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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgcttgaatgttgttacccattcatctcaaataccaccctcttatttctgtaactttataattgatgtttgaacttctaatcagGTAAACCCACATACCCATCAACTCAAGCTATGTGACTTTGGGAGTGCAAAAGTTCTG

Basic information

species Oryza sativa
transcript LOC_Os01g14860.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g14860.3 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM5G835235_T04 (Zea mays), 3'ss of exon 6
gtatgcttgaatgttgttacccattcatctcaaataccaccctcttatt------tctgtaactttataattgatgtttgaacttctaatcagGTAAACCCACATACCCATCAACTCAAGCTATGTGACTTTGGGAGTGCAAAAGTTCTG-------------------------------------------
||||||| | |  || ||  | |||   |||   || ||   ||  ||       | ||  ||||   ||||||| ||  ||||||    ||||| |||||||| ||||| || || ||  ||||||||||||| |||||||||||||||                                           
gtatgct-ggagattctt--ctattttgctcctgtatcattttcagatgaaatggtttggtacttagaaattgattttcaaacttcactacagGTGAACCCACACACCCACCAGCTTAAAATATGTGACTTTGGTAGTGCAAAAGTTCTGGTCAAGGGGGAACCAAACATATCATACATCTGCTCGCGATACT

upper sequence: LOC_Os01g14860.3 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G129482_T01 (Zea mays), 3'ss of exon 2
---------------------------------------------gtatgcttgaatgttgttacccattcatctcaaataccaccctcttatt------tctgtaactttataattgatgtttgaacttctaatcagGTAAACCCACATACCCATCAACTCAAGCTATGTGACTTTGGGAGTGCAAAAGTTCTG
                                             ||||||| | |  || ||  | |||   |||   || ||   ||  ||       | ||  ||||   ||||||| ||  ||||||    ||||| |||||||| ||||| || || || |||||||||||||| |||||||||||    
gtactatcggtgtctgccagagatattaagccacaaaatcttttggtatgct-ggagattctt--ctattttgctcctgtatcattttcagATGAAATTGTTTGGTACTTAGAAATTGATTTTCAAACTTCAGTACAGGTGAACCCACACACCCACCAGCTTAAACTATGTGACTTTGGTAGTGCAAAAGT----

upper sequence: LOC_Os01g14860.3 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G024151_T01 (Zea mays), 3'ss of exon 6
gtatgcttgaatgt-tgttacccattcatctcaaataccaccctcttatttctgta-actttataattgatgtttgaacttctaatcagGTAAACCCACATACCCATCAACTCAAGCTATGTGACTTTGGGAGTGCAAAAGTTCTG-------------------------------------------
||||||| |||  | || ||       |    |  |           | |  | |  |||||  ||||||||||  ||||||    ||||| |||||||| ||||| || || || |||||||||||||| |||||||||||||||                                           
gtatgctggaaaatctgctattttgctactgtatctttttgtaaagaaatgatttgtactttgaaattgatgttcaaacttcactacagGTGAACCCACACACCCACCAGCTTAAACTATGTGACTTTGGCAGTGCAAAAGTTCTGGTCAAGGGGGAACCAAACATATCGTACATCTGCTCCCGATACT

upper sequence: LOC_Os01g14860.3 (Oryza sativa), 3'ss of exon 5
lower sequence: EFJ07923 (Selaginella moellendorffii), 3'ss of exon 6
gtatgcttgaatgttgttacccattcatctcaaataccaccctcttatttctgtaactttataattgatgtttgaacttcta-atcagGTAAACCCACATACCCATCAACTCAAGCTATGTGACTTTGGGAGTGCAAAAGTTCTG
                       |  | | |   |    |  ||   |    | |   ||||  ||    ||||    | |  |||||||||| ||||| || || || |||||||| ||||||||||||||||| |||||  ||
----------------------gtaaaaccctccttgtgctttcgagtcctggaattcttatgcttttcttttgctggtttgcatcagGTAAATCCACACACACACCAGCTCAAGCTCTGTGACTTTGGGAGTGCTAAAGTCTTG

upper sequence: LOC_Os01g14860.3 (Oryza sativa), 3'ss of exon 5
lower sequence: EFJ07216 (Selaginella moellendorffii), 3'ss of exon 6
gtatgcttgaatgttgttacccattcatctcaaataccaccctcttatttctgtaactttataattgatgtttgaacttctaatcagGTAAACCCACATACCCATCAACTCAAGCTATGTGACTTTGGGAGTGCAAAAGTTCTG
               || | || | | | |    |     |||   |||  | |   ||| |  |||     || | |||  |||||||||| ||||| || || || |||||||| ||||||||||||||||| |||||  ||
---------------gtaaaccctccttgtgctttcgagtcctggaattcttatgcttttctt-ttg----ctggatttc--atcagGTAAATCCACACACACACCAGCTCAAGCTCTGTGACTTTGGGAGTGCTAAAGTCTTG

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|58602640|gb|CK013168.1|CK013168
EST:     ATAATAGCATCGGAGTTTGCCACAGAGATATCAAGCCACAGAATCTTCTG                         GTAAACCCACATACCCATCAACTCAAGCTATGTGACTTTGGGAGTGCAAAA
genomic: ATAATAGCATCGGAGTTTGCCACAGAGATATCAAGCCACAGAATCTTCTGgtatgcttga ... ttctaatcagGTAAACCCACATACCCATCAACTCAAGCTATGTGACTTTGGGAGTGCAAAA
EST: gi|58686155|gb|CK074842.1|CK074842
EST:     ATAATAGCATCGGAGTTTGCCACAGAGATATCAAGCCACAGAATCTTCTG                         GTAAACCCACATACCCATCAACTCAAGCTATGTGACTTTGGGAGTGCAAAA
genomic: ATAATAGCATCGGAGTTTGCCACAGAGATATCAAGCCACAGAATCTTCTGgtatgcttga ... ttctaatcagGTAAACCCACATACCCATCAACTCAAGCTATGTGACTTTGGGAGTGCAAAA
EST: gi|2317492|gb|C22546.1|C22546
EST:     ATAATAGCATCGGAGTTTGCCACAGAGATATCAAGCCACAGAATCTTCTG                         GTAAACCCACATACCCATCAACTCAAGCT
genomic: ATAATAGCATCGGAGTTTGCCACAGAGATATCAAGCCACAGAATCTTCTGgtatgcttga ... ttctaatcagGTAAACCCACATACCCATCAACTCAAGCT
EST: gi|58606572|gb|CK034605.1|CK034605
EST:     CGGAGTTTG-CACAGAGATATCAAGCCACAGAATCTTCTG                         GTAAACCCACATACCCATCAACTCAAGCTAGTGGGACTTTGGGAGTGCAAA
genomic: CGGAGTTTGCCACAGAGATATCAAGCCACAGAATCTTCTGgtatgcttga ... ttctaatcagGTAAACCCACATACCCATCAACTCAAGCTA-TGTGACTTTGGGAGTGCAAA
EST: gi|58687307|gb|CK075994.1|CK075994
EST:     ATAATAGCATCGGAGTTTGCCACAGAGATATCAAGCCACAGAATCTTCTG                         GTAAACCCACATACCCATCAACTCAAGCTATGTGACTTTGGGAGTGCAAAA
genomic: ATAATAGCATCGGAGTTTGCCACAGAGATATCAAGCCACAGAATCTTCTGgtatgcttga ... ttctaatcagGTAAACCCACATACCCATCAACTCAAGCTATGTGACTTTGGGAGTGCAAAA
EST: gi|58664832|gb|CK053518.1|CK053518
EST:     ATAATAGCATCGGAGTTTGCCACAGAGATATCAAGCCACAGAATCTTCTG                         GTAAACCCACATACCCATCAACTCAAGCTATGTGACTTTGGGAGT
genomic: ATAATAGCATCGGAGTTTGCCACAGAGATATCAAGCCACAGAATCTTCTGgtatgcttga ... ttctaatcagGTAAACCCACATACCCATCAACTCAAGCTATGTGACTTTGGGAGT
EST: gi|58679602|gb|CK068289.1|CK068289
EST:     ATAATAGCATCGGAGTTTGCCACAGAGATATCAAGCCACAGAATCTTCTG                         GTAAACCCACATACCCATCAACTCAAGCTATGTGACTTTGGGAGTGCAAAA
genomic: ATAATAGCATCGGAGTTTGCCACAGAGATATCAAGCCACAGAATCTTCTGgtatgcttga ... ttctaatcagGTAAACCCACATACCCATCAACTCAAGCTATGTGACTTTGGGAGTGCAAAA
EST: gi|58673993|gb|CK062679.1|CK062679
EST:     ATAATAGCATCGGAGTTTGCCACAGAGATATCAAGCCACAGAATCTTCTG                         GTAAACCCACATACCCATCAACTCAAGCTATGTGACTTTGGGAGTGCAAAA
genomic: ATAATAGCATCGGAGTTTGCCACAGAGATATCAAGCCACAGAATCTTCTGgtatgcttga ... ttctaatcagGTAAACCCACATACCCATCAACTCAAGCTATGTGACTTTGGGAGTGCAAAA
EST: gi|58602991|gb|CK013519.1|CK013519
EST:     ATAATAGCATCGGAGTTTGCCACAGAGATATCAAGCCACAGAATCTTCTG                         GTGGACCCACATACCCATCAACTCAAGCTATGTGACTTTGGGAGTGCAAAA
genomic: ATAATAGCATCGGAGTTTGCCACAGAGATATCAAGCCACAGAATCTTCTGgtatgcttga ... ttctaatcagGTAAACCCACATACCCATCAACTCAAGCTATGTGACTTTGGGAGTGCAAAA
EST: gi|29687086|gb|CB683361.1|CB683361
EST:     ATAATAGCATCGGAGTTTGCCACAGAGATATCAAGCCACAGAATCTTCTG                         GTAAACCCACATACCCATCAACTCAAGCTATGTGACTTTGGGAGTGCAAAA
genomic: ATAATAGCATCGGAGTTTGCCACAGAGATATCAAGCCACAGAATCTTCTGgtatgcttga ... ttctaatcagGTAAACCCACATACCCATCAACTCAAGCTATGTGACTTTGGGAGTGCAAAA
EST: gi|218486932|gb|FG950343.1|FG950343
EST:     ATAATAGCATCGGAGTTTGCCNCAGAGATATCAAGCCACAGAATCTTCTG                         GTAAACCCACATACCCATCAACTCAAGCTATGTGACTTTGGGAGTGCAAAA
genomic: ATAATAGCATCGGAGTTTGCCACAGAGATATCAAGCCACAGAATCTTCTGgtatgcttga ... ttctaatcagGTAAACCCACATACCCATCAACTCAAGCTATGTGACTTTGGGAGTGCAAAA
EST: gi|38469291|gb|CF953422.1|CF953422
EST:     ATAATAGCATCGGAGTTTGCCACAGAGATATCAAGCCACAGAATCTTCTG                         GTAAACCCACATACCCATCAACTCAAGCTATGTGACTTTGGGAGTGCAAAA
genomic: ATAATAGCATCGGAGTTTGCCACAGAGATATCAAGCCACAGAATCTTCTGgtatgcttga ... ttctaatcagGTAAACCCACATACCCATCAACTCAAGCTATGTGACTTTGGGAGTGCAAAA
EST: gi|29677190|gb|CB673465.1|CB673465
EST:     ATAATAGCATCGGAGTTTGCCACAGAGATATCAAGCCACAGAATCTTCTG                         GTAAACCCACATACCCATCAACTCAAGCTATGTGACTTTGGGAGTGCAAAA
genomic: ATAATAGCATCGGAGTTTGCCACAGAGATATCAAGCCACAGAATCTTCTGgtatgcttga ... ttctaatcagGTAAACCCACATACCCATCAACTCAAGCTATGTGACTTTGGGAGTGCAAAA
EST: gi|58679239|gb|CK067926.1|CK067926
EST:     ATAATAGCATCGGAGTTTGCCACAGAGATATCAAGCCACAGAATCTTCTG                         GTAAACCCACATACCCATCAACTCAAGCTATGTGACTTTGGGAGTGCAAAA
genomic: ATAATAGCATCGGAGTTTGCCACAGAGATATCAAGCCACAGAATCTTCTGgtatgcttga ... ttctaatcagGTAAACCCACATACCCATCAACTCAAGCTATGTGACTTTGGGAGTGCAAAA
EST: gi|58671331|gb|CK060017.1|CK060017
EST:     ATAATAGCATCGGAGTTTGCCACAGAGATATCAAGCCACAGAATCTTCTG                         GTAAACCCACATACCCATCAACTCAAGCTATGTGACTTTGGGAGTGCAAAA
genomic: ATAATAGCATCGGAGTTTGCCACAGAGATATCAAGCCACAGAATCTTCTGgtatgcttga ... ttctaatcagGTAAACCCACATACCCATCAACTCAAGCTATGTGACTTTGGGAGTGCAAAA
EST: gi|218496430|gb|FG946684.1|FG946684
EST:     ATAATAGCATCGGAGTTTGCCACAGAGATATCAAGCCACAGAATCTTCTG                         GTAAACCCACATACCCATCAACTCAAGCTATGTGACTTTGGGAGTGCAAAA
genomic: ATAATAGCATCGGAGTTTGCCACAGAGATATCAAGCCACAGAATCTTCTGgtatgcttga ... ttctaatcagGTAAACCCACATACCCATCAACTCAAGCTATGTGACTTTGGGAGTGCAAAA
EST: gi|58675968|gb|CK064655.1|CK064655
EST:     ATAATAGCATCGGAGTTTGCCACAGAGATATCAAGCCACAGAATCTTCTG                         GTAAACCCACATACCCATCAACTCAAGCTATGTGACTTTGGGAGTGCAAAA
genomic: ATAATAGCATCGGAGTTTGCCACAGAGATATCAAGCCACAGAATCTTCTGgtatgcttga ... ttctaatcagGTAAACCCACATACCCATCAACTCAAGCTATGTGACTTTGGGAGTGCAAAA
EST: gi|58682391|gb|CK071078.1|CK071078
EST:     ATAATAGCATCGGAGTTTG-CACAGAGATATCAAGCCACAGAATCTTCTG                         GTAAACCCACATACCCATCAACTCAAGCTATGTGACTTTGGGAGTGCAAAA
genomic: ATAATAGCATCGGAGTTTGCCACAGAGATATCAAGCCACAGAATCTTCTGgtatgcttga ... ttctaatcagGTAAACCCACATACCCATCAACTCAAGCTATGTGACTTTGGGAGTGCAAAA
EST: gi|58679895|gb|CK068582.1|CK068582
EST:     ATAATAGCATCGGAGTTTGCCACAGAGATATCAAGCCACAGAATCTTCTG                         GTAAACCCACATACCCATCAACTCAAGCTATGTGACTTTGGGAGTGCAAAA
genomic: ATAATAGCATCGGAGTTTGCCACAGAGATATCAAGCCACAGAATCTTCTGgtatgcttga ... ttctaatcagGTAAACCCACATACCCATCAACTCAAGCTATGTGACTTTGGGAGTGCAAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aataccaccctcttatttctgtaactttataattgatgtttgaacttctaatcagGTAAACCCACATACCCATCAACTCAAGCTATGTGACTTTGGGAGTGCAAAAGTTCTG
                                            cttct  CT-rich tract
            ttatttctgtaacttt  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
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgcttgaatgttgttacccattcatctcaaataccaccctcttatttctgtaactttataattgatgtttgaacttctaatcagGTAAACCCACATACCCATCAACTCAAGCTATGTGACTTTGGGAGTGCAAAAGTTCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT