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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagctcctcctcctcctccgcctgttcctcgtcgacctccccctacatctctcctctcttctgatgcgcccggtttttgctgcgaggtgcagGGGCGTACAAGTACGTGTCGGAGCTATGGAGGAGGAAGCAGTCGGACGTGATGAGGTTCGTGCAGCGCGTGCGCTGCTGGGAGTACCGCCAGCAGCCGGC

Basic information

species Oryza sativa
transcript LOC_Os05g19370.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g19370.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G024354_T01 (Zea mays), 3'ss of exon 1
gtgagctcctcctcctcctccgcctgttcctcgtcgacctccccctacatctctcctctcttctgatgcgcccggtttttgctgcgaggtgcagGGGCGTACAAGTACGTGTCGGAGCTATGGAGGAGGAAGCAGTCGGACGTGATGAGGTTCGTGCAGCGCGTGCGCTGCTGGGAGTACCGCCAGCAGCCGGC
||||||   |  ||    |  |     |||  |  | |   ||  | |   ||  |||||| |||||  | | | |  | ||        |||||||||||||||||||||||||| |||||||||||||||||||||||||||||| | |||||||||||||||||||||||||||||| | ||||||||| |
gtgagcaaatgttc----tgtggtctctccgtgcaggcgaacctttgcgcgtcgtctctct-ctgata-gtctgttcgtcgc--------gcagGGGCGTACAAGTACGTGTCGGAACTATGGAGGAGGAAGCAGTCGGACGTGATGCGCTTCGTGCAGCGCGTGCGCTGCTGGGAGTACAGGCAGCAGCCGTC

upper sequence: LOC_Os05g19370.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G034794_T02 (Zea mays), 3'ss of exon 1
gtgagctcctcctcctcctccgcctgttcctcgtcgacctccccctacatctctcctctcttctgatgcgcccggtttttgctgcgaggtgcagGGGCGTACAAGTACGTGTCGGAGCTATGGAGGAGGAAGCAGTCGGACGTGATGAGGTTCGTGCAGCGCGTGCGCTGCTGGGAGTACCGCCAGCAGCCGGC
||||||||       | |  |   ||  ||||  |||  | | | | | |   || |  | | ||  |   |   || | ||||   ||  |||| |||||||||||||| |||||||||||| ||||||||||||| || |||||| |||||||||||||||||||||||||||||||| | |||||||||||
gtgagctctcgtatttaccgctgatgg-cctctccga--ttcgcatgcgtgggtcttaccgtgtgtcgtatcattttgtcgctgt--ggcacagGTGCGTACAAGTACGTCTCGGAGCTATGGCGGAGGAAGCAGTCCGATGTGATGCGGTTCGTGCAGCGCGTGCGCTGCTGGGAGTACAGGCAGCAGCCGGC

upper sequence: LOC_Os05g19370.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G180724_T01 (Zea mays), 3'ss of exon 1
gtgagctcctcctcctcctccgcctgttcctcgtcgacctccccctacatctctcctctct-tctgatgcgcccggtttttgctgcgaggtgcagGGGCGTACAAGTACGTGTCGGAGCTATGGAGGAGGAAGCAGTCGGACGTGATGAGGTTCGTGCAGCGCGTGCGCTGCTGGGAGTACCGCCAGCAGCCGGC
|||||       | |||  |  |  |  | ||  |||  | | | | |||   |  |  |  | || |||  | | || | ||||   || ||||||||||||||||| || |||||| |||||||||||||||| || ||||||||| |||||||||||||||||||||||||||||||| | |||||||||||
gtgag-------ttctcggctacaaggccgtctccga--ttcgcatgcatgggtttttacggtatgttgcatc-gtttctcgctgt--ggcgcagGGGCGTACAAGTATGTCTCGGAGTTATGGAGGAGGAAGCAATCCGACGTGATGCGGTTCGTGCAGCGCGTGCGCTGCTGGGAGTACAGGCAGCAGCCGGC

upper sequence: LOC_Os05g19370.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G084757_T01 (Zea mays), 3'ss of exon 1
gtgagctcctcctcctcctccgcctgttcctcgtcgacctccccctacatctctcctctcttctgatgcgcccggtttttgctgcgaggtgcagGGGCGTACAAGTACGTGTCGGAGCTATGGAGGAGGAAGCAGTCGGACGTGATGAGGTTCGTGCAGCGCGTGCGCTGCTGGGAGTACCGCCAGCAGCCGGC
||||| || |   ||| |  |   ||  ||||  |||    |   |      ||   |  |  || ||| || | || | ||||   || |||||||||||||||||||| |||||| ||||||| |||||||| || ||||||||| ||||||| || ||||||||||| ||||||||| | |||||||||||
gtgagttcttggccctaccgctgatgc-cctctccgattcgcatgtgtggggctttacggta-tgttgcacc-gtttctcgctgt--ggcgcagGGGCGTACAAGTACGTCTCGGAGTTATGGAGAAGGAAGCAATCCGACGTGATGCGGTTCGTTCAACGCGTGCGCTGTTGGGAGTACAGGCAGCAGCCGGC

upper sequence: LOC_Os05g19370.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA17G15230.1 (Glycine max), 3'ss of exon 1
--gtgagctcctcctcctcctccgcctgttcctcgtcgacctccccctacatctctcctctcttctgatgcgcccggttt-ttgctgcgaggtgca---gGGGCGTACAAGTACGTGTCGGAGCTATGGAGGAGGAAGCAGTCGGACGTGATGAGGTTCGTGCAGCGCGTGCGCTGCTGGGAGTACCGCCAGCAGCCGGC
   |||  ||       |   | |  ||  | |  |       |   |   |   ||   |    | | ||      | | ||| |    | ||||   || || |||||||| || |||||||||||| | | ||||||||| || || ||||| ||| ||||||| ||| | ||||||||||| |||||||| ||  |
tgctgatttctattagttatgctggttgagctttctatcatagcatttttgttattctagtgaaattaggcattatttgtgttggtttatgttgcaatagGTGCCTACAAGTATGTTTCGGAGCTATGGCGCAAGAAGCAGTCTGATGTTATGAGATTCTTGCAGCGGGTGAGGTGCTGGGAGTATCGCCAGCAACCTTC

upper sequence: LOC_Os05g19370.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA05G04870.1 (Glycine max), 3'ss of exon 1
gtgagctcctcctcctcctccgcctgttcctcgtcgacctccccctacatctctcctctcttctgatgcgc-----ccggtt--tttgctgcgaggtgc------agGGGCGTACAAGTACGTGTCGGAGCTATGGAGGAGGAAGCAGTCGGACGTGATGAGGTTCGTGCAGCGCGTGCGCTGCTGGGAGTACCGCCAGCAGCCGGC
        |   || | |   || | ||     |  |  |     ||    |    | | ||   ||| |        | ||  |||  ||  |  ||       ||| || |||||||| || |||||||||||| | | ||||||||| || || ||||| ||| ||||||| ||| | |||||||||||||||||||| ||  |
-------gcctttctttcatagcatttttgctattcaagtgaaattaggcattgtttgttttggaatgagtgaaaattgattattttattggaatatgttgcaatagGTGCTTACAAGTATGTTTCGGAGCTATGGCGCAAGAAGCAGTCTGATGTTATGAGATTCTTGCAGCGGGTGAGGTGCTGGGAGTACCGCCAGCAACCTTC

upper sequence: LOC_Os05g19370.1 (Oryza sativa), 3'ss of exon 1
lower sequence: AT4G17390.1 (Arabidopsis thaliana), 3'ss of exon 1
gtgagctcctcctcctcctccgcctgttcctcgtcgacctccccctacatctc---tcctctcttctgat--gcgcccggtttttgctgcgaggtgcagGGGCGTACAAGTACGTGTCGGAGCTATGGAGGAGGAAGCAGTCGGACGTGATGAGGTTCGTGCAGCGCGTGCGCTGCTGGGAGTACCGCCAGCAGCCGGC
||  | | |||    |  ||   || |     ||||         |     |    | ||      | ||    |      | |   |      | |||| |||||||| |||||||||||||||||||||| |||||||||||| |||||||||||  | ||| | ||  | || |||||||| |||||||||||  |
gtatgtttctcactattatctctctctcagatgtcgtttctgtattgttcattagattctagaagttaattaaggatgaaatgtgatttttgattacagGTGCGTACAAATACGTGTCGGAGCTATGGAGGAAGAAGCAGTCGGATGTGATGAGGTTTCTTCAGAGGGTTAGGTGTTGGGAGTATCGCCAGCAGCCTTC

upper sequence: LOC_Os05g19370.1 (Oryza sativa), 3'ss of exon 1
lower sequence: AT4G16720.1 (Arabidopsis thaliana), 3'ss of exon 1
----------------------------------------------------gtgagctcctcctcctcctccgcctgttcctcgtcgacctccccctacatctctcctctcttctgatgcgcccggtttttgctgcga--ggtgcagGGGCGTACAAGTACGTGTCGGAGCTATGGAGGAGGAAGCAGTCGGACGTGATGAGGTTCGTGCAGCGCGTGCGCTGCTGGGAGTACCGCCAGCAGCCGGC
                                                    |   | | |  || ||||   |  |||||    |     | |   ||| | |||  | | | |  |       | ||  || |  ||  | |  ||| ||||||||||| || || ||||||||||||| ||| ||||| || |||||||| ||| | ||| | ||  | |||||||||||| | ||||| ||  |
gtaaatccttcttctccatcccttcttctagatcaaatcctctcgtttcttagatcgattcagcttctccattgtttgttcaa-atgatgtttctgttacgtatctgttat-tgcaaactacttagcttaatgatttgattgatatagGTGCGTACAAGTATGTATCTGAGCTATGGAGGAAGAAACAGTCCGATGTGATGAGATTCCTCCAGAGGGTTAGGTGCTGGGAGTACAGACAGCAACCTTC

upper sequence: LOC_Os05g19370.1 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv16s0013g02020.t01 (Vitis vinifera), 3'ss of exon 1
gtgagctcctcctcctcctccgcctgttcctcgtcgacctccccctacatctc----tcctctcttctgatgcgcccggtttttgctg-----cgaggtg----cagGGGCGTACAAGTACGTGTCGGAGCTATGGAGGAGGAAGCAGTCGGACGTGATGAGGTTCGTGCAGCGCGTGCGCTGCTGGGAGTACCGCCAGCAGCCGGC
|| ||| ||      |||| | |    |  |  || || |||      || |     |  ||   | ||  ||  || ||| |||        || ||||     |||||| |||||||||||||||||||||||||||| |||||| || || |||||||||||| ||||| | ||| | ||||||||||| |||||||| ||  |
gtaagcaccaagctttccttcactctctttttctctacttccaagcggatattagggttttccgatttgtggcttcctgttattggcattgttcgtggtggcattagGGGCTTACAAGTACGTGTCGGAGCTATGGAGGAAGAAGCAATCCGATGTGATGAGGTTCTTGCAGAGGGTGAGGTGCTGGGAGTATCGCCAGCACCCTTC

upper sequence: LOC_Os05g19370.1 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv00s0551g00020.t01 (Vitis vinifera), 3'ss of exon 1
-----------gtgagctcctcctcctcctccgcctgttcctcgtcgacctccccctacatctctcctctcttctgatgcgcccggtttttgctgcgaggtgcagGGGCGTACAAGTACGTGTCGGAGCTATGGAGGAGGAAGCAGTCGGACGTGATGAGGTTCGTGCAGCGCGTGCGCTGCTGGGAGTACCGCCAGCAGCCGGC
           ||||        |      |     | |  |  | ||  | ||  |  || |    |   |  | |   |    || |||| |   |     |||||| ||||| |||||||| ||  ||||||||| |||||| || ||||||||||||||| ||||| | ||  | || ||||||||||| || || ||| |
cttaatatgctgtgacagtgctttgaattacattggggtattaatggaggttccattgtatttggagtag-tagtaagttgtggtgtatttggtttaa----tagGGGCTTACAAATACGTGTCCGAATTATGGAGGAAGAAGCAATCAGACGTGATGAGGTTCCTGCAGAGGGTTAGGTGTTGGGAGTACCGTCAACATCCGTC

upper sequence: LOC_Os05g19370.1 (Oryza sativa), 3'ss of exon 1
lower sequence: PP1S152_141V6.1 (Physcomitrella patens), 3'ss of exon 1
--------------------------------------------------------------------------gtgagctcctcctcctcctcc----gcctgttcctcgt---cgacctccccctacatctctcctctcttctgatgcgcccggtttttgctgcgaggtgcagGGGCGTACAAGTACGTGTCGGAGCTATGGAGGAGGAAGCAGTCGGACGTGATGAGGTTCGTGCAGCGCGTGCGCTGCTGGGAGTACCGCCAGCAGCCGGC
                                                                           |    |  |||   ||||      |  ||  |   ||   |||  ||   ||  |  | |  | | || |  |        |||    | |    | |||| |||||||||||| |   |||||| ||||||| ||||||||| || ||| || | ||| ||| ||| |||||||||||||||||| | ||||  || | 
gtattcattcccagctccctctctctctagcgctgcgtagctgcgtagctgcgtttttttattttttttattttttatttttttccctttccttttgaggtttgcgcagtgtgatcgagatctaactggagttttttttttttttttttttttttttttaaatttcc---tccagGTGCGTACAAGTACATCGAGGAGCTGTGGAGGAAGAAGCAGTCTGATGTGCTGCGTTTCTTGCTGCGTGTGCGCTGCTGGGAGTACAGGCAGCTCCCCGG

upper sequence: LOC_Os05g19370.1 (Oryza sativa), 3'ss of exon 1
lower sequence: PP1S7_364V6.1 (Physcomitrella patens), 3'ss of exon 1
----------gtgagctcctcctcctcc-tccgcctgttcctcgtcgacctccccctacatctctcctctcttctgatgcgcccggtttttgctgcgaggtgcagGGGCGTACAAGTACGTGTCGGAGCTATGGAGGAGGAAGCAGTCGGACGTGATGAGGTTCGTGCAGCGCGTGCGCTGCTGGGAGTACCGCCAGCAGCCGGC
          ||  | |     |   || | ||   |||  |           || |  || |    | | || ||    |   |  ||| | | |      |||| |||||||||||| |   |||||||||| ||| ||||||||| |||||| || | ||| |||  || |||||||||||||||||| | || |  || | 
gctttgtgttgtttggtagggttgggccattcgatggttggtgacgagagagtccgttaatgttgggttttttttgtaatgtgtgaatttggttcc-----ccagGCGCGTACAAGTACATTGAGGAGCTATGGCGGAAGAAGCAGTCCGACGTGCTGCGTTTCTTGCTTCGTGTGCGCTGCTGGGAGTACAGACAACTACCCGG

upper sequence: LOC_Os05g19370.1 (Oryza sativa), 3'ss of exon 1
lower sequence: EFJ27946 (Selaginella moellendorffii), 3'ss of exon 1
gtgagctcctcctcctcctccgcctgttcctcgtcgacctccccctaca-tctctcctctcttctgatgcgcccggtttttgctgcgaggtgcagGGGCGTACAAGTACGTGTCGGAGCTATGGAGGAGGAAGCAGTCGGACGTGATGAGGTTCGTGCAGCGCGTGCGCTGCTGGGAGTACCGCCAGCAGCCGGC
                     |   |  |  | |||| |  | |   |  || |   |||||   |      |   ||  | |  |    | |||| || ||||||||| |   |||||||||| ||| |||||| || || |||||| | ||| ||  |||||| |||||||||||||| |||||||  || | 
---------------------gtaagcactgc-tcgatcagctcaggcgctcgcatttctctcgcggctgatcgcattccttcctctctctccagGTGCCTACAAGTACATCGAGGAGCTATGGCGGAAGAAGCAATCCGATGTGATGCGCTTCCTGATGCGCGTCCGCTGCTGGGAGTATCGCCAGCTCCCCGG

upper sequence: LOC_Os05g19370.1 (Oryza sativa), 3'ss of exon 1
lower sequence: EFJ36722 (Selaginella moellendorffii), 3'ss of exon 1
gtgagctcctcctcctcctccgcctgttcctcgtcgacctc---cccctacatctctcctctcttctgatgcgcccggtttttgctgcgaggtgcagGGGCGTACAAGTACGTGTCGGAGCTATGGAGGAGGAAGCAGTCGGACGTGATGAGGTTCGTGCAGCGCGTGCGCTGCTGGGAGTACCGCCAGCAGCCGGC
                         ||| ||||   | |||   | |   ||| |||| || |  ||||| |||    ||  | |  |    | |||| || ||||| ||| |   |||||||||| ||| |||||| || || |||||| | ||| ||  |||||| |||||||||||||| |||||||  || | 
-------------------gtaagcgttgctcgatcagctcaggcgctcgcatttctc-tcgcggctgat-cgc---attccttcctctctctccagGTGCCTACAAATACATCGAGGAGCTATGGCGGAAGAAGCAATCCGATGTGATGCGCTTCCTGATGCGCGTCCGCTGCTGGGAGTATCGCCAGCTCCCCGG

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|25798204|gb|CA754173.1|CA754173
EST:     AGCAAGAGACATGG                         GGGCGTACAAGTACGTGTCGGAGCTATGGAGGAGGAAGCAGTCGGACGTGA
genomic: AGCAAGAGACATGGgtgagctcct ... cgaggtgcagGGGCGTACAAGTACGTGTCGGAGCTATGGAGGAGGAAGCAGTCGGACGTGA
EST: gi|58686451|gb|CK075138.1|CK075138
EST:     AGCAAGAGACATGG                         GGGCGTACAAGTACGTGTCGGAGCTATGGAGGAGGAAGCAGTCGGACGTGA
genomic: AGCAAGAGACATGGgtgagctcct ... cgaggtgcagGGGCGTACAAGTACGTGTCGGAGCTATGGAGGAGGAAGCAGTCGGACGTGA

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: 53 (upstream exon), 62 (downstream exon)
Score: 20

TCTATCTAACCTCCTCCACCACGCGCATCCACGCAAACCCTACCAGCCTCTCTCTCCCGCTCCACCTCCGCCGCCGCCGCCGCCGCAGCAAGAGACATGGgtgagctcct ... cgaggtgcagGGGCGTACAAGTACGTGTCGGAGCTATGGAGGAGGAAGCAGTCGGACGTGATGAGGTTCGTGCAGCGCGTGCGCTGCTGGGAGTACCGCCAGCAGCCGGC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tccccctacatctctcctctcttctgatgcgcccggtttttgctgcgaggtgcagGGGCGTACAAGTACGTGTCGGAGCTATGGAGGAGGAAGCAGTCGGACGTGATGAGGTTCGTGCAGCGCGTGCGCTGCTGGGAGTACCGCCAGCAGCCGGC
                     ttctgat  putative branch site (score: 20)
                                    ttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagctcctcctcctcctccgcctgttcctcgtcgacctccccctacatctctcctctcttctgatgcgcccggtttttgctgcgaggtgcagGGGCGTACAAGTACGTGTCGGAGCTATGGAGGAGGAAGCAGTCGGACGTGATGAGGTTCGTGCAGCGCGTGCGCTGCTGGGAGTACCGCCAGCAGCCGGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT