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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attggttgtttgctttagaagtttataatctcagcaaggacaatgtatacctcttgaacggtttgtcgtcttaaagcttgatgaatatgtgttactgcagAATGGCGCTCAATGAGGAGTACACATACGTGGAGCTGGAGAAGGAGCCTTACTGGCCATTTGAGAAGCTGCGGATCTCGATTACGGGAGCTGGCGGGTTC

Basic information

species Oryza sativa
transcript LOC_Os11g37890.3
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g37890.3 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G138907_T01 (Zea mays), 3'ss of exon 1
attggttgtttgctttaga---agtttataatctcagcaaggacaatgtatac-ctcttgaacggtttgtcgtcttaaagcttgatgaatatgtgttactgcagAATGGCGCTCAATGAGGAGTACACATACGTGGAGCTGGAGAAGGAGCCTTACTGGCCATTTGAGAAGCTGCGGATCTCGATTACGGGAGCTGGCGGGTTC
 | ||||   |    | |     |   || | | |  ||  ||   |||   | || ||       || ||||| ||| ||| |||     | ||    |||||||||||||||||  |||||||||| |||| |||||||||||||||||| |||||||| || |||||||||||| |||| || || || || |||||||||
-tgggtttactctcatggtcatggccgatgagcgctacagagatcgtgttggctctatttggttagttttcgtcctaaggctcgat---cttctgcgtgtgcagAATGGCGCTCAACAAGGAGTACACGTACGCGGAGCTGGAGAAGGAGCCGTACTGGCCGTTCGAGAAGCTGCGGGTCTCCATCACCGGGGCCGGCGGGTTC
















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|88430768|gb|CI596882.1|CI596882
EST:     TCCCCTCCCCAAATCTCGCTCCCACGCCTCTTCCTTCCGACTTGTGACAG                         AATGGCGCTCAATGAGGAGTACACATACGTGGAGCTGGAGAAGGAGCCTTA
genomic: TCCCCTCCCCAAATCTCGCTCCCACGCCTCTTCCTTCCGACTTGTGACAGgtaatgcccc ... gttactgcagAATGGCGCTCAATGAGGAGTACACATACGTGGAGCTGGAGAAGGAGCCTTA
EST: gi|66913986|gb|CX100834.1|CX100834
EST:     TCCCCTCCCCAAATCTCGCTCCCACGCCTCTTCCTTCCGACTTGTGACAG                         AATGGCGCTCAATGAGGAGTACACATACGTGGAGCTGGAGAAGGAGCCTTA
genomic: TCCCCTCCCCAAATCTCGCTCCCACGCCTCTTCCTTCCGACTTGTGACAGgtaatgcccc ... gttactgcagAATGGCGCTCAATGAGGAGTACACATACGTGGAGCTGGAGAAGGAGCCTTA
EST: gi|88738960|gb|CI762468.1|CI762468
EST:     TCCCCTCCCCAAATCTCGCTCCCACGCCTCTTCCTTCCGACTTGTGACAG                         AATGGCGCTCAATGAGGAGTACACATACGTGGAGCTGGAGAAGGAGCCTTA
genomic: TCCCCTCCCCAAATCTCGCTCCCACGCCTCTTCCTTCCGACTTGTGACAGgtaatgcccc ... gttactgcagAATGGCGCTCAATGAGGAGTACACATACGTGGAGCTGGAGAAGGAGCCTTA
EST: gi|88344540|gb|CI637149.1|CI637149
EST:     TCCCCTCCCCAAATCTCGCTCCCACGCCTCTTCCTTCCGACTTGTGAGAG                         AATGGCGCTCAATGAGGAGTAAACATACGTGGAGCTGGAGAAGGAGCGTTA
genomic: TCCCCTCCCCAAATCTCGCTCCCACGCCTCTTCCTTCCGACTTGTGACAGgtaatgcccc ... gttactgcagAATGGCGCTCAATGAGGAGTACACATACGTGGAGCTGGAGAAGGAGCCTTA
EST: gi|29614307|gb|CB619320.1|CB619320
EST:     TCCCCTCCCCAAATCTCGCTCCCACGCCTCTTCCTTCCGACTTGTGACAG                         AATGGCGCACAATGAGGAGTACACATACGTGGAGCTGGAGAAGGAGCCTTA
genomic: TCCCCTCCCCAAATCTCGCTCCCACGCCTCTTCCTTCCGACTTGTGACAGgtaatgcccc ... gttactgcagAATGGCGCTCAATGAGGAGTACACATACGTGGAGCTGGAGAAGGAGCCTTA
EST: gi|88344541|gb|CI637150.1|CI637150
EST:     TCCCCTCCCCAAATCTCGCTCCCACGCCTCTTCCTTCCGACTTGTGACAG                         AATGGCGCTCAATGAGGAGTACACATACGTGGAGCTGGAGAAGGAGCCTTA
genomic: TCCCCTCCCCAAATCTCGCTCCCACGCCTCTTCCTTCCGACTTGTGACAGgtaatgcccc ... gttactgcagAATGGCGCTCAATGAGGAGTACACATACGTGGAGCTGGAGAAGGAGCCTTA
EST: gi|88345921|gb|CI632394.1|CI632394
EST:     TCCCCTCCCCAAATCTCGCTCCCACGCCTCTTCCTTCCGACTTGTGACAG                         AATGGCGCTCAATGAGGAGTACACATACGTGGAGCTGGAGAAGGAGCCTTA
genomic: TCCCCTCCCCAAATCTCGCTCCCACGCCTCTTCCTTCCGACTTGTGACAGgtaatgcccc ... gttactgcagAATGGCGCTCAATGAGGAGTACACATACGTGGAGCTGGAGAAGGAGCCTTA
EST: gi|88694964|gb|CI739002.1|CI739002
EST:     TCCCCTCCCCAAATCTCGCTCCCACGCCTCTTCCTTCCGACTTGTGACAG                         AATGGCGCTCAATGAGGAGTACACATACGTGGAGCTGGAGAAGGAGCCTTA
genomic: TCCCCTCCCCAAATCTCGCTCCCACGCCTCTTCCTTCCGACTTGTGACAGgtaatgcccc ... gttactgcagAATGGCGCTCAATGAGGAGTACACATACGTGGAGCTGGAGAAGGAGCCTTA
EST: gi|88744121|gb|CI767481.1|CI767481
EST:     TCCCCTCCCCAAATCTCGCTCCCACGCCTCTTCCTTCCGACTTGTGACAG                         AATGGCGCTCAATGAGGAGTACACATACGTGGAGCTGGAGAAGGAGCCTTA
genomic: TCCCCTCCCCAAATCTCGCTCCCACGCCTCTTCCTTCCGACTTGTGACAGgtaatgcccc ... gttactgcagAATGGCGCTCAATGAGGAGTACACATACGTGGAGCTGGAGAAGGAGCCTTA
EST: gi|88690516|gb|CI734595.1|CI734595
EST:     TCCCCTCCCCAAATCTCGCTCCCACGCCTCTTCCTTCCGACTTGTGACAG                         AATGGCGCTCAATGAGGAGTACACATACGTGGAGCTGGAGAAGGAGCCTTA
genomic: TCCCCTCCCCAAATCTCGCTCCCACGCCTCTTCCTTCCGACTTGTGACAGgtaatgcccc ... gttactgcagAATGGCGCTCAATGAGGAGTACACATACGTGGAGCTGGAGAAGGAGCCTTA
EST: gi|88412737|gb|CI576001.1|CI576001
EST:     TCCCCTCCCCAAATCTCGCTCCCACGCCTCTTCCTTCCGACTTGTGACAG                         AATGGCGCTCAATGAGGAGTACACATACGTGGAGCTGGAGAAGGAGCCTTA
genomic: TCCCCTCCCCAAATCTCGCTCCCACGCCTCTTCCTTCCGACTTGTGACAGgtaatgcccc ... gttactgcagAATGGCGCTCAATGAGGAGTACACATACGTGGAGCTGGAGAAGGAGCCTTA
EST: gi|88740928|gb|CI763443.1|CI763443
EST:     TCCCCTCCCCAAATCTCGCTCCCACGCCTCTTCCTTCCGACTTGTGACAG                         AATGGCGCTCAATGAGGAGTACACATACGTGGAGCTGGAGAAGGAGCCTTA
genomic: TCCCCTCCCCAAATCTCGCTCCCACGCCTCTTCCTTCCGACTTGTGACAGgtaatgcccc ... gttactgcagAATGGCGCTCAATGAGGAGTACACATACGTGGAGCTGGAGAAGGAGCCTTA
EST: gi|88334898|gb|CI648673.1|CI648673
EST:     TCCCCTCCCCAAATCTCGCTCCCACGCCTCTTCCTTCCGACTTGTGACAG                         AATGGCGCTCAATGAGGAGTACACATACGTGGAGCTGGAGAAGGAGCCTTA
genomic: TCCCCTCCCCAAATCTCGCTCCCACGCCTCTTCCTTCCGACTTGTGACAGgtaatgcccc ... gttactgcagAATGGCGCTCAATGAGGAGTACACATACGTGGAGCTGGAGAAGGAGCCTTA
EST: gi|88401552|gb|CI588493.1|CI588493
EST:     TCCCCTCCCCAAATCTCGCTCCCACGCCTCTTCCTTCCGACTTGTGACAG                         AATGGCGCTCAATGAGGAGTACACATACGTGGAGCTGGAGAAGGAGCCTTA
genomic: TCCCCTCCCCAAATCTCGCTCCCACGCCTCTTCCTTCCGACTTGTGACAGgtaatgcccc ... gttactgcagAATGGCGCTCAATGAGGAGTACACATACGTGGAGCTGGAGAAGGAGCCTTA
EST: gi|88451454|gb|CI565507.1|CI565507
EST:     TCCCCTCCCCAAATCTCGCTCCCACGCCTCTTCCTTCCGACTTGTGACAG                         AATGGCGCTCAATGAGGAGTACACATACGTGGAGCTGGAGAAGGAGCCTTA
genomic: TCCCCTCCCCAAATCTCGCTCCCACGCCTCTTCCTTCCGACTTGTGACAGgtaatgcccc ... gttactgcagAATGGCGCTCAATGAGGAGTACACATACGTGGAGCTGGAGAAGGAGCCTTA
EST: gi|88349583|gb|CI653862.1|CI653862
EST:     TCCCCTCCCCAAATCTCGCTCCCACGCCTCTTCCTTCCGACTTGTGACAG                         AATGGCGCTCAATGAGGAGTACACATACGTGGAGCTGGAGAAGGAGCCTTA
genomic: TCCCCTCCCCAAATCTCGCTCCCACGCCTCTTCCTTCCGACTTGTGACAGgtaatgcccc ... gttactgcagAATGGCGCTCAATGAGGAGTACACATACGTGGAGCTGGAGAAGGAGCCTTA
EST: gi|88827094|gb|CI777659.1|CI777659
EST:     TCCCCTCCCCAAATCTCGCTCCCACGCCTCTTCCTTCCGACTTGTGACAG                         AATGGCGCTCAATGAGGAGTACACATACGTGGAGCTGGAGAAGGAGCCTTA
genomic: TCCCCTCCCCAAATCTCGCTCCCACGCCTCTTCCTTCCGACTTGTGACAGgtaatgcccc ... gttactgcagAATGGCGCTCAATGAGGAGTACACATACGTGGAGCTGGAGAAGGAGCCTTA
EST: gi|88338625|gb|CI644082.1|CI644082
EST:     TCCCCTCCCCAAATCTCGCTCCCACGCCTCTTCCTTCCGACTTGTGACAG                         AATGGCGCTCAATGAGGAGTACACATACGTGGAGCTGGAGAAGGAGCCTTA
genomic: TCCCCTCCCCAAATCTCGCTCCCACGCCTCTTCCTTCCGACTTGTGACAGgtaatgcccc ... gttactgcagAATGGCGCTCAATGAGGAGTACACATACGTGGAGCTGGAGAAGGAGCCTTA
EST: gi|88348917|gb|CI653961.1|CI653961
EST:     TCCCCTCCCCAAATCTCGCTCCCACGCCTCTTCCTTCCGACTTGTGACAG                         AATGGCGCTCAATGAGGAGTACACATACGTGGAGCTGGAGAAGGAGCCTTA
genomic: TCCCCTCCCCAAATCTCGCTCCCACGCCTCTTCCTTCCGACTTGTGACAGgtaatgcccc ... gttactgcagAATGGCGCTCAATGAGGAGTACACATACGTGGAGCTGGAGAAGGAGCCTTA
EST: gi|88316641|gb|CI622887.1|CI622887
EST:     TCCCCTCCCCAAATCTCGCTCCCACGCCTCTTCCTTCCGACTTGTGACAG                         AATGGCGCTCAATGAGGAGTACACATACGTGGAGCTGGAGAAGGAGCCTTA
genomic: TCCCCTCCCCAAATCTCGCTCCCACGCCTCTTCCTTCCGACTTGTGACAGgtaatgcccc ... gttactgcagAATGGCGCTCAATGAGGAGTACACATACGTGGAGCTGGAGAAGGAGCCTTA
EST: gi|88355782|gb|CI626223.1|CI626223
EST:     TCCCCTCCCCAAATCTCGCTCCCACGCCTCTTCCTTCCGACTTGTGACAG                         AATGGCGCTCAATGAGGAGTACACATACGTGGAGCTGGAGAAGGAGCCTTA
genomic: TCCCCTCCCCAAATCTCGCTCCCACGCCTCTTCCTTCCGACTTGTGACAGgtaatgcccc ... gttactgcagAATGGCGCTCAATGAGGAGTACACATACGTGGAGCTGGAGAAGGAGCCTTA
EST: gi|88328093|gb|CI649893.1|CI649893
EST:     TCCCCTCCCCAAATCTCGCTCCCACGCCTCTTCCTTCCGACTTGTGACAG                         AATGGCGCTCAATGAGGAGTACACATACGTGGAGCTGGAGAAGGAGCCTTA
genomic: TCCCCTCCCCAAATCTCGCTCCCACGCCTCTTCCTTCCGACTTGTGACAGgtaatgcccc ... gttactgcagAATGGCGCTCAATGAGGAGTACACATACGTGGAGCTGGAGAAGGAGCCTTA
EST: gi|2428177|gb|C72640.1|C72640
EST:     TCCCCTCCCCAAATCTCGCTCCCACGCCTCTTCCTTCCGACTTGTGACAG                         AATGGCGCTCAATGAGGAGTACACATACGTGGAGCTGGAGAAGGAGCCTTA
genomic: TCCCCTCCCCAAATCTCGCTCCCACGCCTCTTCCTTCCGACTTGTGACAGgtaatgcccc ... gttactgcagAATGGCGCTCAATGAGGAGTACACATACGTGGAGCTGGAGAAGGAGCCTTA
EST: gi|88402293|gb|CI615136.1|CI615136
EST:     TCCCCTCCCCAAATCTCGCTCCCACGCCTCTTCCTTCCGACTTGTGACAG                         AATGGCGCTCAATGAGGAGTACACATACGTGGAGCTGGAGAAGGAGCCTTA
genomic: TCCCCTCCCCAAATCTCGCTCCCACGCCTCTTCCTTCCGACTTGTGACAGgtaatgcccc ... gttactgcagAATGGCGCTCAATGAGGAGTACACATACGTGGAGCTGGAGAAGGAGCCTTA
EST: gi|88407691|gb|CI607825.1|CI607825
EST:     TCCCCTCCCCAAATCTCGCTCCCACGCCTCTTCCTTCCGACTTGTGACAG                         AATGGCGCTCAATGAGGAGTACACATACGTGGAGCTGGAGAAGGAGCCTTA
genomic: TCCCCTCCCCAAATCTCGCTCCCACGCCTCTTCCTTCCGACTTGTGACAGgtaatgcccc ... gttactgcagAATGGCGCTCAATGAGGAGTACACATACGTGGAGCTGGAGAAGGAGCCTTA
EST: gi|88348653|gb|CI634248.1|CI634248
EST:     TCCCCTCCCCAAATCTCGCTCCCACGCCTCTTCCTTCCGACTTGTGACAG                         AATGGCGCTCAATGAGGAGTACACATACGTGGAGCTGGAGAAGGAGCCTTA
genomic: TCCCCTCCCCAAATCTCGCTCCCACGCCTCTTCCTTCCGACTTGTGACAGgtaatgcccc ... gttactgcagAATGGCGCTCAATGAGGAGTACACATACGTGGAGCTGGAGAAGGAGCCTTA
EST: gi|88691229|gb|CI735308.1|CI735308
EST:     TCCCCTCCCCAAATCTCGCTCCCACGCCTCTTCCTTCCGACTTGTGACAG                         AATGGCGCTCAATGAGGAGTACACATACGTGGAGCTGGAGAAGGAGCCTTA
genomic: TCCCCTCCCCAAATCTCGCTCCCACGCCTCTTCCTTCCGACTTGTGACAGgtaatgcccc ... gttactgcagAATGGCGCTCAATGAGGAGTACACATACGTGGAGCTGGAGAAGGAGCCTTA
EST: gi|88353900|gb|CI634691.1|CI634691
EST:     TCCCCTCCCCAAATCTCGCTCCCACGCCTCTTCCTTCCGACTTGTGACAG                         AATGGCGCTCAATGAGGAGTACACATACGTGGAGCTGGAGAAGGAGCCTTA
genomic: TCCCCTCCCCAAATCTCGCTCCCACGCCTCTTCCTTCCGACTTGTGACAGgtaatgcccc ... gttactgcagAATGGCGCTCAATGAGGAGTACACATACGTGGAGCTGGAGAAGGAGCCTTA
EST: gi|86891813|gb|CI310031.1|CI310031
EST:     TCCCCTCCCCAAATCTCGCTCCCACGCCTCTTCCTTCCGACTTGTGACAG                         AATGGCGCTCAATGAGGAGTACACATACGTGGAGCTGGAGAAGGAGCCTTA
genomic: TCCCCTCCCCAAATCTCGCTCCCACGCCTCTTCCTTCCGACTTGTGACAGgtaatgcccc ... gttactgcagAATGGCGCTCAATGAGGAGTACACATACGTGGAGCTGGAGAAGGAGCCTTA
EST: gi|88570264|gb|CI661439.1|CI661439
EST:     TCCCCTCCCCAAATCTCGCTCCCACGCCTCTTCCTTCCGACTTGTGACAG                         AATGGCGCTCAATGAGGAGTACACATACGTGGAGCTGGAGAAGGAGCCTTA
genomic: TCCCCTCCCCAAATCTCGCTCCCACGCCTCTTCCTTCCGACTTGTGACAGgtaatgcccc ... gttactgcagAATGGCGCTCAATGAGGAGTACACATACGTGGAGCTGGAGAAGGAGCCTTA
EST: gi|88352392|gb|CI615646.1|CI615646
EST:     TCCCCTCCCCAAATCTCGCTCCCACGCCTCTTCCTTCCGACTTGTGACAG                         AATGGCGCTCAATGAGGAGTACACATACGTGGAGCTGGAGAAGGAGCCTTA
genomic: TCCCCTCCCCAAATCTCGCTCCCACGCCTCTTCCTTCCGACTTGTGACAGgtaatgcccc ... gttactgcagAATGGCGCTCAATGAGGAGTACACATACGTGGAGCTGGAGAAGGAGCCTTA
EST: gi|58592572|gb|CF990880.1|CF990880
EST:     TCCCCTCCCCAAATCTCGCTCCCACGCCTCTTCCTTCCGACTTGTGACAG                         AATGGCGCACAATGAGGAGTACACATACGTGGAGCTGGAGAAGGAGCCTTA
genomic: TCCCCTCCCCAAATCTCGCTCCCACGCCTCTTCCTTCCGACTTGTGACAGgtaatgcccc ... gttactgcagAATGGCGCTCAATGAGGAGTACACATACGTGGAGCTGGAGAAGGAGCCTTA
EST: gi|88314798|gb|CI608257.1|CI608257
EST:     TCCCCTCCCCAAATCTCGCTCCCACGCCTCTTCCTTCCGACTTGTGACAG                         AATGGCGCTCAATGAGGAGTACACATACGTGGAGCTGGAGAAGGAGCCTTA
genomic: TCCCCTCCCCAAATCTCGCTCCCACGCCTCTTCCTTCCGACTTGTGACAGgtaatgcccc ... gttactgcagAATGGCGCTCAATGAGGAGTACACATACGTGGAGCTGGAGAAGGAGCCTTA
EST: gi|88428654|gb|CI599370.1|CI599370
EST:     TCCCCTCCCCAAATCTCGCTCCCACGCCTCTTCCTTCCGACTTGTGACAG                         AATGGCGCTCAATGAGGAGTACACATACGTGGAGCTGGAGAAGGAGCCTTA
genomic: TCCCCTCCCCAAATCTCGCTCCCACGCCTCTTCCTTCCGACTTGTGACAGgtaatgcccc ... gttactgcagAATGGCGCTCAATGAGGAGTACACATACGTGGAGCTGGAGAAGGAGCCTTA
EST: gi|88333332|gb|CI642369.1|CI642369
EST:     TCCCCTCCCCAAATCTCGCTCCCACGCCTCTTCCTTCCGACTTGTGACAG                         AATGGCGCTCAATGAGGAGTACACATACGTGGAGCTGGAGAAGGAGCCTTA
genomic: TCCCCTCCCCAAATCTCGCTCCCACGCCTCTTCCTTCCGACTTGTGACAGgtaatgcccc ... gttactgcagAATGGCGCTCAATGAGGAGTACACATACGTGGAGCTGGAGAAGGAGCCTTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatacctcttgaacggtttgtcgtcttaaagcttgatgaatatgtgttactgcagAATGGCGCTCAATGAGGAGTACACATACGTGGAGCTGGAGAAGGAGCCTTACTGGCCATTTGAGAAGCTGCGGATCTCGATTACGGGAGCTGGCGGGTTC
                              gcttgat  putative branch site (score: 5)
                                   atgaatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attggttgtttgctttagaagtttataatctcagcaaggacaatgtatacctcttgaacggtttgtcgtcttaaagcttgatgaatatgtgttactgcagAATGGCGCTCAATGAGGAGTACACATACGTGGAGCTGGAGAAGGAGCCTTACTGGCCATTTGAGAAGCTGCGGATCTCGATTACGGGAGCTGGCGGGTTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT