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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTCTGGCATCACAACCCAGACATTGTTAAATCATGCGTGGGCATCTGCAAATCGTCATAACAAAAACAATTCCGATTCAACCTCTGAAGAAGTTCCTAAGgtacgttcacatcaatacttctaatactttttaaggttgtttgtattagttgagttgggcaatattctagttgggttggggactacattttgatatgtgg...

Basic information

species Oryza sativa
transcript LOC_Os02g19510.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g19510.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G119725_T01 (Zea mays), 5'ss of exon 4
CTCTGGCATCACAACCCAGACATTGTTAAATCATGCGTGGGCATCTGCAAATCGTCATAACAAAAACAATTCCGATTCAACCTCTGAAGAAGTTCCTAAGgtacgttcacatcaatacttc--taatactttttaaggttgtttgtattagttgagttgggcaatattctagttgggttggggactacattttgatatgtgg
||||||||||||||||||||||||||| || ||||| ||||||||||||||   |||||| || || | ||| || || | | |||| ||| ||||  |||||| |  ||| || |||| |  |  |   ||   |  ||   |||||   |  |  |  | | |   |||  |  | |   |  |   || |  | |||| 
CTCTGGCATCACAACCCAGACATTGTTGAACCATGCTTGGGCATCTGCAAACAATCATAAAAAGAATAGTTCTGAATCTAACACTGATGAAATTCCCGAGgtacttcaaca-cactactgccttcttgtgttgccatattagctgtatacttatatgtctgtattggcctaaattaggtatcgtatttgttattttttgtg-

upper sequence: LOC_Os02g19510.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G006507_T04 (Zea mays), 5'ss of exon 4
CTCTGGCATCACAACCCAGACATTGTTAAATCATGCGTGGGCATCTGCAAATCGTCATAACAAAAACAATTCCGATTCAACCTCTGAAGAAGTTCCTAAGgtacgttcacatcaatacttctaatactttttaaggttgtttgtattagttgagttgggcaatattctagttgggttggggactacattttgatatgtgg--------
||||||||||||||||||||||||||| || ||||| ||||||||||||||   || ||| || || |  || || || | | |||| ||| |||| ||||||| |  |||         ||| ||| || |   |||| |  |||||||||  |      ||||     ||||  |   |      |||   | |||          
CTCTGGCATCACAACCCAGACATTGTTGAACCATGCTTGGGCATCTGCAAACAATCGTAAAAAGAATAGCTCTGAATCTAACACTGATGAAATTCCCAAGgtacttcaacaca-------ctactaccttcttgtgttgct-atattagttgtatgcttatatatctgtattggcctaaagtaggtctttgattttgttagttattgt
















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|428327|gb|D24475.1|D24475
EST:     ATCGTCATAACAAAAACAATTCCGNTTCAACCTCTGAAGAAGTTCCTAAG                         ATTTATGTTCCCACAAACCCTAAAGGTGCTGAAAGGCTCCCACCAGGCATT
genomic: ATCGTCATAACAAAAACAATTCCGATTCAACCTCTGAAGAAGTTCCTAAGgtacgttcac ... ctttctgcagATTTATGTTCCCACAAACCCTAAAGGTGCTGAAAGGCTCCCACCAGGCATT
EST: gi|88360895|gb|CI625201.1|CI625201
EST:     TAACAAAAACAATTCCGATTCAACCTCTGAAGAAGTTCCTAAG                         ATTTATGTTCCCACAAACCCTAAAGGTGCTGAAAGGCTCCCACCAGGCATT
genomic: TAACAAAAACAATTCCGATTCAACCTCTGAAGAAGTTCCTAAGgtacgttcac ... ctttctgcagATTTATGTTCCCACAAACCCTAAAGGTGCTGAAAGGCTCCCACCAGGCATT
EST: gi|428279|gb|D24427.1|D24427
EST:     ATCGTCATAACAAAAACAATTCCGATTCAACCTCTGAAGAAGTTCCTAAG                         ATTTATGTTCCCACAAACCCTAAAGGTGCTGAAAGGCTCCCACCAGGCATT
genomic: ATCGTCATAACAAAAACAATTCCGATTCAACCTCTGAAGAAGTTCCTAAGgtacgttcac ... ctttctgcagATTTATGTTCCCACAAACCCTAAAGGTGCTGAAAGGCTCCCACCAGGCATT
EST: gi|29646523|gb|CB651530.1|CB651530
EST:     ATCGTCATAACAAAAACAATTCCGATTCAACCTCTGAAGAAGTTCCTAAG                         ATTTATGTTCCCACAAACCCTAAAGGTGCTGAAAGGCTCCCACCAGGCATT
genomic: ATCGTCATAACAAAAACAATTCCGATTCAACCTCTGAAGAAGTTCCTAAGgtacgttcac ... ctttctgcagATTTATGTTCCCACAAACCCTAAAGGTGCTGAAAGGCTCCCACCAGGCATT
EST: gi|428340|gb|D24488.1|D24488
EST:     ATCGTCATAACAAAAACAATTCCGATTCAACCTCTGAAGAAGTTCCTAAG                         ATTTATGTNCCCACAAACCCTAAAGGTGCTGAAAGGCTCCCACCAGGCATT
genomic: ATCGTCATAACAAAAACAATTCCGATTCAACCTCTGAAGAAGTTCCTAAGgtacgttcac ... ctttctgcagATTTATGTTCCCACAAACCCTAAAGGTGCTGAAAGGCTCCCACCAGGCATT
EST: gi|29673248|gb|CB669523.1|CB669523
EST:     ATCGTCATAACAAAAACAATTCCGATTCAACCTCTGAAGAAGTTCCTAAG                         ATTTATGTTCCCACAAACCCTAAAGGTGCTGAAAGGCTCCCACCAGGCATT
genomic: ATCGTCATAACAAAAACAATTCCGATTCAACCTCTGAAGAAGTTCCTAAGgtacgttcac ... ctttctgcagATTTATGTTCCCACAAACCCTAAAGGTGCTGAAAGGCTCCCACCAGGCATT
EST: gi|58659150|gb|CK047830.1|CK047830
EST:     ATCGTCATAACAAAAACAATTCCGATTCAACCTCTGAAGAAGTTCCTAAG                         ATTTATGTTCCCACA
genomic: ATCGTCATAACAAAAACAATTCCGATTCAACCTCTGAAGAAGTTCCTAAGgtacgttcac ... ctttctgcagATTTATGTTCCCACA
EST: gi|29641723|gb|CB646730.1|CB646730
EST:     ATCGTCATAACAAAAACAATTCCGATTCAACCTCTGAAGAAGTTCCTAAG                         ATTTATGTTCCCACAAACCCTAAAGGTGCTGAAAGGCT
genomic: ATCGTCATAACAAAAACAATTCCGATTCAACCTCTGAAGAAGTTCCTAAGgtacgttcac ... ctttctgcagATTTATGTTCCCACAAACCCTAAAGGTGCTGAAAGGCT
EST: gi|29624841|gb|CB629852.1|CB629852
EST:     ATCGTCATAACAAAAACAATTCCGATTCAACCTCTGAAGAAGTTCCTAAG                         ATTTATGTTCCCACAAACCCTAAAGGTGCTGAAAGGCTCCCACCAGGCATT
genomic: ATCGTCATAACAAAAACAATTCCGATTCAACCTCTGAAGAAGTTCCTAAGgtacgttcac ... ctttctgcagATTTATGTTCCCACAAACCCTAAAGGTGCTGAAAGGCTCCCACCAGGCATT
EST: gi|29676038|gb|CB672313.1|CB672313
EST:     ATCGTCATAACAAAAACAATTCCGATTCAACCTCTGAAGAAGTTCCTAAG                         ATTTATGTTCCCACAAACCCTAAAGGTGCTGAAAGGCTCCCACCAGGCATT
genomic: ATCGTCATAACAAAAACAATTCCGATTCAACCTCTGAAGAAGTTCCTAAGgtacgttcac ... ctttctgcagATTTATGTTCCCACAAACCCTAAAGGTGCTGAAAGGCTCCCACCAGGCATT
EST: gi|29673598|gb|CB669873.1|CB669873
EST:     ATCGTCATAACAAAAACAATTCCGATTCAACCTCTGAAGAAGTTCCTAAG                         ATTTATGTTCCCACAAACCCTAAAGGTGCTGAAAGGCTCCCACCAGGCATT
genomic: ATCGTCATAACAAAAACAATTCCGATTCAACCTCTGAAGAAGTTCCTAAGgtacgttcac ... ctttctgcagATTTATGTTCCCACAAACCCTAAAGGTGCTGAAAGGCTCCCACCAGGCATT
EST: gi|29640936|gb|CB645943.1|CB645943
EST:     ATCGTCATAACAAAAACAATTCCGATTCAACCTCTGAAGAAGTTCCTAAG                         ATTTATGTTCCCACAAACCCTAAAGGTGCTGAAAGGCTCCCACCAGGCATT
genomic: ATCGTCATAACAAAAACAATTCCGATTCAACCTCTGAAGAAGTTCCTAAGgtacgttcac ... ctttctgcagATTTATGTTCCCACAAACCCTAAAGGTGCTGAAAGGCTCCCACCAGGCATT
EST: gi|58670226|gb|CK058912.1|CK058912
EST:     ATCGTCATAACAAAAACAATTCCGATTCAACCTCTGAAGAAGTTCCTAAG                         ATTTATGTTCCCACAAACCCTAAAGGTGCTGAAAGGCTCCCACCAGGCATT
genomic: ATCGTCATAACAAAAACAATTCCGATTCAACCTCTGAAGAAGTTCCTAAGgtacgttcac ... ctttctgcagATTTATGTTCCCACAAACCCTAAAGGTGCTGAAAGGCTCCCACCAGGCATT
EST: gi|58691339|gb|CK080026.1|CK080026
EST:     ATCGTCATAACAAAAACAATTCCGATTCAACCTCTGAAGAAGTTCCTAAG                         ATTTATGTTCCCACAAACCCTAAAGGTGCTGAAAGGCTCCCACCAGGCATT
genomic: ATCGTCATAACAAAAACAATTCCGATTCAACCTCTGAAGAAGTTCCTAAGgtacgttcac ... ctttctgcagATTTATGTTCCCACAAACCCTAAAGGTGCTGAAAGGCTCCCACCAGGCATT
EST: gi|66913022|gb|CX099870.1|CX099870
EST:     ATCGTCATAACAAAAACAATTCCGATTCAACCTCTGAAGAAGTTCCTAAG                         ATTTATGTTCCCACAAAACCTAAAGGTGCTGAAAGGCTCCCACCAGGCATT
genomic: ATCGTCATAACAAAAACAATTCCGATTCAACCTCTGAAGAAGTTCCTAAGgtacgttcac ... ctttctgcagATTTATGTTCCCACAAACCCTAAAGGTGCTGAAAGGCTCCCACCAGGCATT
EST: gi|87006680|gb|CI285714.1|CI285714
EST:     CATAACAAAAACAATTCCGATTCAACCTCTGAAGAAGTTCCTAAG                         ATTTATGTTCCCACAAACCCTAAAGGTGCTGAAAGGCTCCCACCAGGCATT
genomic: CATAACAAAAACAATTCCGATTCAACCTCTGAAGAAGTTCCTAAGgtacgttcac ... ctttctgcagATTTATGTTCCCACAAACCCTAAAGGTGCTGAAAGGCTCCCACCAGGCATT
EST: gi|33675555|gb|CF303794.1|CF303794
EST:     ATCGTCATAACAAAAACAATTCCGATTCAACCTCTGAAGAAGTTCCTAAG                         ATTTATGTTCCCACAAACCCTAAAGGTGCTGAAAGGCTCCCACCAGGCATT
genomic: ATCGTCATAACAAAAACAATTCCGATTCAACCTCTGAAGAAGTTCCTAAGgtacgttcac ... ctttctgcagATTTATGTTCCCACAAACCCTAAAGGTGCTGAAAGGCTCCCACCAGGCATT
EST: gi|58605686|gb|CK033719.1|CK033719
EST:     ATCGTCATAACAAAAACAATTCCGATTCAACCTCTGAAGAAGTTCCTAAG                         ATTTATGTTCCCACAAAC
genomic: ATCGTCATAACAAAAACAATTCCGATTCAACCTCTGAAGAAGTTCCTAAGgtacgttcac ... ctttctgcagATTTATGTTCCCACAAAC

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: 70 (upstream exon), 57 (downstream exon)
Score: 26

CTCTGGCATCACAACCCAGACATTGTTAAATCATGCGTGGGCATCTGCAAATCGTCATAACAAAAACAATTCCGATTCAACCTCTGAAGAAGTTCCTAAGgtacgttcac ... ctttctgcagATTTATGTTCCCACAAACCCTAAAGGTGCTGAAAGGCTCCCACCAGGCATTGTTGTTTCTGAAACAGATCTTTTTCCACGGAGATTGTGGGGTGATCCTA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTCTGGCATCACAACCCAGACATTGTTAAATCATGCGTGGGCATCTGCAAATCGTCATAACAAAAACAATTCCGATTCAACCTCTGAAGAAGTTCCTAAGgtacgttcacatcaatacttctaatactttttaaggttgtttgtattagttgagttgggcaatattctagttgggttggggactacattttgatatgtgg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT