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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taaaagaagttgttctctgtcggggcttcttttccccatctttgtcttccactcaccccataacacatcgtgtcctttaactataaaatattttttccagGCTGTTGCTGGTTTAGCTGCAGATGGCAGGCAAATTGTTTCAAGAGCAAAATCGGAAGCGGCCAGTTATGAGAA

Basic information

species Oryza sativa
transcript LOC_Os01g59600.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g59600.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G445100_T01 (Zea mays), 3'ss of exon 4
taaaagaagttgttctctgtcggggcttcttttccccatctttgtcttccactcacc-ccataacacatcgtgtcctttaactataaaatattttt---------tccagGCTGTTGCTGGTTTAGCTGCAGATGGCAGGCAAATTGTTTCAAGAGCAAAATCGGAAGCGGCCAGTTATGAGAA
       |||  | |  | ||      | | || |  | ||   |  |||| |   |    | |   ||| |||   ||  | | ||| || ||||         | ||||| ||||||||||| || ||||||||||||||||||||||||||  | ||||| ||||| ||||||||||| ||
----tccagtgatgccttttca-----tttcttgcaaagctccatgatccattagtcatttttatgaatcatgtgtgttttc-acaaattacttttatgctcgattgcagGCCGTTGCTGGTTTGGCAGCAGATGGCAGGCAAATTGTTTCAAGGACCAAATCAGAAGCTGCCAGTTATGAAAA

upper sequence: LOC_Os01g59600.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G130398_T01 (Zea mays), 3'ss of exon 4
----taaaagaagttgttctctgtcggggcttcttttccccatctttgtcttccactcaccccataacacatcgtgtcctttaactataaaatattttttccagGCTGTTGCTGGTTTAGCTGCAGATGGCAGGCAAATTGTTTCAAGAGCAAAATCGGAAGCGGCCAGTTATGAGAA
     | ||    || || |||      | ||| | | ||  |     | ||  |   |||   |      ||      |     |||    | |  | | |||||||||||||||||||| ||||||||||||||||||||||||||  | ||||| ||||| ||||||||||| ||
tggtgataacctattcttttcttggaaaggttcatgttccatttgccattttttatgaaccatgtgtgttttcacaaattacttttat----tgtcatctgcagGCTGTTGCTGGTTTAGCAGCAGATGGCAGGCAAATTGTTTCAAGGACCAAATCAGAAGCTGCCAGTTATGAAAA

upper sequence: LOC_Os01g59600.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G008623_T01 (Zea mays), 3'ss of exon 4
---taaaagaagttgttctctgtcggggcttcttttccccatctttgtcttccactcaccccataacacatcgtgtcctttaacta--taaaatattttttccagGCTGTTGCTGGTTTAGCTGCAGATGGCAGGCAAATTGTTTCAAGAGCAAAATCGGAAGCGGCCAGTTATGAGAA
   | | | |     || |   ||   | ||| | | ||  |     | ||    | |    || |    | || | |   || ||  |  | |||  ||| |||||||||||||||||||| ||||||||||||||||||||||||||  | || || ||||| ||||||||||| ||
acttgagatagccatttgttcttcaaaggttcatgttccactagccatttttttatga----atcatgt-ttgttttcacaaattacttttattatcatttgcagGCTGTTGCTGGTTTAGCAGCAGATGGCAGGCAAATTGTTTCAAGGACGAAGTCAGAAGCTGCCAGTTATGAAAA

upper sequence: LOC_Os01g59600.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G008623_T02 (Zea mays), 3'ss of exon 4
---taaaagaagttgttctctgtcggggcttcttttccccatctttgtcttccactcaccccataacacatcgtgtcctttaacta--taaaatattttttccagGCTGTTGCTGGTTTAGCTGCAGATGGCAGGCAAATTGTTTCAAGAGCAAAATCGGAAGCGGCCAGTTATGAGAA--------------------------
   | | | |     || |   ||   | ||| | | ||  |     | ||    | |    || |    | || | |   || ||  |  | |||  ||| |||||||||||||||||||| ||||||||||||||||||||||||||  | || || ||||| ||||||||||| ||                          
acttgagatagccatttgttcttcaaaggttcatgttccactagccatttttttatga----atcatgt-ttgttttcacaaattacttttattatcatttgcagGCTGTTGCTGGTTTAGCAGCAGATGGCAGGCAAATTGTTTCAAGGACGAAGTCAGAAGCTGCCAGTTATGAAAAGTAAACACCTTGTCTTTGAGACCATG

upper sequence: LOC_Os01g59600.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G028346_T01 (Zea mays), 3'ss of exon 2
-------taaaagaagttgttctctgtcggggcttcttttccccatctttgtcttccactcaccccataacacatcgtgtcctttaactataaaatattttttccagGCTGTTGCTGGTTTAGCTGCAGATGGCAGGCAAATTGTTTCAAGAGCAAAATCGGAAGCGGCCAGTTATGAGAA
       |    ||  | ||||   ||  | | || |||     |    ||| |   | | ||   |||  | ||  | |  | ||  |||| |   |   || |||| |||||||||||| || ||||||||||| |||||||||||||| || ||||| ||||| ||||||||||| ||
tcttttcttgcggagctcgttcc--gttagcgattttttatg--aatcgtgtgtgaaaattactttata-tatat-atata-tatatatatatatgctcaattgcagGTTGTTGCTGGTTTGGCAGCAGATGGCAGACAAATTGTTTCAAGGGCCAAATCAGAAGCTGCCAGTTATGAAAA

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|33692105|gb|CF320344.1|CF320344
EST:     TGGAGGGATCTAATAGGAGGATCCATTCAGTGCACTGGCACTCTGGCTTG                         GCTGTTGCTGGTTTAGCTGCAGATGGCAGGCAAATTGTTTCAAGAGCAAAA
genomic: TGGAGGGATCTAATAGGAGGATCCATTCAGTGCACTGGCACTCTGGCTTGgtaacatctt ... ttttttccagGCTGTTGCTGGTTTAGCTGCAGATGGCAGGCAAATTGTTTCAAGAGCAAAA
EST: gi|27576784|gb|CA999478.1|CA999478
EST:     GAGGATCCATTCAGTGCACTGGCACTCTGGCTTG                         GCTGTTGCTGGTTTAGCTGCAGATGGCAGGCAAATTGTTTCAAGAGCAAAA
genomic: GAGGATCCATTCAGTGCACTGGCACTCTGGCTTGgtaacatctt ... ttttttccagGCTGTTGCTGGTTTAGCTGCAGATGGCAGGCAAATTGTTTCAAGAGCAAAA
EST: gi|88391006|gb|CI592914.1|CI592914
EST:     TGGAGGGATCTAATAGGAGGATCCATTCAGTGCAGTGGCACTCTGGCTTG                         GCTGTTGCTGGT
genomic: TGGAGGGATCTAATAGGAGGATCCATTCAGTGCACTGGCACTCTGGCTTGgtaacatctt ... ttttttccagGCTGTTGCTGGT
EST: gi|218496122|gb|FG967266.1|FG967266
EST:     TGGAGGGATCTAATAGGAGGATCCATTCAGTGCACTGGCACTCCGGCTTG                         GCTGTTGCTGGTTTAGCTGCAGATGGCAGGCAAATTGTTTCAAGAGCAAAA
genomic: TGGAGGGATCTAATAGGAGGATCCATTCAGTGCACTGGCACTCTGGCTTGgtaacatctt ... ttttttccagGCTGTTGCTGGTTTAGCTGCAGATGGCAGGCAAATTGTTTCAAGAGCAAAA
EST: gi|88425566|gb|CI569290.1|CI569290
EST:     TGGAGGGATCTAATAGGAGGATCCATTCAGTGCACTGGCACTCTGGCTTG                         GCTGTTGCTGGTTTAGCTGCAGATGGCAGGCAAATTGTTTCAAGAGCAAA-
genomic: TGGAGGGATCTAATAGGAGGATCCATTCAGTGCACTGGCACTCTGGCTTGgtaacatctt ... ttttttccagGCTGTTGCTGGTTTAGCTGCAGATGGCAGGCAAATTGTTTCAAGAGCAAAA
EST: gi|58596536|gb|CK007064.1|CK007064
EST:     TGGAGGGATCTAATAGGAGGATCCATTCAGTGCACTGGCACTCCGGCTTG                         GCTGTTGCTGGTTTAGCTGCAGATGGCAGGCAAATTGTTTCAAGAG
genomic: TGGAGGGATCTAATAGGAGGATCCATTCAGTGCACTGGCACTCTGGCTTGgtaacatctt ... ttttttccagGCTGTTGCTGGTTTAGCTGCAGATGGCAGGCAAATTGTTTCAAGAG
EST: gi|58601557|gb|CK012085.1|CK012085
EST:     TGGAGGGATCTAATAGGAGGATCCATTCAGTGCACTGGCACTCCGGCTTG                         GCTGTTGCTGGTTTAGCTGCAGATGGCAGGCAAATTGTTTCAAGAGCAAAA
genomic: TGGAGGGATCTAATAGGAGGATCCATTCAGTGCACTGGCACTCTGGCTTGgtaacatctt ... ttttttccagGCTGTTGCTGGTTTAGCTGCAGATGGCAGGCAAATTGTTTCAAGAGCAAAA
EST: gi|29668732|gb|CB665007.1|CB665007
EST:     TGGAGGGATCTAATAGGAGGATCCATTCAGTGCACTGGCACTCTGGCTTG                         GCTGTTGCTGGTTTAGCTGCAGATGGCAGGCAAATTGTTTCAAGAGCAAAA
genomic: TGGAGGGATCTAATAGGAGGATCCATTCAGTGCACTGGCACTCTGGCTTGgtaacatctt ... ttttttccagGCTGTTGCTGGTTTAGCTGCAGATGGCAGGCAAATTGTTTCAAGAGCAAAA
EST: gi|33657519|gb|CF280133.1|CF280133
EST:     TGGAGGGATCTAATAGGAGGATCCATTCAGTGCACTGGCACTCTGGTTTG                         GCTGGTTGCTGGTTTAGCTGCAGATGGCAGGCAAATTGTTTCAAGAGCAAA
genomic: TGGAGGGATCTAATAGGAGGATCCATTCAGTGCACTGGCACTCTGGCTTGgtaacatctt ... ttttttccagGCTG-TTGCTGGTTTAGCTGCAGATGGCAGGCAAATTGTTTCAAGAGCAAA
EST: gi|12622988|gb|AU173201.1|AU173201
EST:     TGGAGGGATCTAATAGGAGGATCCATTCAGTGCACTGGCACTCTGGCTTG                         GCTGTTGCTGGTTTAGCTGCANATGGCAGGCA
genomic: TGGAGGGATCTAATAGGAGGATCCATTCAGTGCACTGGCACTCTGGCTTGgtaacatctt ... ttttttccagGCTGTTGCTGGTTTAGCTGCAGATGGCAGGCA
EST: gi|88420790|gb|CI564626.1|CI564626
EST:     TGGAGGGATCTAATAGGAGGATCCATTCAGTGCACTGGCACTCTGGCTTG                         GCTGTTGCTGGTTTAGCTGCAGATGGCAGGCAAATTGTTTCAAGAGCAAAA
genomic: TGGAGGGATCTAATAGGAGGATCCATTCAGTGCACTGGCACTCTGGCTTGgtaacatctt ... ttttttccagGCTGTTGCTGGTTTAGCTGCAGATGGCAGGCAAATTGTTTCAAGAGCAAAA
EST: gi|88454340|gb|CI569912.1|CI569912
EST:     TGGAGGGATCTAATAGGAGGATCCATTCAGTGCACTGGCACTCTGGCTTG                         GCTGTTGCTGGTTTAGCTGCAGATGGCAGGCAA-TTGTTTCAAGAGCAAAA
genomic: TGGAGGGATCTAATAGGAGGATCCATTCAGTGCACTGGCACTCTGGCTTGgtaacatctt ... ttttttccagGCTGTTGCTGGTTTAGCTGCAGATGGCAGGCAAATTGTTTCAAGAGCAAAA
EST: gi|29668731|gb|CB665006.1|CB665006
EST:     TGGAGGGATCTAATAGGAGGATCCATTCAGTGCACTGGCACTCTGGCTTG                         GCTGTTGCTGGTTTAGCTGCAGATGGCAGGCAAATTGTTTCAAGAGCAAAA
genomic: TGGAGGGATCTAATAGGAGGATCCATTCAGTGCACTGGCACTCTGGCTTGgtaacatctt ... ttttttccagGCTGTTGCTGGTTTAGCTGCAGATGGCAGGCAAATTGTTTCAAGAGCAAAA
EST: gi|33686716|gb|CF314955.1|CF314955
EST:     GGAGGGATCTAATAGGAGGATCCATTCAGTGCACTGGCACTCTGGCTTTG                         GCTGTTGCTGGTTTAGCTGCAGATGGCAGGCAAATTGTTTCAAGAGCAAA
genomic: GGAGGGATCTAATAGGAGGATCCATTCAGTGCACTGGCACTCTGGCTT-Ggtaacatctt ... ttttttccagGCTGTTGCTGGTTTAGCTGCAGATGGCAGGCAAATTGTTTCAAGAGCAAA
EST: gi|163919763|gb|EG714885.1|EG714885
EST:     TGGAGGGATCTAATAGGAGGATCCATTCAGTGCACTGGCACTCTGGCTTG                         GCTGTTGCTGGTTTAGCTGCAGATGGCAGGCAAATTGTTTCAAGAGCAAAA
genomic: TGGAGGGATCTAATAGGAGGATCCATTCAGTGCACTGGCACTCTGGCTTGgtaacatctt ... ttttttccagGCTGTTGCTGGTTTAGCTGCAGATGGCAGGCAAATTGTTTCAAGAGCAAAA
EST: gi|88694188|gb|CI738226.1|CI738226
EST:     TGGAGGGATCTAATAGGAGGATCCATTCAGTGCACTGGCACTCTGGCTTG                         GCTGTTGCTGGTTTAGCTGCAGATGGCAGGCAAATTGTTTCAAGAGCAAAA
genomic: TGGAGGGATCTAATAGGAGGATCCATTCAGTGCACTGGCACTCTGGCTTGgtaacatctt ... ttttttccagGCTGTTGCTGGTTTAGCTGCAGATGGCAGGCAAATTGTTTCAAGAGCAAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttccactcaccccataacacatcgtgtcctttaactataaaatattttttccagGCTGTTGCTGGTTTAGCTGCAGATGGCAGGCAAATTGTTTCAAGAGCAAAATCGGAAGCGGCCAGTTATGAGAA
                                           tattttttcc  CT-rich tract
                           tcctttaactataaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taaaagaagttgttctctgtcggggcttcttttccccatctttgtcttccactcaccccataacacatcgtgtcctttaactataaaatattttttccagGCTGTTGCTGGTTTAGCTGCAGATGGCAGGCAAATTGTTTCAAGAGCAAAATCGGAAGCGGCCAGTTATGAGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
-aaaagaa
- - - - -ttgttct
- - - - - - - - - - - -ggcttct