGACTATACCAAGAAGGAAACAGAGAGGCTTGAACGCATGTTGGAGAAGgtgggaaaccgtgatcgccaatccaaactttactatcacttgtcatcttacataatgaacgacttgtacttatacaatacttttttattttttttgcttcctgcag

Basic information

species Oryza sativa
transcript LOC_Os01g23740.1
intron # 10
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 10
lower sequence: GRMZM2G128171_T04 (Zea mays), 5'ss of exon 9
GCATGGAAAGGTCTACATTGCCATTGCAAAGAAAATCCTGGACAAAGGTCACGACTATACCAAGAAGGAAACAGAGAGGCTTGAACGCATGTTGGAGAAGgtgggaaaccgtgatcgccaatccaaactttactatcacttgtcatcttacataatgaacgacttgtacttatacaatacttttttattttttttgcttcctgcag
|||||||||||||||  |  |||| |||||||| || || || |||||  |||| |||||  ||||||||||  |||||||||| ||||| ||||||||||||||||||    | | |     |||  | |   || |    || ||||     |  |   ||  ||||  ||   ||   |  |   | ||||| | |  |||||
GCATGGAAAGGTCTATGTAACCATCGCAAAGAAGATTCTAGAGAAAGGCAACGAGTATACTGAGAAGGAAACCAAGAGGCTTGATCGCATCTTGGAGAAGgtgggaaacgcctacctcg----caagatgtctcatgaaacatcctcttttgggacaactcacc-gtacagatttgattactcatatctctttttccctgttgcag
















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|88491028|gb|CI428300.1|CI428300
EST:     AGAAGGAAACAGAGAGGCTTGAACGCATGTTGGAGAAG                         TCCATCAGCCCATCAAAGGCCGATGAATTCATCATCAAGAAGAACGTCCTT
genomic: AGAAGGAAACAGAGAGGCTTGAACGCATGTTGGAGAAGgtgggaaacc ... cttcctgcagTCCATCAGCCCATCAAAGGCCGATGAATTCATCATCAAGAAGAACGTCCTT
EST: gi|88442528|gb|CI544095.1|CI544095
EST:     AAGAAGGAAACAGAGAGGCTTGAACGCATGTTGGAGAAG                         TCCATCAGCCCATCAAAGGCCGATGAATTCATCATCAAGAAGAACGTCCTT
genomic: AAGAAGGAAACAGAGAGGCTTGAACGCATGTTGGAGAAGgtgggaaacc ... cttcctgcagTCCATCAGCCCATCAAAGGCCGATGAATTCATCATCAAGAAGAACGTCCTT
EST: gi|29613480|gb|CB618493.1|CB618493
EST:     ACGACTATACCAAGAAGGAAACAGAGAGGCTTGAACGCATGTTGGAGAAG                         TCCATCAGCCCATCAAAGGCCGATGAATTCATCATCAAGAAGAACGTCCTT
genomic: ACGACTATACCAAGAAGGAAACAGAGAGGCTTGAACGCATGTTGGAGAAGgtgggaaacc ... cttcctgcagTCCATCAGCCCATCAAAGGCCGATGAATTCATCATCAAGAAGAACGTCCTT
EST: gi|86601985|gb|CI258661.1|CI258661
EST:     ACAACTATACCAAGAAGGAAACAGAGAGGCTTGAACGCATGTTGGAGAAG                         TCCATCAGCCCATCAAAGGCCGATGAATTCATCATCAAGAAGAACGTCCTT
genomic: ACGACTATACCAAGAAGGAAACAGAGAGGCTTGAACGCATGTTGGAGAAGgtgggaaacc ... cttcctgcagTCCATCAGCCCATCAAAGGCCGATGAATTCATCATCAAGAAGAACGTCCTT
EST: gi|88965062|gb|CI097930.1|CI097930
EST:     ACGACTATACCAAGAAGGAAACAGAGAGGCTTGAACGCATGTTGGAGAAG                         TCCATCAGCCCATCAAAGGCCGATGAATTCATCATCAAGAAGCACGTCCTT
genomic: ACGACTATACCAAGAAGGAAACAGAGAGGCTTGAACGCATGTTGGAGAAGgtgggaaacc ... cttcctgcagTCCATCAGCCCATCAAAGGCCGATGAATTCATCATCAAGAAGAACGTCCTT
EST: gi|88836436|gb|CI078333.1|CI078333
EST:     ACGACTATACCAAGAAGGAAACAGAGAGGCTTGAACGCATGTTGGAGAAG                         TCCATCAGCCCATCAAAGGCCGATGAATTCATCATCAAGAAGAACGTCCTT
genomic: ACGACTATACCAAGAAGGAAACAGAGAGGCTTGAACGCATGTTGGAGAAGgtgggaaacc ... cttcctgcagTCCATCAGCCCATCAAAGGCCGATGAATTCATCATCAAGAAGAACGTCCTT
EST: gi|86413125|gb|CI067530.1|CI067530
EST:     ACGACTATACCAAGAAGGAAACAGAGAGGCTTGAACGCATGTTGGAGAAG                         TCCATCAGCCCATCAAAGGCCGATGAATTCATCATCAAGAAGAACGTCCTT
genomic: ACGACTATACCAAGAAGGAAACAGAGAGGCTTGAACGCATGTTGGAGAAGgtgggaaacc ... cttcctgcagTCCATCAGCCCATCAAAGGCCGATGAATTCATCATCAAGAAGAACGTCCTT
EST: gi|86878476|gb|CI319666.1|CI319666
EST:     ACGACTATACCAAGAAGGAAACAGAGAGGCTTGAACGCATGTTGGAGAAG                         TCCATCAGCCCATCAAAGGCCGATGAATTCATCATCAAGAAGAACGTCCTT
genomic: ACGACTATACCAAGAAGGAAACAGAGAGGCTTGAACGCATGTTGGAGAAGgtgggaaacc ... cttcctgcagTCCATCAGCCCATCAAAGGCCGATGAATTCATCATCAAGAAGAACGTCCTT
EST: gi|86538091|gb|CI178297.1|CI178297
EST:     ACGACTATACCAAGAAGGAAACAGAGAGGCTTGAACGCATGTTGGAGAAG                         TCCATCAGCCCATCAAAGGCCGATGAATTCATCATCAAGAAGAACGTCCTT
genomic: ACGACTATACCAAGAAGGAAACAGAGAGGCTTGAACGCATGTTGGAGAAGgtgggaaacc ... cttcctgcagTCCATCAGCCCATCAAAGGCCGATGAATTCATCATCAAGAAGAACGTCCTT
EST: gi|88247610|gb|CI247459.1|CI247459
EST:     ACGACTATACCAAGAAGGAAACAGAGAGGCTTGAACGCATGTTGGAGAAG                         TCCATCAGCCCATCAAAGGCCGATGAATTCATCATCAAGAAGAACGTCCTT
genomic: ACGACTATACCAAGAAGGAAACAGAGAGGCTTGAACGCATGTTGGAGAAGgtgggaaacc ... cttcctgcagTCCATCAGCCCATCAAAGGCCGATGAATTCATCATCAAGAAGAACGTCCTT
EST: gi|89183635|gb|CI046200.1|CI046200
EST:     ACGACTATACCAAGAAGGAAACAGAGAGGCTTGAACGCATGTTGGAGAAG                         TCCATCAGCCCATCAAAGGCCGATGAATTCATCATCAAGAAGAACGTCCTT
genomic: ACGACTATACCAAGAAGGAAACAGAGAGGCTTGAACGCATGTTGGAGAAGgtgggaaacc ... cttcctgcagTCCATCAGCCCATCAAAGGCCGATGAATTCATCATCAAGAAGAACGTCCTT
EST: gi|88266700|gb|CI377602.1|CI377602
EST:     ACGACTATACCAAGAAGGAAACAGAGAGGCTTGAACGCATGTTGGAGAAG                         TCCATCAGCCCATCAAAGGCCGATGAATTCATCATCAAGAAGAACGTCCTT
genomic: ACGACTATACCAAGAAGGAAACAGAGAGGCTTGAACGCATGTTGGAGAAGgtgggaaacc ... cttcctgcagTCCATCAGCCCATCAAAGGCCGATGAATTCATCATCAAGAAGAACGTCCTT
EST: gi|87029638|gb|CI257433.1|CI257433
EST:     ACGACTATACCAAGAAGGAAACAGAGAGGCTTGAACGCATGTTGGAGAAG                         TCCATCAGCCCATCAAAGGCCGATGAATTCATCATCAAGAAGAACGTCCTT
genomic: ACGACTATACCAAGAAGGAAACAGAGAGGCTTGAACGCATGTTGGAGAAGgtgggaaacc ... cttcctgcagTCCATCAGCCCATCAAAGGCCGATGAATTCATCATCAAGAAGAACGTCCTT
EST: gi|87034904|gb|CI188707.1|CI188707
EST:     ACGACTATACCAAGAAGGAAACAGAGAGGCTTGAACGCATGTTGGAGAAG                         TCCATCAGCCCATCAAAGGCCGATGAATTCATCATCAAGAAGAACGTCCTT
genomic: ACGACTATACCAAGAAGGAAACAGAGAGGCTTGAACGCATGTTGGAGAAGgtgggaaacc ... cttcctgcagTCCATCAGCCCATCAAAGGCCGATGAATTCATCATCAAGAAGAACGTCCTT
EST: gi|87031239|gb|CI259819.1|CI259819
EST:     ACGACTATACCAAGAAGGAAACAGAGAGGCTTGAACGCATGTTGGAGAAG                         TCCATCAGCCCATCAAAGGCCGATGAATTCATCATCAAGAAGAACGTCCTT
genomic: ACGACTATACCAAGAAGGAAACAGAGAGGCTTGAACGCATGTTGGAGAAGgtgggaaacc ... cttcctgcagTCCATCAGCCCATCAAAGGCCGATGAATTCATCATCAAGAAGAACGTCCTT
EST: gi|88959312|gb|CI093007.1|CI093007
EST:     ACGACTATACCAAGAAGGAAACAGAGAGGCTTGAACGCATGTTGGAGAAG                         TCCATCAGCCCATCAAAGGCCGATGAATTCATCATCAAGAAGAACGTCCTT
genomic: ACGACTATACCAAGAAGGAAACAGAGAGGCTTGAACGCATGTTGGAGAAGgtgggaaacc ... cttcctgcagTCCATCAGCCCATCAAAGGCCGATGAATTCATCATCAAGAAGAACGTCCTT
EST: gi|27548511|gb|CA766443.2|CA766443
EST:     ACGACTATACCAAGAAGGAAACAGAGAGGCTTGAACGCATGTTGGAGAAG                         TCCATCAGCCCATCAAAGGCCGATGAATTCATCATCAAGAAGAACGTCCTT
genomic: ACGACTATACCAAGAAGGAAACAGAGAGGCTTGAACGCATGTTGGAGAAGgtgggaaacc ... cttcctgcagTCCATCAGCCCATCAAAGGCCGATGAATTCATCATCAAGAAGAACGTCCTT
EST: gi|88446785|gb|CI526618.1|CI526618
EST:     TTGAACGCATGTTGGAGAAG                         TCCATCAGCCCATCAAAGGCCGATGAATTCATCATCAAGAAGAACGTCCTT
genomic: TTGAACGCATGTTGGAGAAGgtgggaaacc ... cttcctgcagTCCATCAGCCCATCAAAGGCCGATGAATTCATCATCAAGAAGAACGTCCTT
EST: gi|88250135|gb|CI249984.1|CI249984
EST:     ACGACTATACCAAGAAGGAAACAGAGAGGCTTGAACGCATGTTGGAGAAG                         TCCATCAGCCCATCAAAGGCCGATGAATTCATCATCAAGAAGAACGTCCTT
genomic: ACGACTATACCAAGAAGGAAACAGAGAGGCTTGAACGCATGTTGGAGAAGgtgggaaacc ... cttcctgcagTCCATCAGCCCATCAAAGGCCGATGAATTCATCATCAAGAAGAACGTCCTT
EST: gi|88270195|gb|CI381493.1|CI381493
EST:     CTATACCAAGAAGGAAACAGAGAGGCTTGAACGCATGTTGGAGAAG                         TCCATCAGCCCATCAAAGGCCGATGAATTCATCATCAAGAAGAACGTCCTT
genomic: CTATACCAAGAAGGAAACAGAGAGGCTTGAACGCATGTTGGAGAAGgtgggaaacc ... cttcctgcagTCCATCAGCCCATCAAAGGCCGATGAATTCATCATCAAGAAGAACGTCCTT
EST: gi|86603606|gb|CI112366.1|CI112366
EST:     ACGACTATACCAAGAAGGAAACAGAGAGGCTTGAACGCATGTTGGAGAAG                         TCCATCAGCCCATCAAAGGCCGATGAATTCATCATCAAGAAGAACGTCCTT
genomic: ACGACTATACCAAGAAGGAAACAGAGAGGCTTGAACGCATGTTGGAGAAGgtgggaaacc ... cttcctgcagTCCATCAGCCCATCAAAGGCCGATGAATTCATCATCAAGAAGAACGTCCTT
EST: gi|88266516|gb|CI377418.1|CI377418
EST:     ACGACTATACCAAGAAGGAAACAGAGAGGCTTGAACGCATGTTGGAGAAG                         TCCATCAGCCCATCAAAGGCCGATGAATTCATCATCAAGAAGAACGTCCTT
genomic: ACGACTATACCAAGAAGGAAACAGAGAGGCTTGAACGCATGTTGGAGAAGgtgggaaacc ... cttcctgcagTCCATCAGCCCATCAAAGGCCGATGAATTCATCATCAAGAAGAACGTCCTT
EST: gi|86538109|gb|CI178315.1|CI178315
EST:     ACGACTATACCAAGAAGGAAACAGAGAGGCTTGAACGCATGTTGGAGAAG                         TCCATCAGCCCATCAAAGGCCGATGAATTCATCATCAAGAAGAACGTCCTT
genomic: ACGACTATACCAAGAAGGAAACAGAGAGGCTTGAACGCATGTTGGAGAAGgtgggaaacc ... cttcctgcagTCCATCAGCCCATCAAAGGCCGATGAATTCATCATCAAGAAGAACGTCCTT
EST: gi|89197971|gb|CI117449.1|CI117449
EST:     ACGACTATACCAAGAAGGAAACAGAGAGGCTTGAACGCATGTTGGAGAAG                         TCCATCAGCCCATCAAAGGCCGATGAATTCATCATCAAGAAGAACGTCCTT
genomic: ACGACTATACCAAGAAGGAAACAGAGAGGCTTGAACGCATGTTGGAGAAGgtgggaaacc ... cttcctgcagTCCATCAGCCCATCAAAGGCCGATGAATTCATCATCAAGAAGAACGTCCTT
EST: gi|86503530|gb|CI146163.1|CI146163
EST:     ACGACTATACCAAGAAGGAAACAGAGAGGCTTGAACGCATGTTGGAGAAG                         TCCATCAGCCCATCAAAGGCCGATGAATTCATCATCAAGAAGAACGTCCTT
genomic: ACGACTATACCAAGAAGGAAACAGAGAGGCTTGAACGCATGTTGGAGAAGgtgggaaacc ... cttcctgcagTCCATCAGCCCATCAAAGGCCGATGAATTCATCATCAAGAAGAACGTCCTT
EST: gi|88297767|gb|CI553396.1|CI553396
EST:     CAGAGAGGCTTGAACGCATGTTGGAGAAG                         TCCATCAGCCCATCAAAGGCCGATGAATTCATCATCAAGAAGAACGTCCTT
genomic: CAGAGAGGCTTGAACGCATGTTGGAGAAGgtgggaaacc ... cttcctgcagTCCATCAGCCCATCAAAGGCCGATGAATTCATCATCAAGAAGAACGTCCTT
EST: gi|88828953|gb|CI073823.1|CI073823
EST:     ACGACTATACCAAGAAGGAAACAGAGAGGCTTGAACGCATGTTGGAGAAG                         TCCATCAGCCCATCAAAGGCCGATGAATTCATCATCAAGAAGAACGTCCTT
genomic: ACGACTATACCAAGAAGGAAACAGAGAGGCTTGAACGCATGTTGGAGAAGgtgggaaacc ... cttcctgcagTCCATCAGCCCATCAAAGGCCGATGAATTCATCATCAAGAAGAACGTCCTT
EST: gi|86874759|gb|CI325270.1|CI325270
EST:     ACGACTATACCAAGAAGGAAACAGAGAGGCTTGAACGCATGTTGGAGAAG                         TCCATCAGCCCATCAAAGGCCGATGAATTCATCATCAAGAAGAACGTCCTT
genomic: ACGACTATACCAAGAAGGAAACAGAGAGGCTTGAACGCATGTTGGAGAAGgtgggaaacc ... cttcctgcagTCCATCAGCCCATCAAAGGCCGATGAATTCATCATCAAGAAGAACGTCCTT
EST: gi|88976785|gb|CI257527.1|CI257527
EST:     ACGACTATACCAAGAAGGAAACAGAGAGGCTTGAACGCATGTTGGAGAAG                         TCCATCAGCCCATCAAAGGCCGATGAATTCATCATCAAGAAGAACGTCCTT
genomic: ACGACTATACCAAGAAGGAAACAGAGAGGCTTGAACGCATGTTGGAGAAGgtgggaaacc ... cttcctgcagTCCATCAGCCCATCAAAGGCCGATGAATTCATCATCAAGAAGAACGTCCTT
EST: gi|87016611|gb|CI275613.1|CI275613
EST:     ACGACTATACCAAGAAGGAAACAGAGAGGCTTGAACGCATGTTGGAGAAG                         TCCATCAGCCCATCAAAGGCCGATGAATTCATCATCAAGAAGAACGTCCTT
genomic: ACGACTATACCAAGAAGGAAACAGAGAGGCTTGAACGCATGTTGGAGAAGgtgggaaacc ... cttcctgcagTCCATCAGCCCATCAAAGGCCGATGAATTCATCATCAAGAAGAACGTCCTT
EST: gi|86601984|gb|CI258660.1|CI258660
EST:     ACAACTATACCAAGAAGGAAACAGAGAGGCTTGAACGCATGTTGGAGAAG                         TCCATCAGCCCATCAAAGGCCGATGAATTCATCATCAAGAAGAACGTCCTT
genomic: ACGACTATACCAAGAAGGAAACAGAGAGGCTTGAACGCATGTTGGAGAAGgtgggaaacc ... cttcctgcagTCCATCAGCCCATCAAAGGCCGATGAATTCATCATCAAGAAGAACGTCCTT
EST: gi|88228403|gb|CI227883.1|CI227883
EST:     ATACCAAGAAGGAAACAGAGAGGCTTGAACGCATGTTGGAGAAG                         TCCATCAGCCCATCAAAGGCCGATGAATTCATCATCAAGAAGAACGTCCTT
genomic: ATACCAAGAAGGAAACAGAGAGGCTTGAACGCATGTTGGAGAAGgtgggaaacc ... cttcctgcagTCCATCAGCCCATCAAAGGCCGATGAATTCATCATCAAGAAGAACGTCCTT

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: 33

GCATGGAAAGGTCTACATTGCCATTGCAAAGAAAATCCTGGACAAAGGTCACGACTATACCAAGAAGGAAACAGAGAGGCTTGAACGCATGTTGGAGAAGgtgggaaacc ... cttcctgcagTCCATCAGCCCATCAAAGGCCGATGAATTCATCATCAAGAAGAACGTCCTTTCAACCTTCTCTTCCTAAGGCGATGTCAAACTCCATTCTTATCTTTGGG




<











<


<









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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCATGGAAAGGTCTACATTGCCATTGCAAAGAAAATCCTGGACAAAGGTCACGACTATACCAAGAAGGAAACAGAGAGGCTTGAACGCATGTTGGAGAAGgtgggaaaccgtgatcgccaatccaaactttactatcacttgtcatcttacataatgaacgacttgtacttatacaatacttttttattttttttgcttcctgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA