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

gtatgcagtaatcagttgtatccttctccagcttcagattcttctagcactgcattctactgacgtgaccaaactgataaattcagaagtaacataactcataaaacctttgttgatccatcgatctttacagGCAAATTCTAATTGGCTTTACATCGTGCCATGGGGGATGTACGGATGTGTGAACTACATCAAGCAGAAGTACGGGAATCCGACAGTCGTCATAACTGAAA

Basic information

species Oryza sativa
transcript LOC_Os03g49600.3
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g49600.1 (Oryza sativa), 3'ss of exon 9
lower sequence: AC217401.3_FGT001 (Zea mays), 3'ss of exon 9
gtatgcagtaatcagttgtatccttctccagcttcagat-tcttctagcac-tgcattctactgacgtgaccaaactgataaattcagaagtaacataactcataaaacctttgttgatccatcgatctttacagGCAAATTCTAATTGGCTTTACATCGTGCCATGGGGGATGTACGGATGTGTGAACTACATCAAGCAGAAGTACGGGAATCCGACAGTCGTCATAACTGAAA
       |||   |||| |   ||||  ||  | ||||| || || |  || |     | |     |   |    ||| |  ||| |||| |  |               ||||  | | || | || |   ||||| ||||| || |||||||||||||| |||   ||||||||||| |||||||||||  | ||||| ||||| || ||||| |||||  ||||||| || |
-------gtatgtagttcttcacttcagcatttgcagatatcatccaatacatattacccatcagtggatcagtgctggtggattgagaaatggc---------------tttg--gcttca-caatat---cagGCGAATTCAAAGTGGCTTTACATCGTCCCAGAAGGGATGTACGGTTGTGTGAACTATCTGAAGCACAAGTATGGAAATCCAACAGTTTTCATAACCGAGA

upper sequence: LOC_Os03g49600.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G118003_T04 (Zea mays), 3'ss of exon 1
gtatgcag-taatcagttgtatccttctccagcttcagattcttcta-gcactgcattctac-tgacgtgaccaaactgataaattcagaagtaacataactcataaaacctttgttgatccatcg-atctttac--agGCAAATTCTAATTGGCTTTACATCGTGCCATGGGGGATGTACGGATGTGTGAACTACATCAAGCAGAAGTACGGGAATCCGACAGTCGTCATAACTGAAA
||| || | |  ||  |    ||  ||||        | ||   ||    | |||||  ||    | ||  |   |   |  |||||  |||||    |||  | | ||   ||| | | | | || ||    ||  |||| |||||||| ||||| |||||||  ||   |||||||||||| || ||||||||| ||||| ||||||| |||||||| ||  ||  |||||| || |
gtacgctgctcctccatctactctctctctcatcgttgtttgcactgcatagtgcatggtatgctaggtagcatcagctacgaattctaaagtactgcaaca-agagaatacttgctaaccaaacgcatggacacgtagGCGAATTCTAAGTGGCTCTACATCGCCCCGACGGGGATGTACGGGTGCGTGAACTACCTCAAGGAGAAGTATGGGAATCCAACGATCTACATAACGGAGA

upper sequence: LOC_Os03g49600.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GLYMA09G30910.1 (Glycine max), 3'ss of exon 9
gtatgcagtaatcagttgtatccttctccagcttcagattcttctagcactgcattctactgacgtgaccaaactgataaattcagaagtaacataact-cataaaacctttgttgatccatcgatctttacagGCAAATTCTAATTGGCTTTACATCGTGCCATGGGGGATGTACGGATGTGTGAACTACATCAAGCAGAAGTACGGGAATCCGACAGTCGTCATAACTGAAA
                                            ||    |  | |        |  |   |    ||| |   | ||||   | |||     |    ||   |||     || || ||||||||| |||||| ||||||||||||  || |||||||| ||||||  ||   |||  ||||| ||| |    || || || || || ||  || || ||||||
-------------------------------------------gtaagtttaaacttagtcacagatattcattatatatagatacaagtgcaacaaccatgcattgactaatttgtaagttcaatttttacagGCTAATTCTTATTGGCTTTACAATGTACCATGGGGCATGTACAAATCATTGATGTACATAAAGGAACGTTATGGAAACCCAACTGTTATCTTATCTGAAA

upper sequence: LOC_Os03g49600.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GLYMA07G11310.1 (Glycine max), 3'ss of exon 9
gtatgcagtaatcagttgtatccttctccagcttcagattcttctagcactgcattctactgacgtg-accaaactgataaattcagaagtaaca-taactcataaaacctttgttgatccatcgatctttacagGCAAATTCTAATTGGCTTTACATCGTGCCATGGGGGATGTACGGATGTGTGAACTACATCAAGCAGAAGTACGGGAATCCGACAGTCGTCATAACTGAAA
                                            ||    |  |   || ||||    |   |  | | | || ||   | | ||   |  |||  |    || || |       || |||||||||  ||||| |||||||||||| ||| |||||||| ||||||  ||   |||  ||||| ||| |    || || || || || ||  || || | ||||
-------------------------------------------gtaa-gttttaacttagtgacagatattcattttaaagatacaagtgcaccaaccatgcattgactaatttttaagttg--aatttttacagGCTTATTCTTATTGGCTTTACAACGTACCATGGGGCATGTACAAATCATTGATGTACATAAAGGAACGTTATGGAAACCCAACTGTGTTCTTATCCGAAA

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|86828091|gb|CI274966.1|CI274966
EST:     TTGCGAAAAACGGCAAACCAATTGGACCACAG                         GCAAATTCTAATTGGCTTTACATCGTGCCATGGGGGATGTACGGATGTGTG
genomic: TTGCGAAAAACGGCAAACCAATTGGACCACAGgtatgcagta ... atctttacagGCAAATTCTAATTGGCTTTACATCGTGCCATGGGGGATGTACGGATGTGTG
EST: gi|29638181|gb|CB643190.1|CB643190
EST:     TTGCGAAAAACGGCAAACCAATTGGACCACAG                         GCAAATTCTAATTGGCTTTACATCGTGCCATGGGGGATGTACGGATGTGTG
genomic: TTGCGAAAAACGGCAAACCAATTGGACCACAGgtatgcagta ... atctttacagGCAAATTCTAATTGGCTTTACATCGTGCCATGGGGGATGTACGGATGTGTG
EST: gi|23514367|gb|BU673604.1|BU673604
EST:     TTGCGAAAAACGCCAAACCAAGTGGACCACAG                         GCAAATTCTAATTGGCTTTACATCGTGCCATGGGGGATGTACGGATGTGTG
genomic: TTGCGAAAAACGGCAAACCAATTGGACCACAGgtatgcagta ... atctttacagGCAAATTCTAATTGGCTTTACATCGTGCCATGGGGGATGTACGGATGTGTG
EST: gi|89168841|gb|CI020922.1|CI020922
EST:     TTGCGAAAAACGGCAAACCAATTGGACCACAG                         GCAAATTCTAATTGGCTTTACATCGTGCCATGGGGGATGTACGGATGTGTG
genomic: TTGCGAAAAACGGCAAACCAATTGGACCACAGgtatgcagta ... atctttacagGCAAATTCTAATTGGCTTTACATCGTGCCATGGGGGATGTACGGATGTGTG
EST: gi|8856614|gb|AU093932.1|AU093932
EST:     GAAAAACGGCAANCCCAATTGGACCACAG                         GCAAATTCTAAATTGGCTTTACATCGTGCCATGGGGGATGTACGGATGTGT
genomic: GAAAAACGGCAA-ACCAATTGGACCACAGgtatgcagta ... atctttacagGCAAATTCT-AATTGGCTTTACATCGTGCCATGGGGGATGTACGGATGTGT
EST: gi|29640990|gb|CB645997.1|CB645997
EST:     CGATTGGCAGTTGCGAAAAACGGCAAACCAATTGGACCGCAG                         GCAAATTTTAATTGGCTTTACATCGTGCCATGGGGGATGTACGGATGTGTG
genomic: CGATTGGCAGTTGCGAAAAACGGCAAACCAATTGGACCACAGgtatgcagta ... atctttacagGCAAATTCTAATTGGCTTTACATCGTGCCATGGGGGATGTACGGATGTGTG
EST: gi|88996445|gb|CI259949.1|CI259949
EST:     TTGCGAAAAACGGCAAACCAATTGGACCACAG                         GCAAATTCTAATTGGCTTTACATCGTGCCATGGGGGATGTACGGATGTGTG
genomic: TTGCGAAAAACGGCAAACCAATTGGACCACAGgtatgcagta ... atctttacagGCAAATTCTAATTGGCTTTACATCGTGCCATGGGGGATGTACGGATGTGTG
EST: gi|86593847|gb|CI260076.1|CI260076
EST:     TTGCGAAAAACGGCAAACCAATTGGACCACAG                         GCAAATTCTAATTGGCTTTACATCGTGCCATGGGGGATGTACGGATGTGTG
genomic: TTGCGAAAAACGGCAAACCAATTGGACCACAGgtatgcagta ... atctttacagGCAAATTCTAATTGGCTTTACATCGTGCCATGGGGGATGTACGGATGTGTG
EST: gi|86494154|gb|CI136787.1|CI136787
EST:     TTGCGAAAAACGGCAAACCAATTGGACCACAG                         GCAAATTCTAATTGGCTTTACATCGTGCCATGGGGGATGTACGGATGTGTG
genomic: TTGCGAAAAACGGCAAACCAATTGGACCACAGgtatgcagta ... atctttacagGCAAATTCTAATTGGCTTTACATCGTGCCATGGGGGATGTACGGATGTGTG
EST: gi|29667383|gb|CB663658.1|CB663658
EST:     TTGCGAAAAACGGCAAACCAATTGGACCACAG                         GCAAATTCTAATTGGCTTTACATCGTGCCATGGGGGATGTACGGATGTGTG
genomic: TTGCGAAAAACGGCAAACCAATTGGACCACAGgtatgcagta ... atctttacagGCAAATTCTAATTGGCTTTACATCGTGCCATGGGGGATGTACGGATGTGTG
EST: gi|86433834|gb|CI094177.1|CI094177
EST:     GAAAAACGGCAAACCAATGGGACCACAG                         GCAAATTCTAATGGGCTGTACATCGTGCCATGGGGGATGTACGGATGTGTG
genomic: GAAAAACGGCAAACCAATTGGACCACAGgtatgcagta ... atctttacagGCAAATTCTAATTGGCTTTACATCGTGCCATGGGGGATGTACGGATGTGTG
EST: gi|88844856|gb|CI022210.1|CI022210
EST:     TTGCGAAAAACGGCAAACCAATTGGACCACAG                         GCAAATTCTAATTGGCTTTACATCGTGCCATGGGGGATGTACGGATGTTGT
genomic: TTGCGAAAAACGGCAAACCAATTGGACCACAGgtatgcagta ... atctttacagGCAAATTCTAATTGGCTTTACATCGTGCCATGGGGGATGTACGGATG-TGT
EST: gi|29672037|gb|CB668312.1|CB668312
EST:     TTGCGAAAAACGGCAAACCAATTGGACCACAG                         GCAAATTCTAATTGGCTTTACATCGTGCCATGGGGGATGTACGGATGTGTG
genomic: TTGCGAAAAACGGCAAACCAATTGGACCACAGgtatgcagta ... atctttacagGCAAATTCTAATTGGCTTTACATCGTGCCATGGGGGATGTACGGATGTGTG
EST: gi|58669749|gb|CK058435.1|CK058435
EST:     CAATTGGACCACAG                         GCAAATTCTAATTGGCTTTACATCGTGCCA---GGGATGTACGGATGTGTG
genomic: CAATTGGACCACAGgtatgcagta ... atctttacagGCAAATTCTAATTGGCTTTACATCGTGCCATGGGGGATGTACGGATGTGTG
EST: gi|86495139|gb|CI137772.1|CI137772
EST:     TTGCGAAAAACGGCAAACCAATTGGACCACAG                         GCAAATTCTAATTGGCTTTACATCGTGCCATGGGGGATGTACGGATGTGTG
genomic: TTGCGAAAAACGGCAAACCAATTGGACCACAGgtatgcagta ... atctttacagGCAAATTCTAATTGGCTTTACATCGTGCCATGGGGGATGTACGGATGTGTG
EST: gi|27576307|gb|CA999001.1|CA999001
EST:     TTACCTATGTTTTTGCGAAAAACGGCAAACCAATTGGACCACAG                         GCAAATTCTAATTGGCTTTACATCGTGCCATGGGGGATGTACGGATGTGTG
genomic: TT------G------CGAAAAACGGCAAACCAATTGGACCACAGgtatgcagta ... atctttacagGCAAATTCTAATTGGCTTTACATCGTGCCATGGGGGATGTACGGATGTGTG
EST: gi|86500079|gb|CI142712.1|CI142712
EST:     GCGAAAAACGGCAAACCAATTGGACCACAG                         GCAAATTCTAATTGGCTTTACATCGTGCCATGGGGGATGTACGGATGTGTG
genomic: GCGAAAAACGGCAAACCAATTGGACCACAGgtatgcagta ... atctttacagGCAAATTCTAATTGGCTTTACATCGTGCCATGGGGGATGTACGGATGTGTG
EST: gi|86414783|gb|CI069186.1|CI069186
EST:     AAAAACGGCAAACCAATTGGACCACAG                         GCAAATTCTAATTGGCTTTACATCGTGCCATGGGGGATGTACGGATGTGTG
genomic: AAAAACGGCAAACCAATTGGACCACAGgtatgcagta ... atctttacagGCAAATTCTAATTGGCTTTACATCGTGCCATGGGGGATGTACGGATGTGTG
EST: gi|88245939|gb|CI245788.1|CI245788
EST:     TTGCGAAAAACGGCAAACCAATTGGACCACAG                         GCAAATTCTAATTGGCTTTACATCGTGCCATGGGGGATGTACGGATGTGTG
genomic: TTGCGAAAAACGGCAAACCAATTGGACCACAGgtatgcagta ... atctttacagGCAAATTCTAATTGGCTTTACATCGTGCCATGGGGGATGTACGGATGTGTG
EST: gi|29667349|gb|CB663624.1|CB663624
EST:     TTGCGAAAAACGGCAAACCAATTGGACCACAG                         GCAAATTCTAATTGGCTTTACATCGTGCCATGGGGGATGTACGGATGTGTG
genomic: TTGCGAAAAACGGCAAACCAATTGGACCACAGgtatgcagta ... atctttacagGCAAATTCTAATTGGCTTTACATCGTGCCATGGGGGATGTACGGATGTGTG
EST: gi|86502760|gb|CI145393.1|CI145393
EST:     GCGAAAAACGGCAAACCAATTGGACCACAG                         GCAAATTCTAATTGGCTTTACATCGTGCCATGGGGGATGTACGGATGTGTG
genomic: GCGAAAAACGGCAAACCAATTGGACCACAGgtatgcagta ... atctttacagGCAAATTCTAATTGGCTTTACATCGTGCCATGGGGGATGTACGGATGTGTG
EST: gi|88976936|gb|CI257632.1|CI257632
EST:     TTGCGAAAAACGGCAAACCAATTGGACCACAG                         GCAAATTCTAATTGGCTTTACATCGTGCCATGGGGGATGTACGGATGTGTG
genomic: TTGCGAAAAACGGCAAACCAATTGGACCACAGgtatgcagta ... atctttacagGCAAATTCTAATTGGCTTTACATCGTGCCATGGGGGATGTACGGATGTGTG
EST: gi|88903557|gb|CI089095.1|CI089095
EST:     AACCAATTGGACCACAG                         GCAAATTCTAATNGGCTTTACATCGTGCCATGGGGGATGTACGGATGTGTG
genomic: AACCAATTGGACCACAGgtatgcagta ... atctttacagGCAAATTCTAATTGGCTTTACATCGTGCCATGGGGGATGTACGGATGTGTG
EST: gi|27577942|gb|CB000637.1|CB000637
EST:     TTACCTATGTTTTTGCGAAAAACGGCAAACCAATTGGACCACAG                         GCAAATTCTAATTGGCTTTACATCGTGCCATGGGGGATGTACGGATGTGTG
genomic: TT------G------CGAAAAACGGCAAACCAATTGGACCACAGgtatgcagta ... atctttacagGCAAATTCTAATTGGCTTTACATCGTGCCATGGGGGATGTACGGATGTGTG
EST: gi|89184138|gb|CI046703.1|CI046703
EST:     AACGGCAAACCAATTGGACCACAG                         GCAAATTCTAATTGGCTTTACATCGTGCCATGGGGGATGTACGGATGTGTG
genomic: AACGGCAAACCAATTGGACCACAGgtatgcagta ... atctttacagGCAAATTCTAATTGGCTTTACATCGTGCCATGGGGGATGTACGGATGTGTG
EST: gi|87010187|gb|CI279284.1|CI279284
EST:     TTGCGAAAAACGGCAAACCAATTGGACCACAG                         GCAAATTCTAATTGGCTTTACATCGTGCCATGGGGGATGTACGGATGTGTG
genomic: TTGCGAAAAACGGCAAACCAATTGGACCACAGgtatgcagta ... atctttacagGCAAATTCTAATTGGCTTTACATCGTGCCATGGGGGATGTACGGATGTGTG
EST: gi|8858192|gb|AU095510.1|AU095510
EST:     CGAAAACCGGCAAACCCATTTGGACCACAG                         GC-AATTCTAATTGNCTTTACATCGT-CCNAT-GGGGATTNTACGGATGTG
genomic: CGAAAAACGGCAAA-CCAATTGGACCACAGgtatgcagta ... atctttacagGCAAATTCTAATTGGCTTTACATCGTGCC-ATGGGGGA-TGTACGGATGTG
EST: gi|29678658|gb|CB674933.1|CB674933
EST:     TTGCGAAAAACGGCAAACCAATTGGACCACAG                         GCAAATTCTAATTGGCTTTACATCGTGCCATGGGGGATGTACGGATGTGTG
genomic: TTGCGAAAAACGGCAAACCAATTGGACCACAGgtatgcagta ... atctttacagGCAAATTCTAATTGGCTTTACATCGTGCCATGGGGGATGTACGGATGTGTG
EST: gi|29659818|gb|CB656093.1|CB656093
EST:     TTACCTATGTTTTTGCGAAAAACGGCAAACCAATTGGACCACAG                         GCAAATTCTAATTGGCTTTACATCGTGCCATGGGGGATGTACGGATGTGTG
genomic: TT------G------CGAAAAACGGCAAACCAATTGGACCACAGgtatgcagta ... atctttacagGCAAATTCTAATTGGCTTTACATCGTGCCATGGGGGATGTACGGATGTGTG
EST: gi|29657771|gb|CB654046.1|CB654046
EST:     TTGCGAAAAACGGCAAACCAATTGGACCACAG                         GCAAATTCTAATTGGCTTTACATCGTGCCATGGGGGATGTACGGATGTGTG
genomic: TTGCGAAAAACGGCAAACCAATTGGACCACAGgtatgcagta ... atctttacagGCAAATTCTAATTGGCTTTACATCGTGCCATGGGGGATGTACGGATGTGTG
EST: gi|89197084|gb|CI021924.1|CI021924
EST:     TTGCGAAAAACAGCAAACCAATTGGACCACAG                         GCAAATTCTAATTGGCTTTACATCGTGCCATGGGGGATGTACGGATGTGTG
genomic: TTGCGAAAAACGGCAAACCAATTGGACCACAGgtatgcagta ... atctttacagGCAAATTCTAATTGGCTTTACATCGTGCCATGGGGGATGTACGGATGTGTG
EST: gi|86495823|gb|CI138456.1|CI138456
EST:     TTGCGAAAAACGGCAAACCAATTGGACCACAG                         GCAAATTCTAATTGGCTTTACATCGTGCCATGGGGGATGTACGGATGTGTG
genomic: TTGCGAAAAACGGCAAACCAATTGGACCACAGgtatgcagta ... atctttacagGCAAATTCTAATTGGCTTTACATCGTGCCATGGGGGATGTACGGATGTGTG
EST: gi|89184448|gb|CI047013.1|CI047013
EST:     TTGCGAAAAACGGCAAACCAATTGGACCACAG                         GCAAATTCTAATTGGCTTTACATCGTGCCATGGGGGATGTACGGATGTGTG
genomic: TTGCGAAAAACGGCAAACCAATTGGACCACAGgtatgcagta ... atctttacagGCAAATTCTAATTGGCTTTACATCGTGCCATGGGGGATGTACGGATGTGTG
EST: gi|87038444|gb|CI193066.1|CI193066
EST:     TTGCGAAAAACGGCAAACCAATTGGACCACAG                         GCAAATTCTAATTGGCTTTACATCGTGCCATGGGGGATGTACGGATGTGTG
genomic: TTGCGAAAAACGGCAAACCAATTGGACCACAGgtatgcagta ... atctttacagGCAAATTCTAATTGGCTTTACATCGTGCCATGGGGGATGTACGGATGTGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaattcagaagtaacataactcataaaacctttgttgatccatcgatctttacagGCAAATTCTAATTGGCTTTACATCGTGCCATGGGGGATGTACGGATGTGTGAACTACATCAAGCAGAAGTACGGGAATCCGACAGTCGTCATAACTGAAA
                                              tctttac  CT-rich tract
           taacataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgcagtaatcagttgtatccttctccagcttcagattcttctagcactgcattctactgacgtgaccaaactgataaattcagaagtaacataactcataaaacctttgttgatccatcgatctttacagGCAAATTCTAATTGGCTTTACATCGTGCCATGGGGGATGTACGGATGTGTGAACTACATCAAGCAGAAGTACGGGAATCCGACAGTCGTCATAACTGAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT