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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttgttttctgcaacattctcatgtatccatgctctgttagcatatactgaaatctcgttgctcttttttctttcaacagGTAAAGGATGTGTTATTTGAACCTGTCCGCAAAACACAGGATGCCATGTTCTTCTTTAAGGCTGATGGTGATATGTGGATGCCTTGTGGACCAAAGCAAT

Basic information

species Oryza sativa
transcript LOC_Os01g04814.4
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g04814.3 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G088834_T01 (Zea mays), 3'ss of exon 6
-----------gtaagttgttttctgcaacattctcatgtatccatgctctgt---------tagcatatactgaaatctcgttgctcttttttctttcaac-agGTAAAGGATGTGTTATTTGAACCTGTCCGCAAAACACAGGATGCCATGTTCTTCTTTAAGGCTGATGGTGATATGTGGATGCCTTGTGGACCAAAGCAAT
            | |  |  |   |    |||    |||  ||  ||||| ||         ||  |   | ||||||||  |   | |||||||  || || |||| ||||| |||||||||||||| || |||||||| ||||| |||||||||||||| ||||| || ||||| ||||||||||| |||||||| |||||| 
gtaagtaatttctgaacttgtgcatctgtcatcactatgcttcactgctcagtctcacattgtactaagcaatgaaatctgatacattttttttccctcgaccagGTTAAGGACGTGTTATTTGAACCCGTGCGCAAAACGCAGGACGCCATGTTCTTCTTCAAGGCGGACGGTGACATGTGGATGCCATGTGGACCGAAGCAAC

upper sequence: LOC_Os01g04814.3 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G126860_T01 (Zea mays), 3'ss of exon 6
----------gtaagttgttttctgcaacattctcatgt------atccatgctctgttagcatatactgaaatctcgt-tgctcttttttctttcaacagGTAAAGGATGTGTTATTTGAACCTGTCCGCAAAACACAGGATGCCATGTTCTTCTTTAAGGCTGATGGTGATATGTGGATGCCTTGTGGACCAAAGCAAT
           |    | ||   |    ||||   |||        | ||  |||   || | ||   || ||| |  | || |  || ||  |||||||||| |||||||| |||||||||||||| ||||||||||||||||||||||||||||| ||||| || ||||| ||||||||||| ||||||||||| ||| 
gtaagcaattttggactcttgaatctgtcattactatgctccacagttcagtctcatctatcttactatgcaatttaatctgatacttgtttcttcaacagGTTAAGGATGTCTTATTTGAACCTGTGCGCAAAACACAGGATGCCATGTTCTTCTTCAAGGCAGACGGTGACATGTGGATGCCATGTGGACCAAAACAAC

upper sequence: LOC_Os01g04814.3 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA11G19120.1 (Glycine max), 3'ss of exon 6
gtaagtt-gttttctgca----acattctcatgtatccatgctc----tgttagcatatactgaaatctcgttgctcttttt-------tctttcaacagGTAAAGGATGTGTTATTTGAACCTGTCCGCAAAACACAGGATGCCATGTTCTTCTTTAAGGCTGATGGTGATATGTGGATGCCTTGTGGACCAAAGCAAT
||||||| |  ||||  |    | |      |  |   ||| ||    | || | || |    |  |   | |  |    ||       |  ||| |||||| |||||||| |||||||||||||| |||||||| || ||||||||||| ||||||| |  |  ||  | ||||||||| || ||||| ||||||||| 
gtaagtttgacttctatatttaatacctgattacaataatgatcattttatttggatgtttcaaggtaaaggtaattaaattggacctattattctacagGTGAAGGATGTTTTATTTGAACCTGTTCGCAAAACCCAAGATGCCATGTTTTTCTTTAGGAATCCTGAGGGTATGTGGATCCCATGTGGGCCAAAGCAAC

upper sequence: LOC_Os01g04814.3 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA12G30910.1 (Glycine max), 3'ss of exon 6
gtaagttgt-tttctgca-acattctcatgtatccatgctctgttagcatata---ctgaaatctcgttgctcttttttctttcaacagGTAAAGGATGTGTTATTTGAACCTGTCCGCAAAACACAGGATGCCATGTTCTTCTTTAAGGCTGATGGTGATATGTGGATGCCTTGTGGACCAAAGCAAT
||||||| |  ||||  |   | |  |  || ||  |  |||  ||    ||    || || |        | |        ||  ||||||||||||||||||||||||||||| |||||||| || ||||| ||||||||||| |||  |   |  | ||||||||| || ||||||||||||||| 
gtaagttttacttctatatggaattactggtttcattaatcttatacttaatgaatcttaagtaaaaagtttttggacctcctcttcagGTAAAGGATGTGTTATTTGAACCTGTTCGCAAAACCCAAGATGCAATGTTCTTCTTGAAGAATCCCGAGGGTATGTGGATCCCGTGTGGACCAAAGCAAC

upper sequence: LOC_Os01g04814.3 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA13G39410.1 (Glycine max), 3'ss of exon 7
gtaagtt-----gttttctgcaacattctcatgtatccatgctctg-ttagcatatactgaaatctcgttgctcttttttctttcaacagGTAAAGGATGTGTTATTTGAACCTGTCCGCAAAACACAGGATGCCATGTTCTTCTTTAAGGCTGATGGTGATATGTGGATGCCTTGTGGACCAAAGCAAT
|||||||     | | | || ||        |  ||  ||  | |  ||     ||  | || |        | |        ||  |||||||||||||| |||||||||||||| |||||||| || ||||| |||||||||||||||  |  ||  | ||||||||| || |||||||| |||||| 
gtaagttttactgctatatgaaatgactggtttcattaatcttatacttgatgaatttttaagtaaaaagtttttggacctcctcttcagGTAAAGGATGTTTTATTTGAACCTGTTCGCAAAACCCAAGATGCAATGTTCTTCTTTAAGAATCCTGAGGGTATGTGGATCCCATGTGGACCTAAGCAAC

upper sequence: LOC_Os01g04814.3 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA12G09300.1 (Glycine max), 3'ss of exon 6
gtaagtt-gttttctgca----acattctcatgtatccatgctctgttagcatatactgaaatctcgttgctcttttttctttcaacagGTAAAGGATGTGTTATTTGAACCTGTCCGCAAAACACAGGATGCCATGTTCTTCTTTAAGGCTGATGGTGATATGTGGATGCCTTGTGGACCAAAGCAAT
||||||| |  ||||  |    | |      |  |   ||| ||  ||    |  | |    |          |       ||| |||||| |||||||| |||||||||||||| |||||||| || ||||||||||| ||||||| |  |  ||  ||||||||||| || ||||||||||||||| 
gtaagtttgacttctatatttaatacctggttagaataatgatcattttatttggattagtgttaaaggtaattggacctattctacagGTGAAGGATGTTTTATTTGAACCTGTTCGCAAAACCCAAGATGCCATGTTTTTCTTTAGGAATCCTGAGGATATGTGGATCCCATGTGGACCAAAGCAAC

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|58594912|gb|CF993220.1|CF993220
EST:     GCTTGGCTCGTCGAACAGAGGGGTTTTCTGGTTCGGATATTGCTGTTTGT                         GTAAAGGATGTGTTATTTGAACCTGTCCGCAAAACACAGGATGCCATGTTC
genomic: ACTTGGCTCGTCGAACAGACGGGTTTTCTGGTTCGGATATTGCTGTTTGTgtaagttgtt ... ctttcaacagGTAAAGGATGTGTTATTTGAACCTGTCCGCAAAACACAGGATGCCATGTTC
EST: gi|300215967|gb|HO088593.1|HO088593
EST:     GCTTGGCTCGTCGAACAGACGGGTTTTCTGGTTCGGATATTGCTGTTTGT                         GTAAAGGATGTGTTATTTGAACCTGTCCGCAAAACACAGGATGCCATGTTC
genomic: ACTTGGCTCGTCGAACAGACGGGTTTTCTGGTTCGGATATTGCTGTTTGTgtaagttgtt ... ctttcaacagGTAAAGGATGTGTTATTTGAACCTGTCCGCAAAACACAGGATGCCATGTTC
EST: gi|58588110|gb|CF986418.1|CF986418
EST:     CTTGGCTCGTCGAACAGACGGGTTTTCTGGTGGCGGATATTGCTGTTTGT                         GTAAAGGATGTGTTATTTGAACCTGTCCGCAAAACACAGGATGCCATGTTC
genomic: CTTGGCTCGTCGAACAGACGGGTTTTCTGGTT-CGGATATTGCTGTTTGTgtaagttgtt ... ctttcaacagGTAAAGGATGTGTTATTTGAACCTGTCCGCAAAACACAGGATGCCATGTTC
EST: gi|313080751|gb|HO213548.1|HO213548
EST:     GCTTGGCTCGTCGAACAGACGGGTTTTCTGGTTCGGATATTGCTGTTTGT                         GTAAAGGATGTGTTATTTGAACCTGTCCGCAAAACACAGGATGCCATGTTC
genomic: ACTTGGCTCGTCGAACAGACGGGTTTTCTGGTTCGGATATTGCTGTTTGTgtaagttgtt ... ctttcaacagGTAAAGGATGTGTTATTTGAACCTGTCCGCAAAACACAGGATGCCATGTTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atccatgctctgttagcatatactgaaatctcgttgctcttttttctttcaacagGTAAAGGATGTGTTATTTGAACCTGTCCGCAAAACACAGGATGCCATGTTCTTCTTTAAGGCTGATGGTGATATGTGGATGCCTTGTGGACCAAAGCAAT
                            tctcgttgctcttttt  CT-rich tract
                                       ttttttcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagttgttttctgcaacattctcatgtatccatgctctgttagcatatactgaaatctcgttgctcttttttctttcaacagGTAAAGGATGTGTTATTTGAACCTGTCCGCAAAACACAGGATGCCATGTTCTTCTTTAAGGCTGATGGTGATATGTGGATGCCTTGTGGACCAAAGCAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA