Skip to another splice site:
1  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttcgtgcttttaaattttagtcactaatctctctttcgagatatgaagttttgaagtgcttgagctcatttttttgtgcttttggttctacttttgcagTGGACATGCTGATGCCAGGAAATACAGCAATCTTGCGGAATGCGAGAATCGATATGTTCAAGGGCTCAATGAGGCTTGCTGTCGACAAGTGGGGACGTGT

Basic information

species Oryza sativa
transcript LOC_Os05g15520.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g15520.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM5G825437_T04 (Zea mays), 3'ss of exon 1
----tttcgtgcttttaaattttagtcactaatctctctttc-gagatatgaagttttgaagtgcttgagctcatttttttgtgcttttggttctacttttgcagTGGACATGCTGATGCCAGGAAATACAGCAATCTTGCGGAATGCGAGAATCGATATGTTCAAGGGCTCAATGAGGCTTGCTGTCGACAAGTGGGGACGTGT
    |||| || ||   |   |     ||||||   |||  | | ||| |    ||||| |   |||    ||  | |  ||||||      ||  | |||||||| ||  |||||| ||| |     || |  |||||||| ||||| | |||||| |||||||| || |||||||||||||| || ||||| ||||| ||  |
ttgttttcatggttgctatcatgttcaactaattgttctgactgtgattttttcttttggataactttcagtccgtgtgatgtgcta-----tcctcctttgcagTTGATTTGCTGAAGCCCGATGCCACGGTGATCTTGCGCAATGCCAAAATCGACATGTTCAAAGGATCAATGAGGCTTGCAGTGGACAAATGGGGGCGGAT

upper sequence: LOC_Os05g15520.1 (Oryza sativa), 3'ss of exon 1
lower sequence: AT2G33845.1 (Arabidopsis thaliana), 3'ss of exon 1
tttcgtgct--tttaaattttagtcactaatctctctttcgagatatgaagttttgaagtgcttgagctcatttttttgtgcttttggttctacttttgcagTGGACATGCTGATGCCAGGAAATACAGCAATCTTGCGGAATGCGAGAATCGATATGTTCAAGGGCTCAATGAGGCTTGCTGTCGACAAGTGGGGACGTGT
 || || ||  | |     | | |   | ||   |  |  | |  |   || |||   | |  | |    | | |||  || ||||  || |     |||||||||  || |||  ||||||  ||| |  |   | |||||||| |  || |||||||||||||| ||||||||||||||||| || || ||||| ||  |
atttgttctgctctggtactcaattggtgattcatagt--gggtcacttagctttttgggggctaatacaagtctttcttggtttttattgtgtgggtgcagTGGAATTGATGAAACCAGGAGCTACTGTGAATCTTCGGAATGCAAAGATAGATATGTTCAAGGGATCAATGAGGCTTGCTGTTGATAAATGGGGTCGCAT
















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|86903646|gb|CI300500.1|CI300500
EST:     CGTCGGCGACGAGACCGGGGTCATCGTCTTCACCGCCCGCAACGAGCAAG                         TGGACATGCTGATGCCAGGAAATACAGCAATCTTGCGGAAT
genomic: CGTCGGCGACGAGACCGGGGTCATCGTCTTCACCGCCCGCAACGAGCAAGgtgatgttgc ... acttttgcagTGGACATGCTGATGCCAGGAAATACAGCAATCTTGCGGAAT
EST: gi|89168575|gb|CI038929.1|CI038929
EST:     CGTCGGCGACGAGACCGGGGTCATCGTCTTCACCGCCCGCAACGAGCAAG                         TGGACATGCTGATGCCAGGAAATACAGCAATCTTGCGGAATGCGAGAATCG
genomic: CGTCGGCGACGAGACCGGGGTCATCGTCTTCACCGCCCGCAACGAGCAAGgtgatgttgc ... acttttgcagTGGACATGCTGATGCCAGGAAATACAGCAATCTTGCGGAATGCGAGAATCG
EST: gi|88516397|gb|CI444051.1|CI444051
EST:     CGTCGGCGACGAGACCGGGGTCATCGTCTTCACCGCCCGCAACGAGCAAG                         TGGACATGCTGATGCCAGGAAATACAGCAATCTTGCGGAATGCGAGAATCG
genomic: CGTCGGCGACGAGACCGGGGTCATCGTCTTCACCGCCCGCAACGAGCAAGgtgatgttgc ... acttttgcagTGGACATGCTGATGCCAGGAAATACAGCAATCTTGCGGAATGCGAGAATCG
EST: gi|88349456|gb|CI653735.1|CI653735
EST:     CGTCGGCGACGAGACCGGGGTCATCGTCTTCACCGCCCGCAACGAGCAAG                         TGGACATGCTGATGCCAGGAAATACAGCAATCTTGCGGAATGCGAGAATCG
genomic: CGTCGGCGACGAGACCGGGGTCATCGTCTTCACCGCCCGCAACGAGCAAGgtgatgttgc ... acttttgcagTGGACATGCTGATGCCAGGAAATACAGCAATCTTGCGGAATGCGAGAATCG
EST: gi|88268861|gb|CI377765.1|CI377765
EST:     CGTCGGCGACGAGACCGGGGTCATCGTCTTCACCGCCCGCAACGAGCAAG                         TGGACATGCTGATGCCAGGAAATACAGCAATCTTGCGGAATGCGAGAATCG
genomic: CGTCGGCGACGAGACCGGGGTCATCGTCTTCACCGCCCGCAACGAGCAAGgtgatgttgc ... acttttgcagTGGACATGCTGATGCCAGGAAATACAGCAATCTTGCGGAATGCGAGAATCG
EST: gi|88557640|gb|CI488064.1|CI488064
EST:     TCGGCGACGAGACCGGGGTCATCGTCTTCACCGCCCGCAACGAGCAAG                         TGGACATGCTAATGCCAGGAAATACAGCAATCTTGCGGAATGCGAGAATCA
genomic: TCGGCGACGAGACCGGGGTCATCGTCTTCACCGCCCGCAACGAGCAAGgtgatgttgc ... acttttgcagTGGACATGCTGATGCCAGGAAATACAGCAATCTTGCGGAATGCGAGAATCG
EST: gi|86523739|gb|CI163945.1|CI163945
EST:     CGTCGGCGACGAGACCGGGGTCGTCGTCTTCACCGCCCGCAACGAGCAAG                         TGGACATGCTGATGCCAGGAAATACAGCAATCTTGCGGAATGCGAGAATCG
genomic: CGTCGGCGACGAGACCGGGGTCATCGTCTTCACCGCCCGCAACGAGCAAGgtgatgttgc ... acttttgcagTGGACATGCTGATGCCAGGAAATACAGCAATCTTGCGGAATGCGAGAATCG
EST: gi|88490319|gb|CI427591.1|CI427591
EST:     CGTCGGCGACGAGACCGGGGTCATCGTCTTCACCGCCCGCAACGAGCAAG                         TGGACATGCTGATGCCAGGAAATACAGCAATCTTGCGGAATGCGAGAATCG
genomic: CGTCGGCGACGAGACCGGGGTCATCGTCTTCACCGCCCGCAACGAGCAAGgtgatgttgc ... acttttgcagTGGACATGCTGATGCCAGGAAATACAGCAATCTTGCGGAATGCGAGAATCG
EST: gi|88242012|gb|CI241861.1|CI241861
EST:     CGTCGGCGACGAGACCGGGGTCATCGTCTTCACCGCCCGCAACGAGCAAG                         TGGACATGCTGATGCCAGGAAATACAGCAATCTTGCGGAATGCGAGAATCG
genomic: CGTCGGCGACGAGACCGGGGTCATCGTCTTCACCGCCCGCAACGAGCAAGgtgatgttgc ... acttttgcagTGGACATGCTGATGCCAGGAAATACAGCAATCTTGCGGAATGCGAGAATCG
EST: gi|88575118|gb|CI666887.1|CI666887
EST:     CGTCGGCGACGAGACCGGGGTCATCGTCTTCACCGCCCGCAACGAGCAAG                         TGGACATGCTGATGCCAGGAAATACAGCAATCTTGCGGAA
genomic: CGTCGGCGACGAGACCGGGGTCATCGTCTTCACCGCCCGCAACGAGCAAGgtgatgttgc ... acttttgcagTGGACATGCTGATGCCAGGAAATACAGCAATCTTGCGGAA
EST: gi|88962984|gb|CI025470.1|CI025470
EST:     CGTCGGCGACGAGACCGGGGTCATCGTCTTCACCGCCCGCAACGAGCAAG                         TGGACATGCTGATGCCAGGAAATACAGCAATCTTGCGGAATGCGAGAATCG
genomic: CGTCGGCGACGAGACCGGGGTCATCGTCTTCACCGCCCGCAACGAGCAAGgtgatgttgc ... acttttgcagTGGACATGCTGATGCCAGGAAATACAGCAATCTTGCGGAATGCGAGAATCG
EST: gi|88440928|gb|CI693506.1|CI693506
EST:     CGTCGGCGACGAGACCGGGGTCATCGTCTTCACCGCCCGCAACGAGCAAG                         TGGACATGCTGATGCCAGGAAATACAGCAATCTTGCGGAATGCGAGAATCG
genomic: CGTCGGCGACGAGACCGGGGTCATCGTCTTCACCGCCCGCAACGAGCAAGgtgatgttgc ... acttttgcagTGGACATGCTGATGCCAGGAAATACAGCAATCTTGCGGAATGCGAGAATCG
EST: gi|88482862|gb|CI420133.1|CI420133
EST:     CGGGGTCATCGTCTTCACCGCCCGCAACGAGCAAG                         TGGACATGCTGATGCCAGGAAATACAGCAATCTTGCGGAATGCGAGAATCG
genomic: CGGGGTCATCGTCTTCACCGCCCGCAACGAGCAAGgtgatgttgc ... acttttgcagTGGACATGCTGATGCCAGGAAATACAGCAATCTTGCGGAATGCGAGAATCG
EST: gi|88334787|gb|CI647169.1|CI647169
EST:     CGTCGGCGACGAGACCGGGGTCATCGTCTTCACCGCCCGCAACGAGCAAG                         TGGACATGCTGATGCCAGGAAATACAGCAATCTTGCGGAATGCGAGAATCG
genomic: CGTCGGCGACGAGACCGGGGTCATCGTCTTCACCGCCCGCAACGAGCAAGgtgatgttgc ... acttttgcagTGGACATGCTGATGCCAGGAAATACAGCAATCTTGCGGAATGCGAGAATCG
EST: gi|88482744|gb|CI420015.1|CI420015
EST:     CGTCGGCGACGAGACCGGGGTCATCGTCTTCACCGCCCGCAACGAGCAAG                         TGGACATGCTGATGCCAGGAAATACAGCAATCTTGCGGAATGCGAGAATCG
genomic: CGTCGGCGACGAGACCGGGGTCATCGTCTTCACCGCCCGCAACGAGCAAGgtgatgttgc ... acttttgcagTGGACATGCTGATGCCAGGAAATACAGCAATCTTGCGGAATGCGAGAATCG
EST: gi|88726388|gb|CI750043.1|CI750043
EST:     CGTCGGCGACGAGACCGGGGTCATCGTCTTCACCGCCCGCAACGAGCAAG                         TGGACATGCTGATGCCAGGAAATACAGCAATCTTGCGGAATGCGAGAATCG
genomic: CGTCGGCGACGAGACCGGGGTCATCGTCTTCACCGCCCGCAACGAGCAAGgtgatgttgc ... acttttgcagTGGACATGCTGATGCCAGGAAATACAGCAATCTTGCGGAATGCGAGAATCG
EST: gi|88442015|gb|CI557668.1|CI557668
EST:     GGTCATCGTCTTCACCGCCCGCAACGAGCAAG                         TGGACATGCTGATGCCAGGAAATACAGCAATCTTGCGGAATGCGAGAATCG
genomic: GGTCATCGTCTTCACCGCCCGCAACGAGCAAGgtgatgttgc ... acttttgcagTGGACATGCTGATGCCAGGAAATACAGCAATCTTGCGGAATGCGAGAATCG
EST: gi|9865133|gb|AU100883.1|AU100883
EST:     CGTCGGCGACGAGACCGGGGTCATCGTCTTCACCGCCCGCAACGAGCAAG                         TGGACATGCTGATGCCAGGAAATACAGCAATCTTGCGGAATGCGAGAATCG
genomic: CGTCGGCGACGAGACCGGGGTCATCGTCTTCACCGCCCGCAACGAGCAAGgtgatgttgc ... acttttgcagTGGACATGCTGATGCCAGGAAATACAGCAATCTTGCGGAATGCGAGAATCG
EST: gi|86498980|gb|CI141613.1|CI141613
EST:     CGTCGGCGACGAGACCGGGGTCATCGTCTTCACCGCCCGCAACGAGCAAG                         TGGACATGCTGATGCCAGGAAATACAGCAATTTTGCGGAATGCGAGAATCG
genomic: CGTCGGCGACGAGACCGGGGTCATCGTCTTCACCGCCCGCAACGAGCAAGgtgatgttgc ... acttttgcagTGGACATGCTGATGCCAGGAAATACAGCAATCTTGCGGAATGCGAGAATCG
EST: gi|88544738|gb|CI472864.1|CI472864
EST:     CGTCGGCGACGAGACCGGGGTCATCGTCTTCACCGCCCGCAACGAGCAAG                         TGGACATGCTGATGCCAGGAAATACAGCAATCTTNCGGAATGCGAGAATCG
genomic: CGTCGGCGACGAGACCGGGGTCATCGTCTTCACCGCCCGCAACGAGCAAGgtgatgttgc ... acttttgcagTGGACATGCTGATGCCAGGAAATACAGCAATCTTGCGGAATGCGAGAATCG
EST: gi|88570380|gb|CI661753.1|CI661753
EST:     CGTCGGCGACGAGACCGGGGTCATCGTCTTCACCGCCCGCAACGAGCAAG                         TGGACATGCTGATGCCAGGAAATACAGCGATCTTGCGGAATGCGAGAATCG
genomic: CGTCGGCGACGAGACCGGGGTCATCGTCTTCACCGCCCGCAACGAGCAAGgtgatgttgc ... acttttgcagTGGACATGCTGATGCCAGGAAATACAGCAATCTTGCGGAATGCGAGAATCG
EST: gi|88510059|gb|CI437565.1|CI437565
EST:     CGTCGGCGACGAGACCGGGGTCATCGTCTTCACCGCCCGCAACGAGCAAG                         TGGACATGCTGATGCCAGGAAATACAGCGATCTTGCGGAATGCGAGAATCG
genomic: CGTCGGCGACGAGACCGGGGTCATCGTCTTCACCGCCCGCAACGAGCAAGgtgatgttgc ... acttttgcagTGGACATGCTGATGCCAGGAAATACAGCAATCTTGCGGAATGCGAGAATCG
EST: gi|88214251|gb|CI214100.1|CI214100
EST:     CGTCGGCGACGAGACCGGGGTCATCGTCTTCACCGCCCGCAACGAGCAAG                         TGGACATGCTGATGCCAGGAAATACAGCAATCTTGCGGAATGCGAGAATCG
genomic: CGTCGGCGACGAGACCGGGGTCATCGTCTTCACCGCCCGCAACGAGCAAGgtgatgttgc ... acttttgcagTGGACATGCTGATGCCAGGAAATACAGCAATCTTGCGGAATGCGAGAATCG
EST: gi|88466600|gb|CI532407.1|CI532407
EST:     CGTCGGCGACGAGACCGGGGTCATCGTCTTCACCGCCCGCAACGAGCAAG                         TGGACATGCTGATGCCAGGAAATACAGCAATCTTGCGGAATGCGAGAATCG
genomic: CGTCGGCGACGAGACCGGGGTCATCGTCTTCACCGCCCGCAACGAGCAAGgtgatgttgc ... acttttgcagTGGACATGCTGATGCCAGGAAATACAGCAATCTTGCGGAATGCGAGAATCG
EST: gi|88335705|gb|CI647061.1|CI647061
EST:     CGTCGGCGACGAGACCGGGGTCATCGTCTTCACCGCCCGCAACGAGCAAG                         TGGACATGCTGATGCCAGGAAATACAGCAATCTTGGGGAATGCGAGAATCG
genomic: CGTCGGCGACGAGACCGGGGTCATCGTCTTCACCGCCCGCAACGAGCAAGgtgatgttgc ... acttttgcagTGGACATGCTGATGCCAGGAAATACAGCAATCTTGCGGAATGCGAGAATCG

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: 70 (upstream exon), 65 (downstream exon)
Score: 13

GGGGGCGGCCCGGCCGTCGGATCTCGCCCCGCGCGCATCGCCGAGTGCCTCGTCGGCGACGAGACCGGGGTCATCGTCTTCACCGCCCGCAACGAGCAAGgtgatgttgc ... acttttgcagTGGACATGCTGATGCCAGGAAATACAGCAATCTTGCGGAATGCGAGAATCGATATGTTCAAGGGCTCAATGAGGCTTGCTGTCGACAAGTGGGGACGTGT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaagttttgaagtgcttgagctcatttttttgtgcttttggttctacttttgcagTGGACATGCTGATGCCAGGAAATACAGCAATCTTGCGGAATGCGAGAATCGATATGTTCAAGGGCTCAATGAGGCTTGCTGTCGACAAGTGGGGACGTGT
                                         ttctactttt  CT-rich tract
                     tcattttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttcgtgcttttaaattttagtcactaatctctctttcgagatatgaagttttgaagtgcttgagctcatttttttgtgcttttggttctacttttgcagTGGACATGCTGATGCCAGGAAATACAGCAATCTTGCGGAATGCGAGAATCGATATGTTCAAGGGCTCAATGAGGCTTGCTGTCGACAAGTGGGGACGTGT

- -cgtgctt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - gtgcttg