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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gattgttggcaatgcactatgtagaaaatttgactactatctattatagcgcatatgcttgttgagagacttgtgagcactgaaacacttccatttgcagGGAGTTCCTTATCCAGCTTTGCCTAAGAAGGAAAAACCAAGGCGTGTGGAACTGTATTTCTCAAGTTGGCGTATTAGAGCAG

Basic information

species Oryza sativa
transcript LOC_Os07g08760.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g08760.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G121223_T02 (Zea mays), 3'ss of exon 5
gattgttggcaatgcactatgtagaaaat-ttgactactatctattatagcgcatatgcttgttgagag---acttgtgagcactgaaacacttccattt-gcagGGAGTTCCTTATCCAGCTTTGCCTAAGAAGGAAAAACCAAGGCGTGTGGAACTGTATTTCTCAAGTTGGCGTATTAGAGCAG
        | | | || ||| |  |||    || ||       ||  | ||  | || ||   | || |   |  ||||||| || |    | ||| ||  |||||| ||||| |||||| | ||||| ||||| |||||||| ||||||||||| ||||| ||||||||||||||||||||||| |
-----caaggatttcaatatattaaaatcgctgcctgtagaaaatgtttgctaacatcctatgtaagtgcatatatgtgagcgctcagcagcctccgttccgcagGGTGTTCCATATCCATCATTGCCCAAGAAAGAAAAACCGAGGCGTGTGGAGCTGTACTTCTCAAGTTGGCGTATTAGAGCTG

upper sequence: LOC_Os07g08760.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G124965_T01 (Zea mays), 3'ss of exon 4
--gattgttggcaatgcactatgtagaaaatttgactactatctattatagcgcatatgcttgttgagagacttgtgagcactgaaacacttccatttg-cagGGAGTTCCTTATCCAGCTTTGCCTAAGAAGGAAAAACCAAGGCGTGTGGAACTGTATTTCTCAAGTTGGCGTATTAGAGCAG
   |  | |  ||||  | ||     |   | |    | | | |  ||     | ||||   ||    | |  ||||||| || |   || |||||||| ||||| ||||| |||||| | ||||| ||||| ||||||||||||||||||||  |||| ||||||||||||||||||||||| |
cacaagggtttcaatatattaaaatcactgtgtagaaaatgtttgctaacat-cctatgtaagt--gcatatatgtgagcgctcagcaacctccatttggcagGGTGTTCCATATCCATCATTGCCCAAGAAAGAAAAACCAAGGCGTGTGGAGTTGTACTTCTCAAGTTGGCGTATTAGAGCTG

upper sequence: LOC_Os07g08760.2 (Oryza sativa), 3'ss of exon 3
lower sequence: AT4G14500.1 (Arabidopsis thaliana), 3'ss of exon 4
gattgttggcaatgcactatgtagaaaatttgactactatctattatagcgcatatgcttgttgagagacttgtgagcac-tgaaacac---ttccat-ttgcagGGAGTTCCTTATCCAGCTTTGCCTAAGAAGGAAAAACCAAGGCGTGTGGAACTGTATTTCTCAAGTTGGCGTATTAGAGCAG
 |||      ||||||  | || | |   ||   ||   | |||   ||| |  |     | | | || ||    | ||     |||||   ||| || ||| |||||||||||||||||||| | || |||   || || ||||||||||| || || |||||||||||||||  ||| ||||| |
-attcacaa-aatgcataaggttgtattctttgttag-gtttatc-cagctctaaacaaagctcaaag-ctcagaaccatacttaacacctgttcaatattgtagGGAGTTCCTTATCCAGCTCTACCAAAGCGTGATAAGCCAAGGCGTGTTGAGCTTTATTTCTCAAGTTGGGTTATCAGAGCGG

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|29659937|gb|CB656212.1|CB656212
EST:     TTGGGCGGCGGATATGGGAATCTGGGAAAACTTACTATTGTGTTACAAAG                         GGAGTTCCTTATCCAGCTTTGCCTAAGAAGGAAAAACCAAGGCGTGTGGAA
genomic: TTGGGCGGCGGATATGGGAATCTGGGAAAACTTACTATTGTGTTACAAAGgtatttctac ... ccatttgcagGGAGTTCCTTATCCAGCTTTGCCTAAGAAGGAAAAACCAAGGCGTGTGGAA
EST: gi|86495790|gb|CI138423.1|CI138423
EST:     TTGGGCGCCGGATATGGGAATCTGGGAAAACTTACTATTGTGTTACAAAG                         GGAGTTCCTTATCCAGCTTTGCCTAAGAAGGAAAAACCAAGGCGTGTGGAA
genomic: TTGGGCGGCGGATATGGGAATCTGGGAAAACTTACTATTGTGTTACAAAGgtatttctac ... ccatttgcagGGAGTTCCTTATCCAGCTTTGCCTAAGAAGGAAAAACCAAGGCGTGTGGAA
EST: gi|86494162|gb|CI136795.1|CI136795
EST:     TTGGCCGGCGGATATGGGAATCTGGGAAAACTTACTATTGTGTTACAAAG                         GGAGTTCCTTATCCAGCTTTGCCTAAGAAGGAAAAACCAAGGCGTGTGGAA
genomic: TTGGGCGGCGGATATGGGAATCTGGGAAAACTTACTATTGTGTTACAAAGgtatttctac ... ccatttgcagGGAGTTCCTTATCCAGCTTTGCCTAAGAAGGAAAAACCAAGGCGTGTGGAA
EST: gi|30226837|gb|CB964729.1|CB964729
EST:     TTGGGCGGCGGATATGGGAATCTGGGAAAACTTACTATTGTGTTACAAAG                         GGAGTTCCTTATCCAGCTTTGCCTAAGAAGGAAAAACCAAGGCGTGTGGAA
genomic: TTGGGCGGCGGATATGGGAATCTGGGAAAACTTACTATTGTGTTACAAAGgtatttctac ... ccatttgcagGGAGTTCCTTATCCAGCTTTGCCTAAGAAGGAAAAACCAAGGCGTGTGGAA
EST: gi|14981939|gb|BI306617.1|BI306617
EST:     TTGGGCGGCGGATATGGGAATCTGGGAAAACTTACTATTGTGTTACAAAG                         GGAGTTCCTTATCCAGCTTTGCCTAAGAAGGAAAAACCAAGGCGTGTGGAA
genomic: TTGGGCGGCGGATATGGGAATCTGGGAAAACTTACTATTGTGTTACAAAGgtatttctac ... ccatttgcagGGAGTTCCTTATCCAGCTTTGCCTAAGAAGGAAAAACCAAGGCGTGTGGAA
EST: gi|86503157|gb|CI145790.1|CI145790
EST:     TTGGNCGNCGGATATGGGAATCTGGGAAAACTTACTATTGTGTTACAAAG                         GGAGTTCCTTATCCAGCTTTGCCTAAGAAGGAAAAACCAAGGCGTGTGGAA
genomic: TTGGGCGGCGGATATGGGAATCTGGGAAAACTTACTATTGTGTTACAAAGgtatttctac ... ccatttgcagGGAGTTCCTTATCCAGCTTTGCCTAAGAAGGAAAAACCAAGGCGTGTGGAA
EST: gi|29659876|gb|CB656151.1|CB656151
EST:     TTGGGCGGCGGATATGGGAATCTGGGAAAACTTACTATTGTGTTACAAAG                         GGAGTTCCTTATCCAGCTTTGCCTAAGAAGGAAAAACCAAGGCGTGTGGAA
genomic: TTGGGCGGCGGATATGGGAATCTGGGAAAACTTACTATTGTGTTACAAAGgtatttctac ... ccatttgcagGGAGTTCCTTATCCAGCTTTGCCTAAGAAGGAAAAACCAAGGCGTGTGGAA
EST: gi|30228065|gb|CB965957.1|CB965957
EST:     TTGGGCGGCGGATATGGGAATCTGGGAAAACTTACTATTGTGTTACAAAG                         GGAGTTCCTTATCCAGCTTTGCCTAAGAAGGAAAAACCAAGGCGTGTGGAA
genomic: TTGGGCGGCGGATATGGGAATCTGGGAAAACTTACTATTGTGTTACAAAGgtatttctac ... ccatttgcagGGAGTTCCTTATCCAGCTTTGCCTAAGAAGGAAAAACCAAGGCGTGTGGAA
EST: gi|23512848|gb|BU672864.1|BU672864
EST:     TTGGGCGGCGGATATGGGAATCTGGGAAAACTTACTATTGTGTTACAAAG                         GGAGTTCCTTATCCAGCTTTGCCTAAGAAGGAAAAACCAAGGCGTGTGGAA
genomic: TTGGGCGGCGGATATGGGAATCTGGGAAAACTTACTATTGTGTTACAAAGgtatttctac ... ccatttgcagGGAGTTCCTTATCCAGCTTTGCCTAAGAAGGAAAAACCAAGGCGTGTGGAA
EST: gi|30228719|gb|CB966609.1|CB966609
EST:     TTGGGCGGCGGATATGGGAATCTGGGAAAACTTACTATTGTGTTACAAAG                         GGAGTTCCTTATCCAGCTTTGCCTAAGAAGGAAAAACCAAGGCGTGTGGAA
genomic: TTGGGCGGCGGATATGGGAATCTGGGAAAACTTACTATTGTGTTACAAAGgtatttctac ... ccatttgcagGGAGTTCCTTATCCAGCTTTGCCTAAGAAGGAAAAACCAAGGCGTGTGGAA

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: 71 (upstream exon), 74 (downstream exon)
Score: 35

TTCCCTTTCTTTTGCAGTGACCGTGAATACATTTTTGGGCGGCGGATATGGGAATCTGGGAAAACTTACTATTGTGTTACAAAGgtatttctac ... ccatttgcagGGAGTTCCTTATCCAGCTTTGCCTAAGAAGGAAAAACCAAGGCGTGTGGAACTGTATTTCTCAAGTTGGCGTATTAGAGCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atagcgcatatgcttgttgagagacttgtgagcactgaaacacttccatttgcagGGAGTTCCTTATCCAGCTTTGCCTAAGAAGGAAAAACCAAGGCGTGTGGAACTGTATTTCTCAAGTTGGCGTATTAGAGCAG
                                          cttccattt  CT-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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gattgttggcaatgcactatgtagaaaatttgactactatctattatagcgcatatgcttgttgagagacttgtgagcactgaaacacttccatttgcagGGAGTTCCTTATCCAGCTTTGCCTAAGAAGGAAAAACCAAGGCGTGTGGAACTGTATTTCTCAAGTTGGCGTATTAGAGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
-attgttg
- - - - -caatgca
- - - - - - - - - - gtagaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - gcatatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -cttgttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cttgtga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcactga