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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagttgcaacatctttgggttttcatatatttcaccaatcaccaggaagctaagtagctaacttaacatcattaactctactagcaccactttttttgtatgtagcaaattgttgatacacgataaccttctcttgttaagatgtcctaaatgttcttcatgtctgtaatagtgatatcattttgaccattttcagGCAAAATGTCTGGAGACAGGTGAGACAGTTGCTATCAAGAAGGTTCTTCAGGATAAGCGCTACAAGAACCGTGAGCTTCAGACCATGCGCCTTCTTGACC

Basic information

species Oryza sativa
transcript LOC_Os01g14860.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g14860.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM5G835235_T04 (Zea mays), 3'ss of exon 4
gttagttgcaacatctttgggttttcatatatttcaccaatcaccaggaagctaagtagctaact-taacatcattaactct-actagcaccactttttttgtatgtagcaaattgttgatacacgataaccttctcttgttaagatgtcctaaatgttcttcatgtctgtaatagtgatatcattttgaccattttcagGCAAAATGTCTGGAGACAGGTGAGACAGTTGCTATCAAGAAGGTTCTTCAGGATAAGCGCTACAAGAACCGTGAGCTTCAGACCATGCGCCTTCTTGACC
||||||||||||| ||   |  ||  |||| ||| |                || | ||||| || |   ||   || | |  |||||||    |  | || || ||     || | |  |    |  ||  | || ||  |||        | |||     ||| ||   | | |  ||  |||||   |  ||   |||| || ||| |||| || |||||||| ||||| || |||||||||||||| || ||||| ||||||||||| || || |||||||||||||| |||||||
gttagttgcaacaactcctgacttagatatgttttat---------------tatgcagctatctgtggtattgctatcccggactagcagttttcatgttttaggtctttcatagct--tgtgtgccaaggtcctttttgtaa------tcagatg-----catctcctaatttgcaatgccatttgacctgttcatagGCCAAGTGTTTGGAAACGGGTGAGACTGTTGCCATAAAGAAGGTTCTTCAAGACAAGCGTTACAAGAACCGCGAACTGCAGACCATGCGCCTCCTTGACC

upper sequence: LOC_Os01g14860.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G024151_T01 (Zea mays), 3'ss of exon 4
gttagttgcaacatctttgggttttcatatatttcaccaatcaccaggaagctaagtagctaacttaacatcattaactctactagcaccactttttttgt-atgtagcaaattgttg-atacacgataaccttctcttgttaagatgtcctaaatgttcttcatgtctgtaatagtgatatcattttgaccattttcagGCAAAATGTCTGGAGACAGGTGAGACAGTTGCTATCAAGAAGGTTCTTCAGGATAAGCGCTACAAGAACCGTGAGCTTCAGACCATGCGCCTTCTTGACC
                                       ||   ||  ||  |  ||  || ||||      ||  ||| |  |    || | | |  |||    |  ||    | || | |     ||    |   |   |    ||   |||||   |||  |     ||||   |||  |||||   |  ||   |||| || ||| ||||||| |||||||| ||||| || ||||||||||||||||||||||| ||||||||||| ||| | ||||||||||||||||||||||
------------------------------------gttatttgcaataactt--gtgactgactt--tgatatgtactattatgtagccgcctgtggtgttgctttccacggcgctgcacatgttttagatcttcatatcttgcgtgctataaatcacctttct-----taatca-gatgccatttcacctgttcatagGCTAAGTGTTTGGAGACGGGTGAGACTGTTGCCATAAAGAAGGTTCTTCAGGATAAGCGTTACAAGAACCGCGAGTTGCAGACCATGCGCCTTCTTGACC

upper sequence: LOC_Os01g14860.1 (Oryza sativa), 3'ss of exon 4
lower sequence: PP1S74_168V6.1 (Physcomitrella patens), 3'ss of exon 3
gttagttgcaacatctttgggttttcatatatttcaccaatcaccaggaagctaagtagctaacttaacatcattaactctactagcaccactttttttgtatgtagcaaattgttgatacacgataaccttctcttgttaagatgtcctaaatgttcttcatgtctgtaatagtgatatcattttgaccattttcagGCAAAATGTCTGGAGACAGGTGAGACAGTTGCTATCAAGAAGGTTCTTCAGGATAAGCGCTACAAGAACCGTGAGCTTCAGACCATGCGCCTTCTTGACC
                                                                          |||||  ||| |  |||          |||  ||  ||      | || |  |   |     || ||  |    |||   | | ||| ||   |  |  ||      ||||||    || ||||||||||||  | ||||  || || || || ||||| |||||||| |||||||| ||| | ||||||||||| || ||||||| |||||| || || || |
--------------------------------------------------------------------------taacttcactggagccag-------acatggggctgat---ctgtccatgtgacgttcaaggtggtagaa----ctaggggatgttc-tgatcgcgagggta-----attttg----ttgtcagGCAAAATGCATAGAGAGCGGAGAAACTGTGGCTATTAAGAAGGTGCTTCAGGACAAGAGATACAAGAACCGAGAACTTCAGATCATGCGGCTGCTGGAGC

upper sequence: LOC_Os01g14860.1 (Oryza sativa), 3'ss of exon 4
lower sequence: EFJ04915 (Selaginella moellendorffii), 3'ss of exon 3
gttagttgcaacatctttgggttttcatatatttcaccaatcaccaggaagctaagtagctaacttaacatcattaactctactagcaccactttttttgtatgtagcaaattgttgatacacgataaccttctcttgttaagatgtcctaaatgttcttcatgtctgtaatagtgatatcattttgaccat-tttcagGCAAAATGTCTGGAGACAGGTGAGACAGTTGCTATCAAGAAGGTTCTTCAGGATAAGCGCTACAAGAACCGTGAGCTTCAGACCATGCGCCTTCTTGACC
                                                                                                                                        ||  ||   |   |||   ||||         |||   |  |  |  || | |     || |||| || || || || ||||| ||||| || ||||||||||||||  | ||||| ||| | ||||| ||||| ||||| || |  ||||||||||||||||
-------------------------------------------------------------------------------------------------------------------------------------gtgtgcaaactcgctttaatcattctaggc-----taacgtttcttcctgttgggcttcactttagGCCAAGTGCCTCGAAACAGGAGAGACGGTGGCTATCAAGAAGGTGTTACAGGACAAGAGATACAAAAACCGGGAGCTGCAAATAATGCGCCTTCTTGACC

upper sequence: LOC_Os01g14860.1 (Oryza sativa), 3'ss of exon 4
lower sequence: EFJ07923 (Selaginella moellendorffii), 3'ss of exon 4
gttagttgcaacatctttgggttttcatatatttcaccaatcaccaggaagctaagtagctaacttaacatcattaactctactagcaccactttttttgtatgtagcaaattgttgatacacgataaccttctcttgttaagatgtcctaaatgttcttcatgtctgtaatagtgatatcattttgaccattttcagGCAAAATGTCTGGAGACAGGTGAGACAGTTGCTATCAAGAAGGTTCTTCAGGATAAGCGCTACAAGAACCGTGAGCTTCAGACCATGCGCCTTCTTGACC
                                                                                                              |||| |  | ||    |||  |        |  | |   | |  |||  |  | |||                ||||   ||   ||||| || ||  |||| || || || || || |||||||| ||||| || || || ||||||||||||||||| ||||| ||||  |||||||| || ||||
------------------------------------------------------------------------------------------------------------gtattgctagtcca----aacagtgcaacaaaagcaggcttttatcgtttcttctttct---------------ctttgggaatg--cagGCCAAGTGCTTGGAAACCGGAGAAACCGTGGCTATCAAAAAGGTCCTCCAAGACAAGCGCTACAAGAACCGAGAGCTCCAGATAATGCGCCTCCTCGACC

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|58602831|gb|CK013359.1|CK013359
EST:     ACATGGCTGAGCGTAT-GTAGGGCAAGGTTCATTTGGGATTGTCTTCCAG                         GCAAAATGTCTGGAGACAGGTGAGACAGTTGCTATCAAGAAGGTTCTTCAG
genomic: ACATGGCTGAGCGTATTGTAGGGCAAGGTTCATTTGGGATTGTCTTCCAGgttagttgca ... ccattttcagGCAAAATGTCTGGAGACAGGTGAGACAGTTGCTATCAAGAAGGTTCTTCAG
EST: gi|58685932|gb|CK074619.1|CK074619
EST:     ACATGGCTGAGCGTATTGTAGGGCAAGGTTCATTTGGGATTGTCTTCCAG                         GCAAAATGTCTGGAGACAGGTGAGACAGTTGCTATCAAGAAGGTTCTTCAG
genomic: ACATGGCTGAGCGTATTGTAGGGCAAGGTTCATTTGGGATTGTCTTCCAGgttagttgca ... ccattttcagGCAAAATGTCTGGAGACAGGTGAGACAGTTGCTATCAAGAAGGTTCTTCAG
EST: gi|58661642|gb|CK050322.1|CK050322
EST:     ACATGGCTGAGCGTATTGTAGGGCAAGGTTCATTTGGGATTGTCTTCCAG                         GCAAAATGTCTGGAGACAGGTGAGACAGTTGCTATCAAGAAGGTTCTTCAG
genomic: ACATGGCTGAGCGTATTGTAGGGCAAGGTTCATTTGGGATTGTCTTCCAGgttagttgca ... ccattttcagGCAAAATGTCTGGAGACAGGTGAGACAGTTGCTATCAAGAAGGTTCTTCAG
EST: gi|2317492|gb|C22546.1|C22546
EST:     ACATGGCTGAGCGTATTGTAGGGCAAGGTTCATTTGGGATTGTCTTCCAG                         GCAAAATGTCTGGAGACAGGTGAGACAGTTGCTATCAAGAAGGTTCTTCAG
genomic: ACATGGCTGAGCGTATTGTAGGGCAAGGTTCATTTGGGATTGTCTTCCAGgttagttgca ... ccattttcagGCAAAATGTCTGGAGACAGGTGAGACAGTTGCTATCAAGAAGGTTCTTCAG
EST: gi|58598975|gb|CK009503.1|CK009503
EST:     CATGGCTGAGCGTATTGTAGGGCAAGGTTCATTTGGGATTGTCTTCCANG                         GCAAAATGTCTGGAGACAGGTGAGACAGTTGCTATCAAGAAGGTTCTTCA
genomic: CATGGCTGAGCGTATTGTAGGGCAAGGTTCATTTGGGATTGTCTTCCA-Ggttagttgca ... ccattttcagGCAAAATGTCTGGAGACAGGTGAGACAGTTGCTATCAAGAAGGTTCTTCA
EST: gi|58674441|gb|CK063127.1|CK063127
EST:     ACATGGCTGAGCGTATTGTAGGGCAAGGTTCATTTGGGATTGTCTTCCAG                         GCAAAATGTCTGGAGACAGGTGAGACAGTTGCTATCAAGAAGGTTCTTCAG
genomic: ACATGGCTGAGCGTATTGTAGGGCAAGGTTCATTTGGGATTGTCTTCCAGgttagttgca ... ccattttcagGCAAAATGTCTGGAGACAGGTGAGACAGTTGCTATCAAGAAGGTTCTTCAG
EST: gi|58665294|gb|CK053980.1|CK053980
EST:     ACATGGCTGAGCGTATTGTAGGGCAAGGTTCATTTGGGATTGTCTTCCAG                         GCAAAATGTCTGGAGACAGGTGAGACAGTTGCTATCAAGAAGGTTCTTCAG
genomic: ACATGGCTGAGCGTATTGTAGGGCAAGGTTCATTTGGGATTGTCTTCCAGgttagttgca ... ccattttcagGCAAAATGTCTGGAGACAGGTGAGACAGTTGCTATCAAGAAGGTTCTTCAG
EST: gi|58676495|gb|CK065182.1|CK065182
EST:     ACATGGCTGAGCGTATTGTAGGGCAAGGTTCATTTGGGATTGTCTTCCAG                         GCAAAATGTCTGGAGACAGGTGAGACAGTTGCTATCAAGAAGGTTCTTCAG
genomic: ACATGGCTGAGCGTATTGTAGGGCAAGGTTCATTTGGGATTGTCTTCCAGgttagttgca ... ccattttcagGCAAAATGTCTGGAGACAGGTGAGACAGTTGCTATCAAGAAGGTTCTTCAG
EST: gi|58665103|gb|CK053789.1|CK053789
EST:     ACATGGCTGAGCGTATTGTAGGGCAAGGTTCATTTGGGATTGTCTTCCAG                         GCAAAATGTCTGGAGACAGGTGAGACAGTTGCTATCAAGAAGGTTCTTCAG
genomic: ACATGGCTGAGCGTATTGTAGGGCAAGGTTCATTTGGGATTGTCTTCCAGgttagttgca ... ccattttcagGCAAAATGTCTGGAGACAGGTGAGACAGTTGCTATCAAGAAGGTTCTTCAG
EST: gi|29687086|gb|CB683361.1|CB683361
EST:     ACATGGCTGAGCGTATTGTAGGGCAAGGTTCATTTGGGATTGTCTTCCAG                         GCAAAATGTCTGGAGACAGGTGAGACAGTTGCTATCAAGAAGGTTCTTCAG
genomic: ACATGGCTGAGCGTATTGTAGGGCAAGGTTCATTTGGGATTGTCTTCCAGgttagttgca ... ccattttcagGCAAAATGTCTGGAGACAGGTGAGACAGTTGCTATCAAGAAGGTTCTTCAG
EST: gi|58673516|gb|CK062202.1|CK062202
EST:     ACATGGCTGAGCGTATTGTAGGGCAAGGTTCATTTGGGATTGTCTTCCAG                         GCAAAATGTCTGGAGACAGGTGAGACAGTTGCTATCAAGAAGGTTCTTCAG
genomic: ACATGGCTGAGCGTATTGTAGGGCAAGGTTCATTTGGGATTGTCTTCCAGgttagttgca ... ccattttcagGCAAAATGTCTGGAGACAGGTGAGACAGTTGCTATCAAGAAGGTTCTTCAG
EST: gi|29677190|gb|CB673465.1|CB673465
EST:     ACATGCCTGAGCGTATTGTAGGGCAAGGTTCATTTGGGATTGTCTTCCAG                         GCAAAATGTCTGGAGACAGGTGAGACAGTTGCTATCAAGAAGGTTCTTCAG
genomic: ACATGGCTGAGCGTATTGTAGGGCAAGGTTCATTTGGGATTGTCTTCCAGgttagttgca ... ccattttcagGCAAAATGTCTGGAGACAGGTGAGACAGTTGCTATCAAGAAGGTTCTTCAG
EST: gi|58652484|gb|CK041164.1|CK041164
EST:     ACATGGCTGAGCGTATTGTAGGGCAAGGTTCATTTGGGATTGTCTTCCAG                         GCAAAATGTCTGGAGACAGGTGAGACAGTTGCTATCAAGAAGGTTCTTCAG
genomic: ACATGGCTGAGCGTATTGTAGGGCAAGGTTCATTTGGGATTGTCTTCCAGgttagttgca ... ccattttcagGCAAAATGTCTGGAGACAGGTGAGACAGTTGCTATCAAGAAGGTTCTTCAG
EST: gi|58671331|gb|CK060017.1|CK060017
EST:     ACATGGCTGAGCGTATTGTAGGGCAAGGTTCATTTGGGATTGTCTTCCAG                         GCAAAATGTCTGGAGACAGGTGAGACAGTTGCTATCAAGAAGGTTCTTCAG
genomic: ACATGGCTGAGCGTATTGTAGGGCAAGGTTCATTTGGGATTGTCTTCCAGgttagttgca ... ccattttcagGCAAAATGTCTGGAGACAGGTGAGACAGTTGCTATCAAGAAGGTTCTTCAG
EST: gi|58657986|gb|CK046666.1|CK046666
EST:     ACATGGCTGAGCGTATTGTAGGGCAAGGTTCATTTGGGATTGTCTTCCAG                         GCAAAATGTCTGGAGACAGGTGAGACAGTTGCTATCAAGAAGGTTCTTCAG
genomic: ACATGGCTGAGCGTATTGTAGGGCAAGGTTCATTTGGGATTGTCTTCCAGgttagttgca ... ccattttcagGCAAAATGTCTGGAGACAGGTGAGACAGTTGCTATCAAGAAGGTTCTTCAG
EST: gi|58654229|gb|CK042909.1|CK042909
EST:     ACATGGCTGAGCGTATTGTAGGGCAAGGTTCATTTGGGATTGTCTTCCAG                         GCAAAATGTCTGGAGACAGGTGAGACAGTTGCTATCAAGAAGGTTCTTCAG
genomic: ACATGGCTGAGCGTATTGTAGGGCAAGGTTCATTTGGGATTGTCTTCCAGgttagttgca ... ccattttcagGCAAAATGTCTGGAGACAGGTGAGACAGTTGCTATCAAGAAGGTTCTTCAG
EST: gi|58590979|gb|CF989287.1|CF989287
EST:     ACATGGCTGAGCGTATTGTAGGGCAAGGTTCATTTGGGATTGTCTTCCAG                         GCAAAATGTCTGGAGACAGGTGAGACAGTTGCTATCAAGAAGGTTCTTCAG
genomic: ACATGGCTGAGCGTATTGTAGGGCAAGGTTCATTTGGGATTGTCTTCCAGgttagttgca ... ccattttcagGCAAAATGTCTGGAGACAGGTGAGACAGTTGCTATCAAGAAGGTTCTTCAG
EST: gi|58653056|gb|CK041736.1|CK041736
EST:     ACATGGCTGAGCGTATTGTAGGGCAAGGTTCATTTGGGATTGTCTTCCAG                         GCAAAATGTCTGGAGACAGGTGAGACAGTTGCTATCAAGAAGGTTCTTCAG
genomic: ACATGGCTGAGCGTATTGTAGGGCAAGGTTCATTTGGGATTGTCTTCCAGgttagttgca ... ccattttcagGCAAAATGTCTGGAGACAGGTGAGACAGTTGCTATCAAGAAGGTTCTTCAG
EST: gi|29618976|gb|CB623988.1|CB623988
EST:     ACATGGCTGAGCGTATTGTAGGGCAAGGTTCATTTGGGATTGTCTTCCAG                         GCAAAATGTCTGGAGACAGGTGAGACAGTTGCTATCAAGAAGGTTCTTCAG
genomic: ACATGGCTGAGCGTATTGTAGGGCAAGGTTCATTTGGGATTGTCTTCCAGgttagttgca ... ccattttcagGCAAAATGTCTGGAGACAGGTGAGACAGTTGCTATCAAGAAGGTTCTTCAG
EST: gi|163921584|gb|EG712155.1|EG712155
EST:     ACATGGCTGAGCGTATTGTAGGGCAAGGTTCATTTGGGATTGTCTTCCAG                         GCAAAATGTCTGGAGACAGGTGAGACAGTTGCTATCAAGAAGGTTCTTCAG
genomic: ACATGGCTGAGCGTATTGTAGGGCAAGGTTCATTTGGGATTGTCTTCCAGgttagttgca ... ccattttcagGCAAAATGTCTGGAGACAGGTGAGACAGTTGCTATCAAGAAGGTTCTTCAG
EST: gi|5003279|gb|AU068428.1|AU068428
EST:     ACATGGCTGAGCGTATTGTAGGGCAAGGTTCATTTGGGATTGTCTTCCAG                         GCAAAATGTCTGGAGACAGGTGAGACAGTTGCTATCAAGAAGGTTCTTCAG
genomic: ACATGGCTGAGCGTATTGTAGGGCAAGGTTCATTTGGGATTGTCTTCCAGgttagttgca ... ccattttcagGCAAAATGTCTGGAGACAGGTGAGACAGTTGCTATCAAGAAGGTTCTTCAG
EST: gi|86596734|gb|CI286647.1|CI286647
EST:     ACATGGCTGAGCGTATTGTAGGGCAAGGTTCATTTGGGATTGTCTTCCAG                         GCAAAATGTCTGGAGACAGGTGAGACAGTTGCTATCAAGAAGGTTCTTCAG
genomic: ACATGGCTGAGCGTATTGTAGGGCAAGGTTCATTTGGGATTGTCTTCCAGgttagttgca ... ccattttcagGCAAAATGTCTGGAGACAGGTGAGACAGTTGCTATCAAGAAGGTTCTTCAG
EST: gi|33796677|gb|CF324206.1|CF324206
EST:     ACATGGCTGAGCGTATTGTAGGGCAAGGTTCATTTGGGATTGTCTTCCAG                         GCAAAATGTCTGGAG
genomic: ACATGGCTGAGCGTATTGTAGGGCAAGGTTCATTTGGGATTGTCTTCCAGgttagttgca ... ccattttcagGCAAAATGTCTGGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgtcctaaatgttcttcatgtctgtaatagtgatatcattttgaccattttcagGCAAAATGTCTGGAGACAGGTGAGACAGTTGCTATCAAGAAGGTTCTTCAGGATAAGCGCTACAAGAACCGTGAGCTTCAGACCATGCGCCTTCTTGACC
                                             ccattttc  CT-rich tract
                                 atatcatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagttgcaacatctttgggttttcatatatttcaccaatcaccaggaagctaagtagctaacttaacatcattaactctactagcaccactttttttgtatgtagcaaattgttgatacacgataaccttctcttgttaagatgtcctaaatgttcttcatgtctgtaatagtgatatcattttgaccattttcagGCAAAATGTCTGGAGACAGGTGAGACAGTTGCTATCAAGAAGGTTCTTCAGGATAAGCGCTACAAGAACCGTGAGCTTCAGACCATGCGCCTTCTTGACC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT