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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGAACTTCACCTCGGTGTCAGTGATGCAGGCGGTGGGATCCGTCATGACCAACAAGTACAGCGAGGGGTACCCCGGCGCGAGATACTACGGTGGAAACGAgtacggttgattgcgttctatcggttgcctttgttcagattatttgggtgttaaaaatgtttaatctgaaagagaaatcagtgcctgatgggagtgaatgatgtgaatttctggtggctctgggttttccttgcgtgcag

Basic information

species Oryza sativa
transcript LOC_Os03g52840.3
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g52840.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G135283_T01 (Zea mays), 5'ss of exon 4
AGAACTTCACCTCGGTGTCAGTGATGCAGGCGGTGGGATCCGTCATGACCAACAAGTACAGCGAGGGGTACCCCGGCGCGAGATACTACGGTGGAAACGAgtacggttgattgcgttctatcggttgcctttgttcagattatttgggtgttaaaaatgtttaatctgaaagagaaatcagtgcctgatgggagtgaatgatgtgaatttctggtg--gctctgggttttccttgcgtgcag
|||| ||||| |||||||||||||||||||| ||||| ||||||||||||||||||||||||||||||||||| ||||| ||||||||||| ||||| |||||| |        | ||||||||||| | || |   |||| |||  |||  ||| | |  |         |  || | |||| ||| |  | |||||| || ||||||   | |     |||| || ||| |||   ||||
AGAATTTCACGTCGGTGTCAGTGATGCAGGCAGTGGGTTCCGTCATGACCAACAAGTACAGCGAGGGGTACCCTGGCGCAAGATACTACGGGGGAAATGAgtactgcc----ctgctctatcggttgtcattctcgtgattgtttcagtgg-aaacacgcgt---------gcaaattgagtgactg-tctgggtgaataatctgaattggggtttttattctgtgtgttc-ttggtcgcag

upper sequence: LOC_Os03g52840.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA18G27710.1 (Glycine max), 5'ss of exon 5
AGAACTTCACCTCGGTGTCAGTGATGCAGGCGGTGGGATCCGTCATGACCAACAAGTACAGCGAGGGGTACCCCGGCGCGAGATACTACGGTGGAAACGAgtacggttgattgcgttctatcggttgcctttgttcagattatttgggtgttaaaaatgtttaatctgaaagagaaatcagtgcctgatgggagtgaatgatgtgaatttctggtggctctgggttttccttgcgtgcag
|||| ||||| || ||||| |||||||| || || ||||| || ||||||||||| ||||| ||||||||||| || || ||||| || |||||||| |||||||  |   |   || | ||   | | | |||||| |||    |    |  ||| |   |||| |  |    ||| ||     | ||   |||   ||||| |||                                 
AGAATTTCACTTCTGTGTCTGTGATGCAAGCAGTTGGATCTGTGATGACCAACAAATACAGTGAGGGGTACCCTGGTGCAAGATATTATGGTGGAAATGAgtacgtctctctcacttttttcatctacatgtgttcatatt-caggctcctctaaagttactaatttagagagtaaaaca---tgtaattttagt---tgatgagaa---------------------------------

upper sequence: LOC_Os03g52840.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA08G37270.1 (Glycine max), 5'ss of exon 4
AGAACTTCACCTCGGTGTCAGTGATGCAGGCGGTGGGATCCGTCATGACCAACAAGTACAGCGAGGGGTACCCCGGCGCGAGATACTACGGTGGAAACGAgtacggttgattgcgttctatcggttgcctttgttcagattatttgggtgttaaaaatgtttaatctgaaagagaaatcagtgcctgatgggagtgaatgatgtgaatttctggtggctctgggttttccttgcgtgcag
|||| |||||||| ||||| |||||||| ||||| ||||| || ||||||||||| ||||| ||||||||||| || || ||||| || |||||||| ||||| |  |   |   || |  |   | | | | |||| | |         ||| |  |  | | |  || ||  |||  |||   |   |     ||                                           
AGAATTTCACCTCTGTGTCTGTGATGCAAGCGGTTGGATCGGTTATGACCAACAAATACAGTGAGGGGTACCCTGGTGCAAGATATTATGGTGGAAATGAgtatgtgtctctcactttttgcatctacatgttttcatactcaggctcctttatagttactaacttagagagtaaaacaagtaattttagtttacgagaa----------------------------------------

upper sequence: LOC_Os03g52840.1 (Oryza sativa), 5'ss of exon 4
lower sequence: Vv00s0211g00160.t01 (Vitis vinifera), 5'ss of exon 4
AGAACTTCACCTCGGTGTCAGTGATGCAGGCGGTGGGATCCGTCATGACCAACAAGTACAGCGAGGGGTACCCCGGCGCGAGATACTACGGTGGAAACGAgtacgg-----ttgattgcgttctatcggttgcctttgttcagattatt--tgggtgttaaaaat-gtttaatctgaaagagaaatcagtgcctgatgggagtgaatgatgtga-atttctg--gtggctctgggttttccttgcgtgcag-------------------------------------------------
|||||||||| || |||||||| ||||| || || || ||  | ||||| |||||||||||||| || || || ||||| |||||||| || ||||| ||||| |      || ||| | || |   | ||  ||||  |   |||  |  ||  | ||    || ||   || || ||     ||  ||   || |   | | |    | | | |||| ||  ||   |    || ||| ||   |                                                     
AGAACTTCACTTCTGTGTCAGTTATGCAAGCTGTTGGGTCTATTATGACAAACAAGTACAGCGAAGGATATCCAGGCGCTAGATACTATGGAGGAAATGAgtaagaagatattaatttccttatcatgattttctttcgtggtatttgtaatgtttattggtcatcgtggtatttgtaatgtctattggtcattgttatcatttagcattatcatatttatgtagtcagttccagtgttcattcttttggatttcctggttagtactgaagtagaaagagtgaaaccttttatctttcag

upper sequence: LOC_Os03g52840.1 (Oryza sativa), 5'ss of exon 4
lower sequence: Vv00s0211g00120.t01 (Vitis vinifera), 5'ss of exon 4
AGAACTTCACCTCGGTGTCAGTGATGCAGGCGGTGGGATCCGTCATGACCAACAAGTACAGCGAGGGGTACCCCGGCGCGAGATACTACGGTGGAAACGAgtacgg-----ttgattgcgttctatcggttgcctttgttcagattatt--tgggtgttaaaaat-gtttaatctgaaagagaaatcagtgcctgatgggagtgaatgatgtga-atttctg--gtggctctgggttttccttgcgtgcag-------------------------------------------------
|||||||||| || |||||||| ||||| || || || ||  | ||||| |||||||||||||| || || || ||||| |||||||| || ||||| ||||| |      || ||| | || |   | ||  ||||  |   |||  |  ||  | ||    || ||   || || ||     ||  ||   || |   | | |    | | | |||| ||  ||   |    || ||| ||   |                                                     
AGAACTTCACTTCTGTGTCAGTTATGCAAGCTGTTGGGTCTATTATGACAAACAAGTACAGCGAAGGATATCCAGGCGCTAGATACTATGGAGGAAATGAgtaagaagatattaatttccttatcatgattttctttcgtggtatttgtaatgtttattggtcatcgtggtatttgtaatgtttattggtcattgttatcatttagcattatcatatttatgtagtcagttccagtgttcattcttttggatttcctggttagtactgaagtagaaagagtgaaaccttttatctttcag

upper sequence: LOC_Os03g52840.1 (Oryza sativa), 5'ss of exon 4
lower sequence: EDO97448 (Chlamydomonas reinhardtii), 5'ss of exon 5
AGAACTTCACCTCGGTGTCAGTGATGCAGGCGGTGGGATCCGTCATGACCAACAAGTACAGCGAGGGGTACCCCGGCGCGAGATACTACGGTGGAAACGAgtacggttgattgcgttctatcggttgcctttgttcagattatttgggtgttaaaaatgtttaatctgaaagagaaatcagtgcctgatgggagtgaatgatgtgaatttctggtggctctgggttttccttgcgtgcag
                               ||||||   ||||||||||||||||||||||||||| |||||||||||  | |||||||| || ||||||| |  ||||    |    | ||  ||     | |  || |  | ||||    |   |||||| |  |     |    |   |     |||  |   |    | |  || ||||||| ||| ||   | |  | || |  
-------------------------------GGTGGGCAGCGTCATGACCAACAAGTACAGCGAGGGCTACCCCGGCGCCCGCTACTACGGCGGCAACGAGTTCA-TTGACCAGGCAG-AGCGCCTGTGCCAGgtgggaat-ctggggtccgcaggctgtttagtgggttgcggtgggcgaggggccgtggacgctga----ggggcttgctggtggatcttggacctgcgcgggttc--

upper sequence: LOC_Os03g52840.1 (Oryza sativa), 5'ss of exon 4
lower sequence: PP1S51_296V6.1 (Physcomitrella patens), 5'ss of exon 3
----------------------AGAACTTCACCTCGGTGTCAGTGATGCAGGCGGTGGGATCCGTCATGACCAACAAGTACAGCGAGGGGTACCCCGGCGCGAGATACTACGGTGGAAACGAgtacggttgattgcgttctatcggttgcctttgttcagattatttgggtgttaaaaatgtttaatctgaaagagaaatcagtgcctgatgggagtgaatgatgtgaatttctggtggctctgggttttccttgcgtgcag
                      |||| ||||| || || ||||| |||||||| || || |||||||||||||| |||||||| || || || || || ||    || |||||||| ||||| | ||  |  |  | ||||       | ||||  ||   ||  ||       | | || || | |  || |  | |   | |   |                                                      
GGCCTCGAGTTGATCCCATCAGAGAATTTCACGTCTGTTTCAGTTATGCAGGCAGTAGGTTCCGTCATGACCAATAAGTACAGTGAAGGATATCCTGGTgctctctagtacggtggtaacgaatgcgtcttctccccttct------cgtctttaatcgattttctt-----caacacatcttcactgcgacattggatgtaatttttcc----------------------------------------------------

upper sequence: LOC_Os03g52840.1 (Oryza sativa), 5'ss of exon 4
lower sequence: PP1S21_270V6.1 (Physcomitrella patens), 5'ss of exon 4
AGAACTTCACCTCGGTGTCAGTGATGCAGGCGGTGGGATCCGTCATGACCAACAAGTACAGCGAGGGGTACCCCGGCGCGAGATACTACGGTGGAAACGAgtacggttgattgcgttctatcggttgcctttgttcagattatttgggtgttaaaaatgtttaatctgaaagagaaatcagtgcctgatgggagtgaatgatgtgaatttctggtggctctgggttttccttgcgtgcag
| |||||||||||  | ||||| |||||||| ||||| || |||||||||||||||||||| ||||| |||||||| ||  | ||||||||||| |||||||| |     |  | || | || | | |   || |   ||||  ||   ||||||  |  ||| | |     |    | |||   || |||  ||  | | |||||     ||  ||||    |   | |  |   ||||
AAAACTTCACCTCCCTCTCAGTTATGCAGGCAGTGGGGTCAGTCATGACCAACAAGTACAGTGAGGGTTACCCCGGGGCTCGTTACTACGGTGGCAACGAgtatg-----tcaccttttctctgcttcg--tggtgttattacatga-cgttaaacttcattactattttccaagtgt-agt-tttggtggtcgtttacg-tgtgatcagttg--ggctgacagcgctacccgtccgcag

upper sequence: LOC_Os03g52840.1 (Oryza sativa), 5'ss of exon 4
lower sequence: PP1S79_54V6.1 (Physcomitrella patens), 5'ss of exon 4
AGAACTTCACCTCGGTGTCAGTGATGCAGGCGGTGGGATCCGTCATGACCAACAAGTACAGCGAGGGGTACCCCGGCGCGAGATACTACGGTGGAAACGAgtacggttgattgcgttctatcggttgcctttg---ttcagattatttgggtgtt-----aaaaatgtttaatctgaaagagaaatcagtgcctgatgggagtgaatgatgtgaatttctggtggctctgggttttccttgcgtgcag
|||| || || || || ||||| |||||||| ||||| || ||||||||||| |||||||| || || |||||||| ||  | || |||||||| ||||||| ||     |  | || |      |  ||||    |  |  || | ||  |  |     | |||  |||| |     |  || ||   |||    ||    |||||  |  |   |  ||    ||||         | |       
AGAATTTTACGTCCGTATCAGTTATGCAGGCAGTGGGTTCAGTCATGACCAATAAGTACAGTGAAGGTTACCCCGGTGCTCGCTATTACGGTGGCAACGAgtgcgtagtttctcattttcctctctctctttaaaatataacttgtctgtattctttttcataaacctttatt----gattgagatttttgctc--tgttcatgaatagttaggtatattgacacctctacacaaatgtag-------

upper sequence: LOC_Os03g52840.1 (Oryza sativa), 5'ss of exon 4
lower sequence: EFJ16660 (Selaginella moellendorffii), 5'ss of exon 4
AGAACTTCACCTCGGTGTCAGTGATGCAGGCGGTGGGATCCGTCATGACCAACAAGTACAGCGAGGGGTACCCCGGCGCGAGATACTACGGTGGAAACGAgtacggttgattgcgttctatcggttgcctttgttcagattatttgggtgttaaaaatgtttaatctgaaagagaaatcagtgcctgatgggagtgaatgatgtgaatttctggtggctctgggttttccttgcgtgcag
|||| || || ||    ||||| ||||| || ||||||||| |||||||||||||||| |||||||| || || || ||  | |||||||||||||| ||||| ||| | ||    |  |   ||  | | |     ||    ||   | ||     ||||   |||                                                                         
AGAATTTTACTTCAACTTCAGTCATGCAAGCAGTGGGATCCATCATGACCAACAAGTATAGCGAGGGCTATCCAGGAGCTCGTTACTACGGTGGAAATGAgta-ggtcgttttttcttcacaagtgacgtcta---ggaacgcttaa-tatt-----tgttcgttctag-----------------------------------------------------------------------

upper sequence: LOC_Os03g52840.1 (Oryza sativa), 5'ss of exon 4
lower sequence: EFJ32604 (Selaginella moellendorffii), 5'ss of exon 4
AGAACTTCACCTCGGTGTCAGTGATGCAGGCGGTGGGATCCGTCATGACCAACAAGTACAGCGAGGGGTACCCCGGCGCGAGATACTACGGTGGAAACGAgtacggttgattgcgttctatcggttgcctttgttcagattatttgggtgttaaaaatgtttaatctgaaagagaaatcagtgcctgatgggagtgaatgatgtgaatttctggtggctctgggttttccttgcgtgcag
|||| || || ||    ||||| ||||| || ||||||||| |||||||||||||||| |||||||| || || || ||  | |||||||||||||| ||||| ||| | ||    |  |   ||| | | |    |   |   ||  ||||     ||||   |||                                                                         
AGAATTTTACTTCAACTTCAGTCATGCAAGCAGTGGGATCCATCATGACCAACAAGTATAGCGAGGGCTATCCAGGAGCTCGTTACTACGGTGGAAATGAgta-ggtcgttttttcttcacaagttacgtctaggaacgcttaatgtttgtt-----tgttcgttctag-----------------------------------------------------------------------

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|25798315|gb|CA754276.1|CA754276
EST:     GTACAGCGAGGGGTACCCCGGCGCGAGATACTACGGTGGAAACGA                         ATACATTGATATGGCCGAGTCATTGTGCCAGAAACGTGCTTTGGAGGCCTT
genomic: GTACAGCGAGGGGTACCCCGGCGCGAGATACTACGGTGGAAACGAgtacggttga ... ttgcgtgcagATACATTGATATGGCCGAGTCATTGTGCCAGAAACGTGCTTTGGAGGCCTT
EST: gi|58689542|gb|CK078229.1|CK078229
EST:     GATACTACGGTGGAAACGA                         ATACATTGATATGGCCGAGTCATTGTGCCAGAAACGTGCTTTGGAGGCCTT
genomic: GATACTACGGTGGAAACGAgtacggttga ... ttgcgtgcagATACATTGATATGGCCGAGTCATTGTGCCAGAAACGTGCTTTGGAGGCCTT
EST: gi|29681406|gb|CB677681.1|CB677681
EST:     GGGGTACCCCGGCGCGAGATACTACGGTGGAAACGA                         ATACATTGATATGGCCGAGTCATTGTGCCAGAAACGTGCTTTGGAGGCCTT
genomic: GGGGTACCCCGGCGCGAGATACTACGGTGGAAACGAgtacggttga ... ttgcgtgcagATACATTGATATGGCCGAGTCATTGTGCCAGAAACGTGCTTTGGAGGCCTT
EST: gi|14571290|gb|BI118658.1|BI118658
EST:     ACCCCGGCGCGAGATACTACGGTGGAAACGA                         ATACATTGATATGGCCGAGTCATTGTGCCAGAAACGTGCTTTGGAGGCCTT
genomic: ACCCCGGCGCGAGATACTACGGTGGAAACGAgtacggttga ... ttgcgtgcagATACATTGATATGGCCGAGTCATTGTGCCAGAAACGTGCTTTGGAGGCCTT
EST: gi|38472219|gb|CF956350.1|CF956350
EST:     GCGAGATACTACGGTGGAAACGA                         ATACATTGATATGGCCGAGTCATTGTGCCAGAAACGTGCTTTGGAGGCCTT
genomic: GCGAGATACTACGGTGGAAACGAgtacggttga ... ttgcgtgcagATACATTGATATGGCCGAGTCATTGTGCCAGAAACGTGCTTTGGAGGCCTT
EST: gi|29674038|gb|CB670313.1|CB670313
EST:     ACCCCGGCGCGAGATACTACGGTGGAAACGA                         ATACATTGATATGGCCGAGTCATTGTGCCAGAAACGTGCTTTGGAGGCCTT
genomic: ACCCCGGCGCGAGATACTACGGTGGAAACGAgtacggttga ... ttgcgtgcagATACATTGATATGGCCGAGTCATTGTGCCAGAAACGTGCTTTGGAGGCCTT
EST: gi|29681405|gb|CB677680.1|CB677680
EST:     GGGGTACCCCGGCTCTAGATACTACGGTGGAAACGA                         ATACATTGATATGGCCGAGTCATTGTGCCAGAAACGTGCTTTGGAGGCCTT
genomic: GGGGTACCCCGGCGCGAGATACTACGGTGGAAACGAgtacggttga ... ttgcgtgcagATACATTGATATGGCCGAGTCATTGTGCCAGAAACGTGCTTTGGAGGCCTT
EST: gi|84117692|gb|CD285458.1|CD285458
EST:     GTACCCCGGCGCGAGATACTACGGTGGAAACGA                         ATACATTGATATGGCCGAGTCATTGTGCCAGAAACGTGCTTTGGAGGCCTT
genomic: GTACCCCGGCGCGAGATACTACGGTGGAAACGAgtacggttga ... ttgcgtgcagATACATTGATATGGCCGAGTCATTGTGCCAGAAACGTGCTTTGGAGGCCTT
EST: gi|33381615|gb|CF196958.1|CF196958
EST:     AACAAGTACAGCGAGGGGTACCCCGGCGCGAGATACTACGGTGGAAACGA                         ATACATTGATATGGCCGAGTCATTGTGCCAGAAACGTGCTTTGGAGGCCTT
genomic: AACAAGTACAGCGAGGGGTACCCCGGCGCGAGATACTACGGTGGAAACGAgtacggttga ... ttgcgtgcagATACATTGATATGGCCGAGTCATTGTGCCAGAAACGTGCTTTGGAGGCCTT
EST: gi|4714773|gb|AU055890.1|AU055890
EST:     AACAAGTACAGCGAGGGGTACCCCGGCGCGAGATACTACGGTGGAAACGA                         ATACATTGATATGGCCGAGTCATTGTGCCAGAAACGTGCTTTGGAGGCCTT
genomic: AACAAGTACAGCGAGGGGTACCCCGGCGCGAGATACTACGGTGGAAACGAgtacggttga ... ttgcgtgcagATACATTGATATGGCCGAGTCATTGTGCCAGAAACGTGCTTTGGAGGCCTT
EST: gi|88413328|gb|CI581343.1|CI581343
EST:     AACAAGTACAGCGAGGGGTACCCCGGCGCGAGAAACTACGGTGGAAACGA                         ATACATTGATATGGCCGAGTCATTGTGCCAGAAACGTGCTTTGGAGGCCTT
genomic: AACAAGTACAGCGAGGGGTACCCCGGCGCGAGATACTACGGTGGAAACGAgtacggttga ... ttgcgtgcagATACATTGATATGGCCGAGTCATTGTGCCAGAAACGTGCTTTGGAGGCCTT
EST: gi|29674139|gb|CB670414.1|CB670414
EST:     ACCCCGGCGCGAGATACTACGGTGGAAACGA                         ATACATTGATATGGCCGAGTCATTGTGCCAGAAACGTGCTTTGGAGGCCTT
genomic: ACCCCGGCGCGAGATACTACGGTGGAAACGAgtacggttga ... ttgcgtgcagATACATTGATATGGCCGAGTCATTGTGCCAGAAACGTGCTTTGGAGGCCTT
EST: gi|11442623|gb|BF430526.1|BF430526
EST:     AACAAGTACAGCGAGGGGTACCCCGGCGCGAGATACTACGGTGGAAACGA                         ATACATTGATATGGCCGAGTCATTGTGCCAGAAACGTGCTTTGGAGGCCTT
genomic: AACAAGTACAGCGAGGGGTACCCCGGCGCGAGATACTACGGTGGAAACGAgtacggttga ... ttgcgtgcagATACATTGATATGGCCGAGTCATTGTGCCAGAAACGTGCTTTGGAGGCCTT

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: 75 (upstream exon), 75 (downstream exon)
Score: 262

AGAACTTCACCTCGGTGTCAGTGATGCAGGCGGTGGGATCCGTCATGACCAACAAGTACAGCGAGGGGTACCCCGGCGCGAGATACTACGGTGGAAACGAgtacggttga ... ttgcgtgcagATACATTGATATGGCCGAGTCATTGTGCCAGAAACGTGCTTTGGAGGCCTTCCGCTTGGACCCAGCGAAATGGGGAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGAACTTCACCTCGGTGTCAGTGATGCAGGCGGTGGGATCCGTCATGACCAACAAGTACAGCGAGGGGTACCCCGGCGCGAGATACTACGGTGGAAACGAgtacggttgattgcgttctatcggttgcctttgttcagattatttgggtgttaaaaatgtttaatctgaaagagaaatcagtgcctgatgggagtgaatgatgtgaatttctggtggctctgggttttccttgcgtgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA