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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtaatggtatagaatgctatttatcttcagaaatggtacagaataatggtttttgccagttttttgtcgttccctagcccctattaccgtgcgactgatgtggcactggcatttcagGTTGCTGTTGTCACTGTGGCATTCCCTGCCACACCTCTGCTCCTTGCAAGGGCGCGCATCTGCATTTCTGCTTCGCACACTAGGGAGGACCTGATAAAAG

Basic information

species Oryza sativa
transcript LOC_Os11g31640.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g31640.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G030862_T01 (Zea mays), 3'ss of exon 9
gttagtaatggtatagaatgctatttatcttcagaaatggtacagaataatggtttttgccagttttttgtcgttccctagcccctattaccgtgcgactga---tgtggcactggcatttcagGTTGCTGTTGTCACTGTGGCATTCCCTGCCACACCTCTGCTCCTTGCAAGGGCGCGCATCTGCATTTCTGCTTCGCACACTAGGGAGGACCTGATAAAAG
                                       ||    | |  | |  |||| |          |  ||   ||  || | || |    ||| ||   | | |  || ||  | |||||||| ||| |||||||||| || ||||  || ||||| || || ||||| || ||  |||||||||| |||||||||||||||||||||||||  ||||
---------------------------------------gttattagtgctagagtttgtcgacg---aaacactctgaagatccgaatagcaattgacagaattttttgtgctagc--tgcagGTTGCCGTTATCACTGTGGCGTTTCCTGTGACTCCTCTCCTTCTCGCAAGAGCACGTTTCTGCATTTCAGCTTCGCACACTAGGGAGGACCTGACGAAAG

upper sequence: LOC_Os11g31640.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G067257_T01 (Zea mays), 3'ss of exon 11
gttagtaatggtatagaatgctatttatcttcagaaatggtacagaataatggtttttgccagttttttgtcgttccctagcccctattaccgtgcgactgatgtggcactggcatttcagGTTGCTGTTGTCACTGTGGCATTCCCTGCCACACCTCTGCTCCTTGCAAGGGCGCGCATCTGCATTTCTGCTTCGCACACTAGGGAGGACCTGATAAAAG
  || ||    ||| | |||   |  || | ||  | |  |       | |||||||     ||| ||        |||| |      |  | ||  ||| ||  |  |||    |||||||||| |||||| ||||| || || ||||| |||||||| || ||||| ||||| ||||| |||||||||||||| || ||||||||||||||||| ||||
-ctaatagcaatat-gcatgtagtccatttccatcactatttgcacccactggtttt-----gttctt--------cctatc------tgtcatggtacttataagatacttatctttcagGTTGTTGTTGTTACTGTTGCGTTTCCTGCGACACCTCTTCTTCTTGCTAGGGCACGCATATGCATTTCTGCTTCACATACTAGGGAGGACCTGATTAAAG

upper sequence: LOC_Os11g31640.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G157249_T01 (Zea mays), 3'ss of exon 3
--------------------------------------------------------------------------------gttagtaatggtatagaatgctatttatcttcagaa-atggtacagaataatggtttttgccagttttttgtcgttccctagcccctattaccgtgcgactgatgtggcactggcatttcagGTTGCTGTTGTCACTGTGGCATTCCCTGCCACACCTCTGCTCCTTGCAAGGGCGCGCATCTGCATTTCTGCTTCGCACACTAGGGAGGACCTGATAAAAG
                                                                                 ||  |   |   |    ||||| |     || | |  | || || |   ||   | ||  ||     | ||  |||  |   ||    |  | ||  ||| ||  |  |||    |||||||||| |||||| ||||| |  || ||||| |||||||| || ||||| ||||| ||||| |||||||||||||| || ||||||||| ||||||| ||||
gttagtagtagagttcgtcagaatattctgaagatccaaatagcactatgcttttggtatacttttttcttaaaaaatactttgtttgagaattgtggtgctaatagcaatctgcatgtagtccatatccatcactatttgcacccactggt--ttcgttcttcctatctgtcatggtacttataagatacttatctttcagGTTGTTGTTGTTACTGTTGTGTTTCCTGCGACACCTCTTCTTCTTGCTAGGGCACGCATATGCATTTCTGCTTCACATACTAGGGAGCACCTGATTAAAG

upper sequence: LOC_Os11g31640.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G357734_T03 (Zea mays), 3'ss of exon 15
--------------------------------------------------------------------------------gttagtaatggtatagaatgctatttatcttcagaa-atggtacagaataatggtttttgccagttttttgtcgttccctagcccctattaccgtgcgactgatgtggcactggcatttcagGTTGCTGTTGTCACTGTGGCATTCCCTGCCACACCTCTGCTCCTTGCAAGGGCGCGCATCTGCATTTCTGCTTCGCACACTAGGGAGGACCTGATAAAAG
                                                                                 ||  |   |   |    ||||| |     || | |  | || ||     ||   | ||  ||     | ||  |   ||   ||    |  | ||  ||| ||  |  |||    |||||||||| |||||| ||||| || || ||||| |||||||| || ||||| ||||| ||||| |||||||||||||| || ||||||||||||||||| ||||
gttagtagtagagtttgtcaggatattctgaagatccaaatagcactatgcttttggtatactttttttttttaaaatactttgtttgagaattgtggtgctaatagcaatctgcatgtagtccatttccatcactatttgcacccactggttttgttct--tcctatctgtcatggtacttataagatacttatctttcagGTTGTTGTTGTTACTGTTGCGTTTCCTGCGACACCTCTTCTTCTTGCTAGGGCACGCATATGCATTTCTGCTTCACATACTAGGGAGGACCTGATTAAAG

upper sequence: LOC_Os11g31640.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G152888_T01 (Zea mays), 3'ss of exon 10
gttagtaatggtatagaatgctatttatcttcagaaatggtacagaataatggtttttgccagttttttgtcgttccctagcccctattaccgtgcgactgatgtggcactggcatttcagGTTGCTGTTGTCACTGTGGCATTCCCTGCCACACCTCTGCTCCTTGCAAGGGCGCGCATCTGCATTTCTGCTTCGCACACTAGGGAGGACCTGATAAAAG
                  |  ||   |||| || |  | || || |   ||   | ||  ||     | ||  |||  |   ||    |  | ||  ||| ||  |  |||    || |||||||||||||| ||||| || || ||||| |||||||| || ||||| ||||| ||||| |||||||||||||| || ||||||||||||||||| ||||
-----------------ctaatagcaatctgcata--tagtccatatccatcactatttgcacccactggt--ttcgttcttcctatctgtcatggtacttataagatacttatcttccagGTTGCTGTTGTTACTGTTGCGTTTCCTGCGACACCTCTTCTTCTTGCTAGGGCACGCATATGCATTTCTGCTTCACATACTAGGGAGGACCTGATGAAAG

upper sequence: LOC_Os11g31640.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G142030_T01 (Zea mays), 3'ss of exon 10
----------------------------------------------------------------------------gttagtaatggta-tagaatgctatttatcttcagaaatggtacagaataatggtttttgccagttttttgtcgttccctagcccctattaccgtgcgactgatgtggcactggcatttcagGTTGCTGTTGTCACTGTGGCATTCCCTGCCACACCTCTGCTCCTTGCAAGGGCGCGCATCTGCATTTCTGCTTCGCACACTAGGGAGGACCTGATAAAAG
                                                                             ||| |    | | |    ||||| |     |   |  | || |  |   ||   | ||  ||    |  ||  |   ||   ||   ||  | |||| || ||  | ||||   ||||||||| || ||||| || ||||| || || || |||||||| || ||||| ||||| |||||||||||||| ||||| ||||||||||||||  |||| ||||
gtcagtcatagagtttgtcagactattctgaagatccagatagcactatgcttttggtacagttttcttttaaaatattactttgagaagtctggtgctaatagcagttgcatgtagtccttatccatcactatttgcacccatcggttttgttct--tcctctttgtcatgcggctaataagacacttatatttcagGTCGCCGTTGTTACCGTGGCGTTTCCAGCAACACCTCTTCTTCTTGCTAGGGCACGCATCTGCATTTCGGCTTCACACACTAGGGAGGATTTGATGAAAG

upper sequence: LOC_Os11g31640.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GLYMA02G07250.1 (Glycine max), 3'ss of exon 10
gttagtaatggtatagaatgctatttatcttcagaaatggtacagaataatggtttttgccagttttttgtcgttccctagcccctattaccgtgcgactgatgtggcactggcatttcagGTTGCTGTTGTCACTGTGGCATTCCCTGCCACACCTCTGCTCCTTGCAAGGGCGCGCATCTGCATTTCTGCTTCGCACACTAGGGAGGACCTGATAAAAG
                   |  |   | | ||| | ||   ||    || || |  |||    |    |          ||     |||        | || |       |   |||||||||||||||||| || |||||||| ||||| || || ||||| || || || || ||||| ||||| |||||  | ||  | ||||| ||||| || ||||
-------------------gtga--gaacatcaaatatccaactatcta-tgctccttgttgataccctacatcatataagaatgaatttgttaattaatgtttacaattttttatttcagGTTGCTGTTGTGACAGTGGCATTTCCTGCAACCCCACTGCTACTGGCTAGAGCACGCATATGCATATCTGCAGCTCATTCAAGGGAAGACCTTATCAAAG

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|89193136|gb|CI050434.1|CI050434
EST:     ACAATCCAGCCAAAATTCCAGCTTTTTCCAGGGAGTGCCTTAGACAAAAG                         GTTGCTGTTGTCACTGTGGCATTCCCTGCCACACCTCTGCTCCTTGCAAGG
genomic: ACAATCCAGCCAAAATTCCAGCTTTTTCCAGGGAGTGCCTTAGACAAAAGgttagtaatg ... ggcatttcagGTTGCTGTTGTCACTGTGGCATTCCCTGCCACACCTCTGCTCCTTGCAAGG
EST: gi|29628852|gb|CB633863.1|CB633863
EST:     ACAATCCAGCCAAAATTCCAGCTTTTTCCAGGGAGTGCCTTAGACAGAAG                         GTTGCTGTTGTCACTGTGGCATTCCCTGCCACACCTCTGCTCCTTGCAAGG
genomic: ACAATCCAGCCAAAATTCCAGCTTTTTCCAGGGAGTGCCTTAGACAAAAGgttagtaatg ... ggcatttcagGTTGCTGTTGTCACTGTGGCATTCCCTGCCACACCTCTGCTCCTTGCAAGG
EST: gi|29671691|gb|CB667966.1|CB667966
EST:     ACAATCCAGCCAAAATTCCAGCTTTTTCCAGGGAGTGCCTTAGACAAAAG                         GTTGCTGTTGTCACTGTGGCATTCCCTGCCACACCTTTGCTCCTTGCAAGG
genomic: ACAATCCAGCCAAAATTCCAGCTTTTTCCAGGGAGTGCCTTAGACAAAAGgttagtaatg ... ggcatttcagGTTGCTGTTGTCACTGTGGCATTCCCTGCCACACCTCTGCTCCTTGCAAGG
EST: gi|86872762|gb|CI341972.1|CI341972
EST:     CAGCCAAAA-TCCA-CTTTTTCCAGGGAGTGCCTTAGACAAAAG                         GTTGCTG-TGTCACTGT-GCATTCCCTGCCACACCTCTGCTCCTTGCAAGG
genomic: CAGCCAAAATTCCAGCTTTTTCCAGGGAGTGCCTTAGACAAAAGgttagtaatg ... ggcatttcagGTTGCTGTTGTCACTGTGGCATTCCCTGCCACACCTCTGCTCCTTGCAAGG
EST: gi|29675002|gb|CB671277.1|CB671277
EST:     ACAATCCAGCCAAAATTCCAGCTTTTTCCAGGGAGTGCCTTAGACAAAAG                         GTTGCTGTTGTCACTGTGGCATTCCCTGCCACACCTCTGCTCCTTGCAAGG
genomic: ACAATCCAGCCAAAATTCCAGCTTTTTCCAGGGAGTGCCTTAGACAAAAGgttagtaatg ... ggcatttcagGTTGCTGTTGTCACTGTGGCATTCCCTGCCACACCTCTGCTCCTTGCAAGG
EST: gi|86592303|gb|CI250957.1|CI250957
EST:     AGTGCCTTAGACAAAAG                         GTTGCTGTTGTCACTGTGGCATTCCCTGCCACACCTCTGCTCCTTGCAAGG
genomic: AGTGCCTTAGACAAAAGgttagtaatg ... ggcatttcagGTTGCTGTTGTCACTGTGGCATTCCCTGCCACACCTCTGCTCCTTGCAAGG
EST: gi|29615692|gb|CB620704.1|CB620704
EST:     ACAATCCAGCCAAAATTCCAGCTTTTTCCAGGGAGTGCCTTAGACAAAAG                         GTTGCTGTTGTCACTGTGGCATTCCCTGCCACACCTCTGCTCCTTGCAAGG
genomic: ACAATCCAGCCAAAATTCCAGCTTTTTCCAGGGAGTGCCTTAGACAAAAGgttagtaatg ... ggcatttcagGTTGCTGTTGTCACTGTGGCATTCCCTGCCACACCTCTGCTCCTTGCAAGG
EST: gi|88993224|gb|CI108852.1|CI108852
EST:     TTTTTCCAGGGAGTGCCTTAGACAAAAG                         GTTGCTGTTGTCACTGTGGCATTCCCTGCCACACCTCTGCTCCTTGCAAGG
genomic: TTTTTCCAGGGAGTGCCTTAGACAAAAGgttagtaatg ... ggcatttcagGTTGCTGTTGTCACTGTGGCATTCCCTGCCACACCTCTGCTCCTTGCAAGG
EST: gi|29659061|gb|CB655336.1|CB655336
EST:     ACAATCCAGCCAAAATTCCAGCTTTTTCCAGGGAGTGCCTTAGACAAAAG                         GTTGCTGTTGTCACTGTGGCATTCCCTGCCACACCTCTGCTCCTTGCAAGG
genomic: ACAATCCAGCCAAAATTCCAGCTTTTTCCAGGGAGTGCCTTAGACAAAAGgttagtaatg ... ggcatttcagGTTGCTGTTGTCACTGTGGCATTCCCTGCCACACCTCTGCTCCTTGCAAGG
EST: gi|86866454|gb|CI343422.1|CI343422
EST:     ACAATCCAGCCAAAATTCCAGCTTTTTCCAGGGAGTGCCTTAGACAAAAG                         GTTGCTGTTGTCACTGTGGCATTCCCTGCCACACCTCTGCTCCTTGCAA-G
genomic: ACAATCCAGCCAAAATTCCAGCTTTTTCCAGGGAGTGCCTTAGACAAAAGgttagtaatg ... ggcatttcagGTTGCTGTTGTCACTGTGGCATTCCCTGCCACACCTCTGCTCCTTGCAAGG
EST: gi|86415690|gb|CI029701.1|CI029701
EST:     AGCTTTTTCCAGGGAGTGCCTTAGACAAAAG                         GTTGCTGTTGTCACTGTGGCATTCCCTGCCACACCTCTGCTCCTTGCAAGG
genomic: AGCTTTTTCCAGGGAGTGCCTTAGACAAAAGgttagtaatg ... ggcatttcagGTTGCTGTTGTCACTGTGGCATTCCCTGCCACACCTCTGCTCCTTGCAAGG
EST: gi|89183664|gb|CI046229.1|CI046229
EST:     AGGGAGTGCCTTAGACCAAAG                         GTTGCTGTTGTCACTGTGGCATTCCCTGCCACACCTCTGCTCCTTGCAAGG
genomic: AGGGAGTGCCTTAGACAAAAGgttagtaatg ... ggcatttcagGTTGCTGTTGTCACTGTGGCATTCCCTGCCACACCTCTGCTCCTTGCAAGG
EST: gi|18385894|gb|BM419093.1|BM419093
EST:     CAATCCAGCC-AAATTCCAGCTTTTTCCAGGGAGTGCCCTTAGACAAAAG                         GTTGCTGTTGTCACTGTGGCATTCCCTGCCACACCTCTGCTCCTTGCAAGG
genomic: CAATCCAGCCAAAATTCCAGCTTTTTCCAGGGAGTG-CCTTAGACAAAAGgttagtaatg ... ggcatttcagGTTGCTGTTGTCACTGTGGCATTCCCTGCCACACCTCTGCTCCTTGCAAGG
EST: gi|86903309|gb|CI313672.1|CI313672
EST:     TTTCCA-GGAGTGCC-TAGACGAAAG                         GTTGCTGTTGTCACTGTGCCATTCCCTGCCACACCTCTGCTCCTTGCAAGG
genomic: TTTCCAGGGAGTGCCTTAGACAAAAGgttagtaatg ... ggcatttcagGTTGCTGTTGTCACTGTGGCATTCCCTGCCACACCTCTGCTCCTTGCAAGG
EST: gi|29672757|gb|CB669032.1|CB669032
EST:     ACAATCCAGCCAAAATTCCAGCTTTTTCCAGGGAGTGCCTTAGACAAAAG                         GTTGCTGTTGTCACTGTGGCATTCCCTGCCACACCTCTGCTCCTTGCAAGG
genomic: ACAATCCAGCCAAAATTCCAGCTTTTTCCAGGGAGTGCCTTAGACAAAAGgttagtaatg ... ggcatttcagGTTGCTGTTGTCACTGTGGCATTCCCTGCCACACCTCTGCTCCTTGCAAGG
EST: gi|29626773|gb|CB631784.1|CB631784
EST:     ACAATCCAGCCAAAATTCCAGCTTTTTCCAGGGAGTGCCTTAGACAGAAG                         GTTGCTGTTGTCACTGTGGCATTCCCTGCCACACCTCTGCTCCTTGCAAGG
genomic: ACAATCCAGCCAAAATTCCAGCTTTTTCCAGGGAGTGCCTTAGACAAAAGgttagtaatg ... ggcatttcagGTTGCTGTTGTCACTGTGGCATTCCCTGCCACACCTCTGCTCCTTGCAAGG
EST: gi|29615730|gb|CB620742.1|CB620742
EST:     ACAATCCAGCCAAAATTCCAGCTTTTTCCAGGGAGTGCCTTAGACAAAAG                         GTTGCTGTTGTCACTGTGGCATTCCCTGCCACACCTCTGCTCCTTGCAAGG
genomic: ACAATCCAGCCAAAATTCCAGCTTTTTCCAGGGAGTGCCTTAGACAAAAGgttagtaatg ... ggcatttcagGTTGCTGTTGTCACTGTGGCATTCCCTGCCACACCTCTGCTCCTTGCAAGG
EST: gi|29633292|gb|CB638301.1|CB638301
EST:     AGGGAGTGCCTTAGACAAAAG                         GTTGCTGTTGTCACTGTGGCATTCCCTGCCACACCTCTGCTCCTTGCAAGG
genomic: AGGGAGTGCCTTAGACAAAAGgttagtaatg ... ggcatttcagGTTGCTGTTGTCACTGTGGCATTCCCTGCCACACCTCTGCTCCTTGCAAGG
EST: gi|94362891|gb|CI053052.1|CI053052
EST:     ATTCCAGCTTTTTCCAGGGAGTGCCTTAGACAAAAG                         GTTGCTGTTGTCACTGTGGCATTCCCTGCCACACCTCTGCTCCTTGCAAGG
genomic: ATTCCAGCTTTTTCCAGGGAGTGCCTTAGACAAAAGgttagtaatg ... ggcatttcagGTTGCTGTTGTCACTGTGGCATTCCCTGCCACACCTCTGCTCCTTGCAAGG
EST: gi|86869808|gb|CI316536.1|CI316536
EST:     TTCCAGC-TTTTCCAGGGAGTGCCTTAGACAAAAG                         GTTGCTGTTGTCACTGTGGCATTCCCTGCCACACCTCTGCTCCTTGCCAAG
genomic: TTCCAGCTTTTTCCAGGGAGTGCCTTAGACAAAAGgttagtaatg ... ggcatttcagGTTGCTGTTGTCACTGTGGCATTCCCTGCCACACCTCTGCTCCTTG-CAAG
EST: gi|86494972|gb|CI137605.1|CI137605
EST:     CAATCCAGCCAAAATTCCAGCTTTTTCACAGGGAGTGCCTTAGACAAAAG                         GTTGCTGTTGTCACTGTGGCATTCCCTGCCACACCTCTGCTCCTTGCAAGG
genomic: CAATCCAGCCAAAATTCCAGCTTTTTC-CAGGGAGTGCCTTAGACAAAAGgttagtaatg ... ggcatttcagGTTGCTGTTGTCACTGTGGCATTCCCTGCCACACCTCTGCTCCTTGCAAGG

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: 39 (upstream exon), 75 (downstream exon)
Score: 13

TTTTGAGGTTCTCGGAGACAATGACTCTCCAGTTATGCCAATAATGCTCTACAATCCAGCCAAAATTCCAGCTTTTTCCAGGGAGTGCCTTAGACAAAAGgttagtaatg ... ggcatttcagGTTGCTGTTGTCACTGTGGCATTCCCTGCCACACCTCTGCTCCTTGCAAGGGCGCGCATCTGCATTTCTGCTTCGCACACTAGGGAGGACCTGATAAAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgtcgttccctagcccctattaccgtgcgactgatgtggcactggcatttcagGTTGCTGTTGTCACTGTGGCATTCCCTGCCACACCTCTGCTCCTTGCAAGGGCGCGCATCTGCATTTCTGCTTCGCACACTAGGGAGGACCTGATAAAAG
                              gactgat  putative branch site (score: 13)
                   tatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagtaatggtatagaatgctatttatcttcagaaatggtacagaataatggtttttgccagttttttgtcgttccctagcccctattaccgtgcgactgatgtggcactggcatttcagGTTGCTGTTGTCACTGTGGCATTCCCTGCCACACCTCTGCTCCTTGCAAGGGCGCGCATCTGCATTTCTGCTTCGCACACTAGGGAGGACCTGATAAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA